Starting phenix.real_space_refine on Wed Nov 15 06:53:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8g_10121/11_2023/6s8g_10121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8g_10121/11_2023/6s8g_10121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8g_10121/11_2023/6s8g_10121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8g_10121/11_2023/6s8g_10121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8g_10121/11_2023/6s8g_10121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8g_10121/11_2023/6s8g_10121_updated.pdb" } resolution = 3.5 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= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3414 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 44 5.16 5 C 4836 2.51 5 N 1290 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 21": "OD1" <-> "OD2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A ASP 108": "OD1" <-> "OD2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F ARG 295": "NH1" <-> "NH2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G ASP 63": "OD1" <-> "OD2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 7530 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "B" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1867 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1845 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1875 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LMD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.65, per 1000 atoms: 0.62 Number of scatterers: 7530 At special positions: 0 Unit cell: (111.54, 79.092, 89.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 6 15.00 O 1354 8.00 N 1290 7.00 C 4836 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: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1768 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 6 sheets defined 41.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.509A pdb=" N ALA A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 78' Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.718A pdb=" N GLU A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.500A pdb=" N VAL A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.792A pdb=" N ARG A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.677A pdb=" N VAL A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 50 Processing helix chain 'B' and resid 72 through 78 removed outlier: 3.509A pdb=" N ALA B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 78' Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.718A pdb=" N GLU B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU B 123 " --> pdb=" O ASN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 130 No H-bonds generated for 'chain 'B' and resid 128 through 130' Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.915A pdb=" N ALA B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 181 removed outlier: 3.792A pdb=" N ARG B 178 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.676A pdb=" N VAL B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 37 removed outlier: 3.581A pdb=" N THR F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 18 " --> pdb=" O SER F 14 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 22 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 30 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 4.212A pdb=" N GLY F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 59 No H-bonds generated for 'chain 'F' and resid 56 through 59' Processing helix chain 'F' and resid 63 through 81 removed outlier: 4.048A pdb=" N LEU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 69 " --> pdb=" O PRO F 65 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET F 74 " --> pdb=" O LEU F 70 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 91 removed outlier: 3.518A pdb=" N CYS F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 118 removed outlier: 3.512A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 125 removed outlier: 3.674A pdb=" N SER F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 121 through 125' Processing helix chain 'F' and resid 274 through 281 removed outlier: 3.553A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 310 removed outlier: 3.643A pdb=" N LEU F 308 " --> pdb=" O LEU F 304 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 310 " --> pdb=" O TYR F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 No H-bonds generated for 'chain 'F' and resid 330 through 333' Processing helix chain 'F' and resid 337 through 344 removed outlier: 4.215A pdb=" N ALA F 342 " --> pdb=" O TYR F 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 14 Processing helix chain 'G' and resid 16 through 40 removed outlier: 4.152A pdb=" N MET G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 57 No H-bonds generated for 'chain 'G' and resid 54 through 57' Processing helix chain 'G' and resid 62 through 65 No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 68 through 85 removed outlier: 3.790A pdb=" N LEU G 74 " --> pdb=" O MET G 70 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.749A pdb=" N SER G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 120 removed outlier: 4.147A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 3.571A pdb=" N LEU G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 removed outlier: 3.611A pdb=" N ARG G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 257 Processing helix chain 'G' and resid 282 through 292 removed outlier: 3.557A pdb=" N ALA G 286 " --> pdb=" O PRO G 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 287 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 323 removed outlier: 4.009A pdb=" N PHE G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR G 320 " --> pdb=" O GLY G 316 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP G 323 " --> pdb=" O PHE G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 340 No H-bonds generated for 'chain 'G' and resid 337 through 340' Processing helix chain 'G' and resid 343 through 355 removed outlier: 3.633A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 59 through 62 removed outlier: 5.765A pdb=" N VAL A 22 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.714A pdb=" N ARG A 206 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU A 35 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR A 208 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 219 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 217 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 80 through 83 removed outlier: 7.722A pdb=" N LYS A 157 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LEU A 83 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 10.078A pdb=" N ILE A 159 " --> pdb=" O LEU A 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 59 through 62 removed outlier: 5.766A pdb=" N VAL B 22 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.715A pdb=" N ARG B 206 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 35 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR B 208 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 219 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 217 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 80 through 83 removed outlier: 7.721A pdb=" N LYS B 157 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LEU B 83 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 10.077A pdb=" N ILE B 159 " --> pdb=" O LEU B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 181 hydrogen bonds defined for protein. 528 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: 1.95 Time building geometry restraints manager: 3.28 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: 2392 1.34 - 1.46: 1408 1.46 - 1.58: 3775 1.58 - 1.70: 4 1.70 - 1.82: 84 Bond restraints: 7663 Sorted by residual: bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" O3A ANP A 401 " pdb=" PB ANP A 401 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 1.795 1.677 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 1.795 1.677 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" O5' ANP B 401 " pdb=" PA ANP B 401 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 7658 not shown) Histogram of bond angle deviations from ideal: 96.48 - 103.99: 135 103.99 - 111.51: 3289 111.51 - 119.02: 3012 119.02 - 126.53: 3825 126.53 - 134.04: 128 Bond angle restraints: 10389 Sorted by residual: angle pdb=" PB ANP B 401 " pdb=" N3B ANP B 401 " pdb=" PG ANP B 401 " ideal model delta sigma weight residual 126.95 100.50 26.45 3.00e+00 1.11e-01 7.77e+01 angle pdb=" PB ANP A 401 " pdb=" N3B ANP A 401 " pdb=" PG ANP A 401 " ideal model delta sigma weight residual 126.95 100.56 26.39 3.00e+00 1.11e-01 7.74e+01 angle pdb=" CB LYS A 14 " pdb=" CG LYS A 14 " pdb=" CD LYS A 14 " ideal model delta sigma weight residual 111.30 126.05 -14.75 2.30e+00 1.89e-01 4.11e+01 angle pdb=" CB LYS B 14 " pdb=" CG LYS B 14 " pdb=" CD LYS B 14 " ideal model delta sigma weight residual 111.30 126.04 -14.74 2.30e+00 1.89e-01 4.10e+01 angle pdb=" C ILE B 62 " pdb=" N ASP B 63 " pdb=" CA ASP B 63 " ideal model delta sigma weight residual 121.54 132.41 -10.87 1.91e+00 2.74e-01 3.24e+01 ... (remaining 10384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 4181 23.00 - 46.00: 337 46.00 - 69.01: 51 69.01 - 92.01: 11 92.01 - 115.01: 3 Dihedral angle restraints: 4583 sinusoidal: 1841 harmonic: 2742 Sorted by residual: dihedral pdb=" CA PRO B 156 " pdb=" C PRO B 156 " pdb=" N LYS B 157 " pdb=" CA LYS B 157 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA PRO A 156 " pdb=" C PRO A 156 " pdb=" N LYS A 157 " pdb=" CA LYS A 157 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LYS B 157 " pdb=" C LYS B 157 " pdb=" N PHE B 158 " pdb=" CA PHE B 158 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 4580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 863 0.056 - 0.112: 293 0.112 - 0.169: 62 0.169 - 0.225: 11 0.225 - 0.281: 4 Chirality restraints: 1233 Sorted by residual: chirality pdb=" C3' ANP A 401 " pdb=" C2' ANP A 401 " pdb=" C4' ANP A 401 " pdb=" O3' ANP A 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A 173 " pdb=" CA VAL A 173 " pdb=" CG1 VAL A 173 " pdb=" CG2 VAL A 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1230 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 169 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO A 170 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 170 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 170 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 169 " -0.064 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO B 170 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 64 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO F 65 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO F 65 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 65 " 0.039 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2294 2.82 - 3.34: 6399 3.34 - 3.86: 11645 3.86 - 4.38: 14248 4.38 - 4.90: 23912 Nonbonded interactions: 58498 Sorted by model distance: nonbonded pdb=" OG SER A 139 " pdb=" OE1 GLU A 142 " model vdw 2.294 2.440 nonbonded pdb=" OG SER B 139 " pdb=" OE1 GLU B 142 " model vdw 2.294 2.440 nonbonded pdb=" O SER A 186 " pdb=" OG SER A 186 " model vdw 2.315 2.440 nonbonded pdb=" O SER B 186 " pdb=" OG SER B 186 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR G 10 " pdb=" OE1 GLU G 88 " model vdw 2.322 2.440 ... (remaining 58493 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 2 and (name CA or name C or name O or name CB )) or resid \ 3 through 239 or resid 401)) selection = (chain 'B' and (resid 2 through 239 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 1.700 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.400 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.010 0.154 7663 Z= 0.642 Angle : 1.323 26.452 10389 Z= 0.673 Chirality : 0.061 0.281 1233 Planarity : 0.008 0.097 1292 Dihedral : 17.192 115.010 2815 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.74 % Favored : 85.15 % Rotamer: Outliers : 3.86 % Allowed : 12.58 % Favored : 83.56 % 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: -6.67 (0.17), residues: 943 helix: -4.89 (0.08), residues: 478 sheet: -2.08 (0.67), residues: 42 loop : -4.01 (0.24), residues: 423 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 0.881 Fit side-chains outliers start: 31 outliers final: 8 residues processed: 246 average time/residue: 0.2560 time to fit residues: 80.6202 Evaluate side-chains 179 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1353 time to fit residues: 3.0782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN B 27 ASN B 155 ASN F 15 GLN F 46 ASN F 116 ASN F 267 ASN F 313 GLN G 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7663 Z= 0.182 Angle : 0.701 7.596 10389 Z= 0.363 Chirality : 0.043 0.368 1233 Planarity : 0.006 0.071 1292 Dihedral : 9.819 141.787 1054 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.09 % Favored : 87.80 % Rotamer: Outliers : 2.37 % Allowed : 18.56 % Favored : 79.08 % 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: -5.39 (0.21), residues: 943 helix: -3.59 (0.16), residues: 488 sheet: -1.74 (0.70), residues: 52 loop : -3.71 (0.26), residues: 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 0.894 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 188 average time/residue: 0.2231 time to fit residues: 54.8285 Evaluate side-chains 174 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0743 time to fit residues: 3.1154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 0.0370 chunk 75 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 overall best weight: 3.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 195 HIS B 113 GLN B 195 HIS B 218 HIS F 127 HIS F 313 GLN F 346 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7663 Z= 0.393 Angle : 0.805 10.071 10389 Z= 0.406 Chirality : 0.047 0.231 1233 Planarity : 0.005 0.071 1292 Dihedral : 9.269 130.408 1054 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 15.27 % Favored : 84.62 % Rotamer: Outliers : 3.36 % Allowed : 22.91 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.23), residues: 943 helix: -2.84 (0.19), residues: 504 sheet: -1.30 (0.78), residues: 48 loop : -3.83 (0.27), residues: 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 168 time to evaluate : 1.067 Fit side-chains outliers start: 27 outliers final: 14 residues processed: 186 average time/residue: 0.2326 time to fit residues: 55.8372 Evaluate side-chains 168 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 154 time to evaluate : 0.820 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0723 time to fit residues: 2.9857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7663 Z= 0.245 Angle : 0.711 8.994 10389 Z= 0.356 Chirality : 0.044 0.190 1233 Planarity : 0.005 0.062 1292 Dihedral : 9.019 134.109 1054 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.20 % Favored : 87.70 % Rotamer: Outliers : 2.37 % Allowed : 24.78 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.24), residues: 943 helix: -2.34 (0.21), residues: 502 sheet: -1.31 (0.76), residues: 48 loop : -3.70 (0.27), residues: 393 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 0.855 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 178 average time/residue: 0.2292 time to fit residues: 53.0530 Evaluate side-chains 166 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0719 time to fit residues: 2.5427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 155 ASN F 127 HIS F 290 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7663 Z= 0.289 Angle : 0.737 13.522 10389 Z= 0.364 Chirality : 0.046 0.356 1233 Planarity : 0.005 0.063 1292 Dihedral : 8.863 131.160 1054 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.15 % Favored : 86.74 % Rotamer: Outliers : 2.62 % Allowed : 25.03 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.25), residues: 943 helix: -2.12 (0.21), residues: 515 sheet: -1.22 (0.79), residues: 48 loop : -3.87 (0.27), residues: 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 0.984 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 171 average time/residue: 0.2311 time to fit residues: 51.1728 Evaluate side-chains 164 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0706 time to fit residues: 2.7511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 155 ASN F 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7663 Z= 0.276 Angle : 0.730 11.342 10389 Z= 0.358 Chirality : 0.045 0.298 1233 Planarity : 0.005 0.061 1292 Dihedral : 8.798 131.893 1054 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.94 % Favored : 86.96 % Rotamer: Outliers : 2.24 % Allowed : 26.15 % Favored : 71.61 % 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: -3.92 (0.25), residues: 943 helix: -1.86 (0.22), residues: 509 sheet: -1.25 (0.79), residues: 48 loop : -3.82 (0.27), residues: 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.940 Fit side-chains outliers start: 18 outliers final: 6 residues processed: 167 average time/residue: 0.2239 time to fit residues: 48.6443 Evaluate side-chains 156 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0740 time to fit residues: 1.8667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 55 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 GLN B 27 ASN B 126 HIS F 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7663 Z= 0.160 Angle : 0.674 11.021 10389 Z= 0.327 Chirality : 0.043 0.386 1233 Planarity : 0.004 0.055 1292 Dihedral : 8.419 132.247 1054 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.77 % Favored : 88.12 % Rotamer: Outliers : 1.99 % Allowed : 27.40 % Favored : 70.61 % 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: -3.50 (0.26), residues: 943 helix: -1.49 (0.23), residues: 509 sheet: -1.72 (0.67), residues: 66 loop : -3.63 (0.29), residues: 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 0.786 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 171 average time/residue: 0.2249 time to fit residues: 50.1454 Evaluate side-chains 154 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0734 time to fit residues: 1.7601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN A 196 ASN B 27 ASN F 127 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7663 Z= 0.392 Angle : 0.802 9.893 10389 Z= 0.395 Chirality : 0.048 0.349 1233 Planarity : 0.005 0.071 1292 Dihedral : 8.761 130.720 1054 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.85 % Favored : 85.05 % Rotamer: Outliers : 1.87 % Allowed : 27.27 % Favored : 70.86 % 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: -3.59 (0.26), residues: 943 helix: -1.57 (0.23), residues: 503 sheet: -1.43 (0.78), residues: 53 loop : -3.64 (0.28), residues: 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 0.926 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 159 average time/residue: 0.2387 time to fit residues: 49.1177 Evaluate side-chains 164 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.846 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0727 time to fit residues: 3.0253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 27 ASN F 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7663 Z= 0.246 Angle : 0.727 10.020 10389 Z= 0.354 Chirality : 0.045 0.347 1233 Planarity : 0.005 0.071 1292 Dihedral : 8.660 133.778 1054 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.30 % Favored : 87.59 % Rotamer: Outliers : 0.12 % Allowed : 28.02 % Favored : 71.86 % 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: -3.38 (0.26), residues: 943 helix: -1.40 (0.23), residues: 507 sheet: -1.48 (0.75), residues: 58 loop : -3.54 (0.29), residues: 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.953 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.2323 time to fit residues: 46.5097 Evaluate side-chains 146 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 61 optimal weight: 0.0980 chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 58 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7663 Z= 0.155 Angle : 0.671 9.287 10389 Z= 0.329 Chirality : 0.043 0.352 1233 Planarity : 0.004 0.062 1292 Dihedral : 8.131 132.843 1054 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.24 % Favored : 88.65 % Rotamer: Outliers : 0.37 % Allowed : 29.76 % Favored : 69.86 % 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: -2.98 (0.27), residues: 943 helix: -1.03 (0.24), residues: 499 sheet: -1.36 (0.69), residues: 68 loop : -3.43 (0.29), residues: 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 160 time to evaluate : 0.829 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 162 average time/residue: 0.2211 time to fit residues: 47.0615 Evaluate side-chains 152 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0719 time to fit residues: 1.5776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108940 restraints weight = 9920.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.112126 restraints weight = 6026.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.114186 restraints weight = 4436.283| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 7663 Z= 0.390 Angle : 0.791 9.544 10389 Z= 0.387 Chirality : 0.048 0.403 1233 Planarity : 0.005 0.066 1292 Dihedral : 8.495 131.153 1054 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.00 % Favored : 85.90 % Rotamer: Outliers : 0.75 % Allowed : 29.39 % Favored : 69.86 % 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: -3.20 (0.27), residues: 943 helix: -1.22 (0.23), residues: 506 sheet: -1.53 (0.76), residues: 58 loop : -3.49 (0.29), residues: 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.25 seconds wall clock time: 32 minutes 31.94 seconds (1951.94 seconds total)