Starting phenix.real_space_refine on Mon Mar 11 14:32:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e9y_27968/03_2024/8e9y_27968_updated.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5423 2.51 5 N 1437 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 138": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8479 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2173 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1658 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2498 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1741 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'WE9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.61 Number of scatterers: 8479 At special positions: 0 Unit cell: (88, 118.8, 124.96, 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) Cl 1 17.00 S 56 16.00 O 1562 8.00 N 1437 7.00 C 5423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 32.5% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 68 through 95 removed outlier: 3.750A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.571A pdb=" N LEU A 108 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 115 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 116 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 119 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 140 through 171 removed outlier: 4.122A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 145 " --> pdb=" O CYS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 No H-bonds generated for 'chain 'A' and resid 182 through 185' Processing helix chain 'A' and resid 187 through 205 removed outlier: 3.747A pdb=" N SER A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 207 through 210 No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.544A pdb=" N TYR A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.879A pdb=" N ALA A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 523 through 539 removed outlier: 4.205A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 535 " --> pdb=" O TRP A 531 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER A 537 " --> pdb=" O CYS A 533 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.565A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.682A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.674A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 No H-bonds generated for 'chain 'B' and resid 160 through 163' Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.827A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 196 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL B 198 " --> pdb=" O ARG B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 243 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.558A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 138 through 141 removed outlier: 3.966A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASN B 80 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU B 36 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS B 82 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU B 38 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE B 84 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 79 through 83 removed outlier: 3.628A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.015A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.748A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.817A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.661A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.395A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.738A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.727A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.233A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ARG E 168 " --> pdb=" O PRO E 173 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 143 through 147 344 hydrogen bonds defined for protein. 951 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: 2.53 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2169 1.33 - 1.45: 1827 1.45 - 1.58: 4589 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 8664 Sorted by residual: bond pdb=" N VAL B 186 " pdb=" CA VAL B 186 " ideal model delta sigma weight residual 1.461 1.502 -0.041 1.17e-02 7.31e+03 1.22e+01 bond pdb=" N VAL B 198 " pdb=" CA VAL B 198 " ideal model delta sigma weight residual 1.457 1.487 -0.030 9.30e-03 1.16e+04 1.04e+01 bond pdb=" N PRO B 184 " pdb=" CA PRO B 184 " ideal model delta sigma weight residual 1.474 1.450 0.024 7.40e-03 1.83e+04 1.02e+01 bond pdb=" N ASP B 183 " pdb=" CA ASP B 183 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.28e+00 bond pdb=" N ASP B 199 " pdb=" CA ASP B 199 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.27e-02 6.20e+03 8.88e+00 ... (remaining 8659 not shown) Histogram of bond angle deviations from ideal: 98.08 - 105.27: 134 105.27 - 112.46: 4489 112.46 - 119.65: 2782 119.65 - 126.84: 4284 126.84 - 134.03: 120 Bond angle restraints: 11809 Sorted by residual: angle pdb=" N TYR B 191 " pdb=" CA TYR B 191 " pdb=" C TYR B 191 " ideal model delta sigma weight residual 113.38 104.98 8.40 1.23e+00 6.61e-01 4.67e+01 angle pdb=" N ILE B 193 " pdb=" CA ILE B 193 " pdb=" C ILE B 193 " ideal model delta sigma weight residual 110.42 103.98 6.44 9.60e-01 1.09e+00 4.50e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 117.38 124.90 -7.52 1.18e+00 7.18e-01 4.06e+01 angle pdb=" N ILE B 200 " pdb=" CA ILE B 200 " pdb=" C ILE B 200 " ideal model delta sigma weight residual 110.62 104.23 6.39 1.02e+00 9.61e-01 3.92e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 113.20 107.44 5.76 9.60e-01 1.09e+00 3.60e+01 ... (remaining 11804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.68: 4720 20.68 - 41.36: 304 41.36 - 62.03: 28 62.03 - 82.71: 11 82.71 - 103.39: 2 Dihedral angle restraints: 5065 sinusoidal: 1805 harmonic: 3260 Sorted by residual: dihedral pdb=" CA ASN D 24 " pdb=" C ASN D 24 " pdb=" N ILE D 25 " pdb=" CA ILE D 25 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.48 21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR E 161 " pdb=" C TYR E 161 " pdb=" N LEU E 162 " pdb=" CA LEU E 162 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1090 0.054 - 0.108: 243 0.108 - 0.162: 34 0.162 - 0.215: 4 0.215 - 0.269: 5 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CA ILE B 193 " pdb=" N ILE B 193 " pdb=" C ILE B 193 " pdb=" CB ILE B 193 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA GLU B 182 " pdb=" N GLU B 182 " pdb=" C GLU B 182 " pdb=" CB GLU B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE B 200 " pdb=" N ILE B 200 " pdb=" C ILE B 200 " pdb=" CB ILE B 200 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1373 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 212 " 0.063 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO B 213 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 193 " -0.018 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE B 193 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE B 193 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG B 194 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.94e+00 pdb=" C GLU E 222 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.019 2.00e-02 2.50e+03 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1193 2.75 - 3.29: 8493 3.29 - 3.83: 14170 3.83 - 4.36: 17096 4.36 - 4.90: 29115 Nonbonded interactions: 70067 Sorted by model distance: nonbonded pdb=" O SER B 44 " pdb=" ND2 ASN B 144 " model vdw 2.217 2.520 nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.220 2.440 nonbonded pdb=" NH2 ARG A 177 " pdb=" OH TYR B 243 " model vdw 2.242 2.520 nonbonded pdb=" OH TYR C 264 " pdb=" O ALA C 299 " model vdw 2.243 2.440 nonbonded pdb=" O ALA B 41 " pdb=" OG SER B 44 " model vdw 2.244 2.440 ... (remaining 70062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.350 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.750 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.005 0.041 8664 Z= 0.303 Angle : 0.810 13.182 11809 Z= 0.493 Chirality : 0.048 0.269 1376 Planarity : 0.004 0.096 1490 Dihedral : 13.488 103.391 2950 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.12 % Allowed : 1.16 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.06 (0.25), residues: 1105 helix: -0.41 (0.26), residues: 374 sheet: -0.27 (0.32), residues: 259 loop : -1.06 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 504 HIS 0.014 0.002 HIS B 82 PHE 0.024 0.002 PHE B 84 TYR 0.017 0.002 TYR B 170 ARG 0.006 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.915 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 172 average time/residue: 0.8277 time to fit residues: 155.2982 Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 chunk 33 optimal weight: 0.0980 chunk 51 optimal weight: 0.0060 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 overall best weight: 0.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8664 Z= 0.153 Angle : 0.570 7.361 11809 Z= 0.294 Chirality : 0.042 0.145 1376 Planarity : 0.004 0.065 1490 Dihedral : 6.764 101.887 1212 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.39 % Allowed : 10.75 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.47 (0.26), residues: 1105 helix: 0.49 (0.27), residues: 372 sheet: -0.24 (0.31), residues: 267 loop : -0.91 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 526 HIS 0.010 0.001 HIS B 82 PHE 0.016 0.001 PHE B 84 TYR 0.022 0.002 TYR B 170 ARG 0.005 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 1.001 Fit side-chains REVERT: B 35 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6984 (mtm-85) REVERT: C 251 ARG cc_start: 0.7418 (mtt180) cc_final: 0.7204 (mtt90) REVERT: C 335 PHE cc_start: 0.7996 (m-80) cc_final: 0.7635 (m-80) REVERT: E 79 LEU cc_start: 0.7633 (pt) cc_final: 0.7194 (pt) REVERT: E 95 TYR cc_start: 0.8348 (m-80) cc_final: 0.7781 (m-80) outliers start: 12 outliers final: 3 residues processed: 165 average time/residue: 0.9187 time to fit residues: 164.1530 Evaluate side-chains 160 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain E residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.0030 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 33 optimal weight: 0.0370 chunk 79 optimal weight: 0.7980 overall best weight: 0.3068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8664 Z= 0.159 Angle : 0.531 7.174 11809 Z= 0.274 Chirality : 0.041 0.131 1376 Planarity : 0.003 0.054 1490 Dihedral : 6.472 96.791 1211 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.08 % Allowed : 14.34 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1105 helix: 0.78 (0.28), residues: 378 sheet: -0.12 (0.31), residues: 268 loop : -0.98 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.009 0.001 HIS B 82 PHE 0.016 0.001 PHE B 84 TYR 0.023 0.001 TYR A 176 ARG 0.003 0.000 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 0.967 Fit side-chains REVERT: B 242 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6274 (mm-30) REVERT: C 335 PHE cc_start: 0.8006 (m-80) cc_final: 0.7648 (m-80) REVERT: E 79 LEU cc_start: 0.7573 (pt) cc_final: 0.7163 (pt) REVERT: E 95 TYR cc_start: 0.8380 (m-80) cc_final: 0.7817 (m-80) REVERT: E 167 GLN cc_start: 0.8425 (tt0) cc_final: 0.8043 (tt0) outliers start: 18 outliers final: 8 residues processed: 167 average time/residue: 0.8950 time to fit residues: 162.4964 Evaluate side-chains 167 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.0050 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.0980 overall best weight: 0.2532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8664 Z= 0.151 Angle : 0.522 6.686 11809 Z= 0.267 Chirality : 0.040 0.130 1376 Planarity : 0.003 0.045 1490 Dihedral : 6.377 95.482 1211 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.62 % Allowed : 17.46 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.18 (0.26), residues: 1105 helix: 0.87 (0.28), residues: 379 sheet: -0.03 (0.31), residues: 268 loop : -0.94 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 99 HIS 0.008 0.001 HIS B 82 PHE 0.015 0.001 PHE B 84 TYR 0.017 0.001 TYR A 176 ARG 0.008 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 1.017 Fit side-chains REVERT: B 242 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6192 (mm-30) REVERT: B 244 ASN cc_start: 0.8049 (m110) cc_final: 0.7637 (m110) REVERT: C 335 PHE cc_start: 0.7953 (m-80) cc_final: 0.7700 (m-80) REVERT: E 79 LEU cc_start: 0.7510 (pt) cc_final: 0.7112 (pt) REVERT: E 95 TYR cc_start: 0.8398 (m-80) cc_final: 0.7980 (m-80) REVERT: E 167 GLN cc_start: 0.8383 (tt0) cc_final: 0.8058 (tt0) outliers start: 14 outliers final: 7 residues processed: 165 average time/residue: 0.8450 time to fit residues: 152.0932 Evaluate side-chains 167 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 160 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 177 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 17 GLN C 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8664 Z= 0.419 Angle : 0.669 8.520 11809 Z= 0.347 Chirality : 0.046 0.143 1376 Planarity : 0.004 0.051 1490 Dihedral : 6.497 82.883 1211 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.61 % Favored : 94.21 % Rotamer: Outliers : 2.43 % Allowed : 17.92 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.25), residues: 1105 helix: 0.54 (0.27), residues: 381 sheet: -0.16 (0.31), residues: 270 loop : -1.10 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 211 HIS 0.011 0.003 HIS B 209 PHE 0.026 0.003 PHE A 222 TYR 0.022 0.003 TYR A 534 ARG 0.010 0.001 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 1.037 Fit side-chains REVERT: B 35 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7177 (mtm-85) REVERT: B 242 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6234 (mm-30) REVERT: B 244 ASN cc_start: 0.8113 (m110) cc_final: 0.7712 (m110) REVERT: C 22 ARG cc_start: 0.7013 (mtt180) cc_final: 0.6809 (mtt180) outliers start: 21 outliers final: 11 residues processed: 160 average time/residue: 0.8442 time to fit residues: 147.4543 Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 0.0060 chunk 26 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8664 Z= 0.200 Angle : 0.571 6.981 11809 Z= 0.293 Chirality : 0.042 0.159 1376 Planarity : 0.004 0.045 1490 Dihedral : 6.278 84.637 1211 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.25 % Favored : 95.57 % Rotamer: Outliers : 2.43 % Allowed : 20.46 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.36 (0.26), residues: 1105 helix: 0.71 (0.27), residues: 381 sheet: -0.11 (0.31), residues: 268 loop : -1.06 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 133 HIS 0.008 0.002 HIS B 82 PHE 0.025 0.002 PHE A 222 TYR 0.022 0.002 TYR A 176 ARG 0.010 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.107 Fit side-chains REVERT: B 35 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7109 (mtm-85) REVERT: B 242 GLU cc_start: 0.6487 (mm-30) cc_final: 0.6209 (mm-30) REVERT: B 244 ASN cc_start: 0.8075 (m110) cc_final: 0.7668 (m110) outliers start: 21 outliers final: 9 residues processed: 164 average time/residue: 0.8955 time to fit residues: 160.1465 Evaluate side-chains 163 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 0.0040 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8664 Z= 0.192 Angle : 0.570 8.493 11809 Z= 0.292 Chirality : 0.041 0.133 1376 Planarity : 0.004 0.048 1490 Dihedral : 6.338 86.754 1211 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 2.20 % Allowed : 21.62 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.30 (0.26), residues: 1105 helix: 0.76 (0.27), residues: 381 sheet: -0.12 (0.31), residues: 269 loop : -0.99 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.008 0.002 HIS B 82 PHE 0.015 0.001 PHE B 81 TYR 0.020 0.002 TYR A 176 ARG 0.012 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 0.987 Fit side-chains REVERT: A 189 ILE cc_start: 0.7410 (mm) cc_final: 0.7199 (tp) REVERT: A 246 ILE cc_start: 0.8137 (mp) cc_final: 0.7869 (mt) REVERT: B 35 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.7078 (mtm-85) REVERT: B 242 GLU cc_start: 0.6469 (mm-30) cc_final: 0.6175 (mm-30) REVERT: B 244 ASN cc_start: 0.8069 (m110) cc_final: 0.7664 (m110) REVERT: C 212 ASP cc_start: 0.7551 (t70) cc_final: 0.7004 (t70) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 0.8484 time to fit residues: 152.7096 Evaluate side-chains 169 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN C 17 GLN C 230 ASN E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8664 Z= 0.202 Angle : 0.566 7.148 11809 Z= 0.290 Chirality : 0.042 0.140 1376 Planarity : 0.004 0.052 1490 Dihedral : 6.348 87.506 1211 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.77 % Allowed : 20.92 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.26 (0.26), residues: 1105 helix: 0.81 (0.28), residues: 375 sheet: -0.12 (0.31), residues: 269 loop : -0.95 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 169 HIS 0.007 0.002 HIS B 82 PHE 0.030 0.002 PHE A 222 TYR 0.020 0.002 TYR A 534 ARG 0.012 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.022 Fit side-chains REVERT: A 189 ILE cc_start: 0.7408 (mm) cc_final: 0.7196 (tp) REVERT: A 246 ILE cc_start: 0.8126 (mp) cc_final: 0.7856 (mt) REVERT: B 35 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7081 (mtm-85) REVERT: B 242 GLU cc_start: 0.6448 (mm-30) cc_final: 0.6146 (mm-30) REVERT: B 244 ASN cc_start: 0.8067 (m110) cc_final: 0.7672 (m110) REVERT: E 79 LEU cc_start: 0.7740 (pt) cc_final: 0.7276 (pt) outliers start: 24 outliers final: 13 residues processed: 166 average time/residue: 0.8513 time to fit residues: 154.3017 Evaluate side-chains 171 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 42 optimal weight: 0.0870 chunk 76 optimal weight: 0.4980 chunk 30 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN E 82 GLN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8664 Z= 0.151 Angle : 0.552 8.862 11809 Z= 0.281 Chirality : 0.041 0.184 1376 Planarity : 0.004 0.052 1490 Dihedral : 6.301 90.407 1211 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.08 % Allowed : 21.62 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.26), residues: 1105 helix: 0.85 (0.28), residues: 375 sheet: -0.08 (0.31), residues: 269 loop : -0.91 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.006 0.001 HIS B 82 PHE 0.030 0.001 PHE A 222 TYR 0.018 0.002 TYR A 534 ARG 0.013 0.000 ARG C 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 1.022 Fit side-chains REVERT: A 189 ILE cc_start: 0.7348 (mm) cc_final: 0.7137 (tp) REVERT: A 246 ILE cc_start: 0.8041 (mp) cc_final: 0.7785 (mt) REVERT: B 242 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6136 (mm-30) REVERT: E 79 LEU cc_start: 0.7585 (pt) cc_final: 0.7118 (pt) REVERT: E 95 TYR cc_start: 0.8257 (m-80) cc_final: 0.7743 (m-80) REVERT: E 167 GLN cc_start: 0.8396 (tt0) cc_final: 0.8123 (tt0) outliers start: 18 outliers final: 10 residues processed: 164 average time/residue: 0.8244 time to fit residues: 147.4420 Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 chunk 108 optimal weight: 0.1980 chunk 99 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8664 Z= 0.166 Angle : 0.551 6.642 11809 Z= 0.281 Chirality : 0.041 0.146 1376 Planarity : 0.004 0.057 1490 Dihedral : 6.254 89.656 1211 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.27 % Allowed : 22.89 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.15 (0.26), residues: 1105 helix: 0.89 (0.28), residues: 375 sheet: -0.05 (0.31), residues: 269 loop : -0.88 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 169 HIS 0.006 0.001 HIS B 82 PHE 0.017 0.001 PHE E 68 TYR 0.019 0.002 TYR A 534 ARG 0.013 0.000 ARG C 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.068 Fit side-chains REVERT: A 189 ILE cc_start: 0.7346 (mm) cc_final: 0.7137 (tp) REVERT: A 246 ILE cc_start: 0.8047 (mp) cc_final: 0.7790 (mt) REVERT: B 242 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6128 (mm-30) REVERT: E 79 LEU cc_start: 0.7595 (pt) cc_final: 0.7130 (pt) outliers start: 11 outliers final: 10 residues processed: 155 average time/residue: 0.8929 time to fit residues: 150.7765 Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.161127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141360 restraints weight = 11806.176| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.79 r_work: 0.3745 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8664 Z= 0.242 Angle : 0.588 8.631 11809 Z= 0.301 Chirality : 0.042 0.132 1376 Planarity : 0.004 0.057 1490 Dihedral : 6.239 87.276 1211 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.50 % Allowed : 22.89 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.20 (0.26), residues: 1105 helix: 0.83 (0.27), residues: 375 sheet: -0.05 (0.31), residues: 269 loop : -0.92 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 144 HIS 0.007 0.002 HIS B 82 PHE 0.032 0.002 PHE A 222 TYR 0.019 0.002 TYR A 507 ARG 0.013 0.000 ARG C 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3456.15 seconds wall clock time: 62 minutes 27.45 seconds (3747.45 seconds total)