Starting phenix.real_space_refine on Mon Mar 11 13:49:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6p_32331/03_2024/7w6p_32331_updated.pdb" } resolution = 3.47 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= 0.004 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5364 2.51 5 N 1435 2.21 5 O 1552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H ASP 62": "OD1" <-> "OD2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ASP 90": "OD1" <-> "OD2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 125": "OD1" <-> "OD2" Residue "H TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R ARG 240": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 386": "NH1" <-> "NH2" Residue "R PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 450": "NH1" <-> "NH2" 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: 8408 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1604 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 201} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2572 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "H" Number of atoms: 1770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1770 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2044 Unusual residues: {'W96': 1} Classifications: {'peptide': 258, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 248, None: 1} Not linked: pdbres="CYS R 457 " pdbres="W96 R 501 " Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 4.78, per 1000 atoms: 0.57 Number of scatterers: 8408 At special positions: 0 Unit cell: (88.4, 113.9, 120.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1552 8.00 N 1435 7.00 C 5364 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 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: 3.18 Conformation dependent library (CDL) restraints added in 1.6 seconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 14 sheets defined 31.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 29 removed outlier: 3.522A pdb=" N ASN A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.340A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.222A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.768A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.541A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'R' and resid 47 through 73 removed outlier: 4.132A pdb=" N VAL R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 107 removed outlier: 3.610A pdb=" N LEU R 85 " --> pdb=" O PRO R 82 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE R 86 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE R 102 " --> pdb=" O THR R 99 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 118 through 150 removed outlier: 3.656A pdb=" N ILE R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 159 Processing helix chain 'R' and resid 162 through 178 Processing helix chain 'R' and resid 211 through 219 Processing helix chain 'R' and resid 221 through 241 Processing helix chain 'R' and resid 380 through 411 Proline residue: R 404 - end of helix Processing helix chain 'R' and resid 423 through 440 removed outlier: 3.689A pdb=" N SER R 434 " --> pdb=" O GLY R 430 " (cutoff:3.500A) Proline residue: R 438 - end of helix Processing helix chain 'R' and resid 446 through 456 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.805A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 202 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY A 40 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.739A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.659A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.887A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 232 through 234 Processing sheet with id= F, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.741A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.876A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 249 through 253 removed outlier: 4.052A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.715A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 4 through 6 Processing sheet with id= K, first strand: chain 'H' and resid 114 through 117 removed outlier: 3.922A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL H 97 " --> pdb=" O HIS H 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 134 through 136 removed outlier: 7.034A pdb=" N LYS H 232 " --> pdb=" O VAL H 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'H' and resid 146 through 148 Processing sheet with id= N, first strand: chain 'H' and resid 214 through 219 removed outlier: 5.875A pdb=" N LEU H 166 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU H 175 " --> pdb=" O LEU H 166 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 918 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: 2.10 Time building geometry restraints manager: 3.47 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: 1895 1.33 - 1.45: 1924 1.45 - 1.57: 4683 1.57 - 1.69: 1 1.69 - 1.81: 79 Bond restraints: 8582 Sorted by residual: bond pdb=" C PHE R 405 " pdb=" O PHE R 405 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.16e-02 7.43e+03 5.84e+00 bond pdb=" C3 W96 R 501 " pdb=" C4 W96 R 501 " ideal model delta sigma weight residual 1.376 1.423 -0.047 2.00e-02 2.50e+03 5.55e+00 bond pdb=" N THR B 274 " pdb=" CA THR B 274 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.38e-02 5.25e+03 5.48e+00 bond pdb=" C TYR R 409 " pdb=" O TYR R 409 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.25e-02 6.40e+03 5.06e+00 bond pdb=" N PHE R 405 " pdb=" CA PHE R 405 " ideal model delta sigma weight residual 1.459 1.481 -0.021 1.18e-02 7.18e+03 3.24e+00 ... (remaining 8577 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.87: 128 105.87 - 112.90: 4633 112.90 - 119.94: 2784 119.94 - 126.98: 3992 126.98 - 134.01: 97 Bond angle restraints: 11634 Sorted by residual: angle pdb=" CA TYR R 409 " pdb=" CB TYR R 409 " pdb=" CG TYR R 409 " ideal model delta sigma weight residual 113.90 121.85 -7.95 1.80e+00 3.09e-01 1.95e+01 angle pdb=" C12 W96 R 501 " pdb=" C3 W96 R 501 " pdb=" N2 W96 R 501 " ideal model delta sigma weight residual 108.11 120.84 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C PHE R 405 " pdb=" CA PHE R 405 " pdb=" CB PHE R 405 " ideal model delta sigma weight residual 110.95 104.43 6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" N PHE R 406 " pdb=" CA PHE R 406 " pdb=" C PHE R 406 " ideal model delta sigma weight residual 111.28 106.81 4.47 1.09e+00 8.42e-01 1.68e+01 angle pdb=" C PHE R 406 " pdb=" N PHE R 407 " pdb=" CA PHE R 407 " ideal model delta sigma weight residual 120.28 115.25 5.03 1.34e+00 5.57e-01 1.41e+01 ... (remaining 11629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4511 17.30 - 34.60: 447 34.60 - 51.89: 77 51.89 - 69.19: 10 69.19 - 86.49: 7 Dihedral angle restraints: 5052 sinusoidal: 1919 harmonic: 3133 Sorted by residual: dihedral pdb=" CB CYS R 121 " pdb=" SG CYS R 121 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual -86.00 -172.49 86.49 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 5049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 979 0.045 - 0.090: 272 0.090 - 0.135: 71 0.135 - 0.180: 8 0.180 - 0.225: 1 Chirality restraints: 1331 Sorted by residual: chirality pdb=" CB VAL H 64 " pdb=" CA VAL H 64 " pdb=" CG1 VAL H 64 " pdb=" CG2 VAL H 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CG LEU B 286 " pdb=" CB LEU B 286 " pdb=" CD1 LEU B 286 " pdb=" CD2 LEU B 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1328 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO R 404 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.94e+00 pdb=" C PRO R 404 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO R 404 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE R 405 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 98 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C ALA R 98 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA R 98 " -0.016 2.00e-02 2.50e+03 pdb=" N THR R 99 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 97 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C VAL R 97 " 0.039 2.00e-02 2.50e+03 pdb=" O VAL R 97 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA R 98 " -0.013 2.00e-02 2.50e+03 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 694 2.74 - 3.28: 8816 3.28 - 3.82: 14039 3.82 - 4.36: 16652 4.36 - 4.90: 28591 Nonbonded interactions: 68792 Sorted by model distance: nonbonded pdb=" OE2 GLU A 20 " pdb=" NZ LYS B 89 " model vdw 2.196 2.520 nonbonded pdb=" O ALA A 41 " pdb=" NZ LYS A 46 " model vdw 2.234 2.520 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.248 2.520 nonbonded pdb=" O ARG H 67 " pdb=" OG1 THR H 84 " model vdw 2.256 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.266 2.440 ... (remaining 68787 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 7.130 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.170 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8582 Z= 0.265 Angle : 0.700 12.728 11634 Z= 0.394 Chirality : 0.044 0.225 1331 Planarity : 0.004 0.056 1468 Dihedral : 13.782 80.650 3024 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1061 helix: 1.20 (0.28), residues: 344 sheet: -1.72 (0.31), residues: 254 loop : -1.31 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 169 HIS 0.007 0.001 HIS A 189 PHE 0.028 0.002 PHE B 234 TYR 0.028 0.002 TYR R 409 ARG 0.012 0.000 ARG H 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 47 TRP cc_start: 0.3248 (t60) cc_final: 0.2947 (t60) REVERT: H 218 MET cc_start: -0.0933 (ttt) cc_final: -0.1655 (ttt) REVERT: R 437 ASN cc_start: 0.3830 (m-40) cc_final: 0.3292 (m-40) outliers start: 1 outliers final: 1 residues processed: 97 average time/residue: 0.2107 time to fit residues: 28.4227 Evaluate side-chains 72 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 54 optimal weight: 0.3980 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN R 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1525 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8582 Z= 0.181 Angle : 0.593 7.434 11634 Z= 0.308 Chirality : 0.043 0.156 1331 Planarity : 0.004 0.058 1468 Dihedral : 5.573 77.753 1171 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.89 % Allowed : 8.88 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.26), residues: 1061 helix: 1.46 (0.27), residues: 362 sheet: -1.47 (0.32), residues: 247 loop : -1.38 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 339 HIS 0.007 0.001 HIS H 35 PHE 0.024 0.002 PHE R 387 TYR 0.016 0.002 TYR R 409 ARG 0.004 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 HIS cc_start: 0.2089 (t-90) cc_final: 0.1329 (t-90) REVERT: H 47 TRP cc_start: 0.4212 (t60) cc_final: 0.3456 (t60) REVERT: R 173 TRP cc_start: 0.4792 (m100) cc_final: 0.2616 (t60) REVERT: R 381 GLN cc_start: 0.0612 (mm-40) cc_final: 0.0247 (pp30) outliers start: 8 outliers final: 6 residues processed: 72 average time/residue: 0.2141 time to fit residues: 22.0859 Evaluate side-chains 69 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain R residue 135 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.0070 chunk 26 optimal weight: 0.0770 chunk 96 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1873 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8582 Z= 0.170 Angle : 0.563 6.060 11634 Z= 0.295 Chirality : 0.043 0.209 1331 Planarity : 0.004 0.059 1468 Dihedral : 5.318 77.288 1171 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.44 % Allowed : 12.43 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.26), residues: 1061 helix: 1.58 (0.27), residues: 353 sheet: -1.20 (0.34), residues: 233 loop : -1.49 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS A 189 PHE 0.016 0.002 PHE R 387 TYR 0.016 0.002 TYR H 60 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 342 ILE cc_start: 0.4685 (mt) cc_final: 0.4124 (mt) REVERT: B 285 LEU cc_start: 0.0567 (OUTLIER) cc_final: 0.0323 (tp) REVERT: H 47 TRP cc_start: 0.4078 (t60) cc_final: 0.3209 (t60) REVERT: H 83 MET cc_start: 0.5136 (mmm) cc_final: 0.4703 (mmm) REVERT: R 138 HIS cc_start: 0.5119 (OUTLIER) cc_final: 0.3512 (m170) REVERT: R 173 TRP cc_start: 0.5169 (m100) cc_final: 0.2638 (t60) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 0.2205 time to fit residues: 22.7944 Evaluate side-chains 68 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 138 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.0570 chunk 46 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 0.0770 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1777 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8582 Z= 0.123 Angle : 0.503 7.530 11634 Z= 0.260 Chirality : 0.040 0.149 1331 Planarity : 0.004 0.059 1468 Dihedral : 5.024 75.003 1170 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.55 % Allowed : 13.54 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1061 helix: 1.67 (0.28), residues: 355 sheet: -1.02 (0.34), residues: 232 loop : -1.47 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 189 PHE 0.015 0.001 PHE R 387 TYR 0.011 0.001 TYR R 409 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1600 (ptp) cc_final: -0.3272 (mmp) REVERT: A 342 ILE cc_start: 0.4611 (mt) cc_final: 0.4075 (mt) REVERT: B 45 MET cc_start: 0.1108 (mtt) cc_final: -0.0077 (ttm) REVERT: B 285 LEU cc_start: 0.0617 (OUTLIER) cc_final: 0.0220 (tp) REVERT: H 47 TRP cc_start: 0.3766 (t60) cc_final: 0.2735 (t60) REVERT: R 173 TRP cc_start: 0.5180 (m100) cc_final: 0.2368 (t60) outliers start: 14 outliers final: 4 residues processed: 77 average time/residue: 0.2060 time to fit residues: 22.6764 Evaluate side-chains 61 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 0.0030 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 340 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2077 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8582 Z= 0.166 Angle : 0.572 13.885 11634 Z= 0.292 Chirality : 0.041 0.159 1331 Planarity : 0.004 0.058 1468 Dihedral : 5.035 68.371 1170 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.11 % Allowed : 15.65 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1061 helix: 1.66 (0.28), residues: 354 sheet: -0.97 (0.35), residues: 224 loop : -1.53 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS H 220 PHE 0.013 0.002 PHE R 427 TYR 0.016 0.002 TYR H 60 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1423 (ptp) cc_final: -0.3003 (mmp) REVERT: B 295 ASN cc_start: 0.4977 (OUTLIER) cc_final: 0.4685 (m-40) REVERT: H 47 TRP cc_start: 0.3701 (t60) cc_final: 0.2639 (t60) REVERT: R 138 HIS cc_start: 0.5423 (OUTLIER) cc_final: 0.3571 (m170) REVERT: R 173 TRP cc_start: 0.5357 (m100) cc_final: 0.2571 (t60) outliers start: 19 outliers final: 9 residues processed: 76 average time/residue: 0.1948 time to fit residues: 21.5701 Evaluate side-chains 68 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 223 TYR Chi-restraints excluded: chain R residue 138 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 102 optimal weight: 0.0070 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2335 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8582 Z= 0.199 Angle : 0.632 12.875 11634 Z= 0.324 Chirality : 0.042 0.172 1331 Planarity : 0.005 0.061 1468 Dihedral : 5.259 59.743 1170 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.44 % Allowed : 15.54 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.26), residues: 1061 helix: 1.53 (0.28), residues: 354 sheet: -1.01 (0.36), residues: 197 loop : -1.70 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.012 0.002 HIS B 62 PHE 0.013 0.002 PHE R 427 TYR 0.022 0.002 TYR H 60 ARG 0.005 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1851 (ptp) cc_final: -0.3078 (mmp) REVERT: A 342 ILE cc_start: 0.4911 (mt) cc_final: 0.4700 (mt) REVERT: H 36 TRP cc_start: 0.3324 (m100) cc_final: 0.2886 (m100) REVERT: H 47 TRP cc_start: 0.3795 (t60) cc_final: 0.2756 (t60) REVERT: R 138 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.3760 (m170) REVERT: R 173 TRP cc_start: 0.5474 (m100) cc_final: 0.2511 (t60) outliers start: 22 outliers final: 11 residues processed: 78 average time/residue: 0.1955 time to fit residues: 22.4414 Evaluate side-chains 70 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 chunk 74 optimal weight: 0.0020 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 0.0010 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.2412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2143 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 8582 Z= 0.147 Angle : 0.548 11.566 11634 Z= 0.276 Chirality : 0.041 0.161 1331 Planarity : 0.004 0.052 1468 Dihedral : 4.896 60.835 1170 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.44 % Allowed : 15.98 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.26), residues: 1061 helix: 1.68 (0.28), residues: 355 sheet: -1.17 (0.36), residues: 200 loop : -1.64 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.017 0.001 HIS R 138 PHE 0.011 0.001 PHE R 387 TYR 0.011 0.001 TYR A 320 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1890 (ptp) cc_final: -0.3475 (mmp) REVERT: A 320 TYR cc_start: 0.1726 (m-10) cc_final: 0.1114 (t80) REVERT: B 273 ILE cc_start: 0.0719 (OUTLIER) cc_final: -0.0214 (mp) REVERT: B 286 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.5418 (mp) REVERT: H 36 TRP cc_start: 0.3324 (m100) cc_final: 0.2745 (m100) REVERT: H 47 TRP cc_start: 0.3677 (t60) cc_final: 0.2833 (t60) REVERT: R 173 TRP cc_start: 0.5398 (m100) cc_final: 0.2540 (t60) outliers start: 22 outliers final: 13 residues processed: 82 average time/residue: 0.1856 time to fit residues: 22.2922 Evaluate side-chains 74 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2551 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8582 Z= 0.223 Angle : 0.671 9.834 11634 Z= 0.346 Chirality : 0.045 0.169 1331 Planarity : 0.004 0.053 1468 Dihedral : 5.441 63.277 1170 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.55 % Allowed : 16.43 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1061 helix: 1.51 (0.28), residues: 345 sheet: -1.33 (0.35), residues: 217 loop : -1.73 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 82 HIS 0.011 0.002 HIS H 220 PHE 0.024 0.002 PHE B 235 TYR 0.024 0.002 TYR H 60 ARG 0.005 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: -0.1659 (ptp) cc_final: -0.3110 (mmt) REVERT: B 273 ILE cc_start: 0.1094 (OUTLIER) cc_final: 0.0618 (mp) REVERT: B 286 LEU cc_start: 0.6957 (mp) cc_final: 0.5848 (mp) REVERT: H 36 TRP cc_start: 0.3722 (m100) cc_final: 0.2957 (m100) REVERT: R 138 HIS cc_start: 0.6304 (OUTLIER) cc_final: 0.4181 (m170) REVERT: R 159 LYS cc_start: 0.4356 (mtmt) cc_final: 0.3803 (mptt) REVERT: R 173 TRP cc_start: 0.5547 (m100) cc_final: 0.2531 (t60) outliers start: 23 outliers final: 16 residues processed: 83 average time/residue: 0.1688 time to fit residues: 20.9524 Evaluate side-chains 74 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 56 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0070 chunk 97 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 41 optimal weight: 0.0770 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.0370 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2371 moved from start: 0.6274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 8582 Z= 0.151 Angle : 0.593 10.383 11634 Z= 0.297 Chirality : 0.042 0.164 1331 Planarity : 0.004 0.073 1468 Dihedral : 5.085 67.196 1170 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.33 % Allowed : 17.54 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1061 helix: 1.71 (0.28), residues: 352 sheet: -1.22 (0.35), residues: 206 loop : -1.70 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.011 0.001 HIS B 62 PHE 0.012 0.001 PHE B 241 TYR 0.012 0.001 TYR H 178 ARG 0.016 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1774 (ptp) cc_final: -0.3456 (mmp) REVERT: B 19 ARG cc_start: 0.6237 (mpt-90) cc_final: 0.5986 (mpt180) REVERT: B 273 ILE cc_start: 0.1047 (OUTLIER) cc_final: 0.0566 (mp) REVERT: B 286 LEU cc_start: 0.6783 (mp) cc_final: 0.5601 (mp) REVERT: H 36 TRP cc_start: 0.3548 (m100) cc_final: 0.2745 (m100) REVERT: H 47 TRP cc_start: 0.3465 (t60) cc_final: 0.2871 (t60) REVERT: R 138 HIS cc_start: 0.5519 (OUTLIER) cc_final: 0.3940 (m170) REVERT: R 159 LYS cc_start: 0.4131 (mtmt) cc_final: 0.3613 (mptt) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.2030 time to fit residues: 20.8143 Evaluate side-chains 70 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 105 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2552 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8582 Z= 0.184 Angle : 0.605 9.792 11634 Z= 0.307 Chirality : 0.042 0.163 1331 Planarity : 0.004 0.063 1468 Dihedral : 5.114 69.542 1170 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.78 % Allowed : 17.31 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.26), residues: 1061 helix: 1.72 (0.28), residues: 352 sheet: -1.22 (0.35), residues: 212 loop : -1.77 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.008 0.002 HIS B 62 PHE 0.013 0.002 PHE H 108 TYR 0.015 0.001 TYR H 60 ARG 0.010 0.000 ARG B 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: -0.1443 (ptp) cc_final: -0.3367 (tpt) REVERT: A 323 MET cc_start: 0.5095 (tpp) cc_final: 0.2324 (mtp) REVERT: B 19 ARG cc_start: 0.6402 (mpt-90) cc_final: 0.6142 (mpt180) REVERT: B 183 HIS cc_start: 0.2468 (OUTLIER) cc_final: 0.1229 (m90) REVERT: B 273 ILE cc_start: 0.1025 (OUTLIER) cc_final: 0.0538 (mp) REVERT: B 286 LEU cc_start: 0.6932 (mp) cc_final: 0.5832 (mp) REVERT: H 36 TRP cc_start: 0.3655 (m100) cc_final: 0.2782 (m100) REVERT: H 47 TRP cc_start: 0.3412 (t60) cc_final: 0.2720 (t60) REVERT: H 180 MET cc_start: 0.2961 (ptt) cc_final: 0.2555 (ptt) REVERT: R 59 MET cc_start: 0.5724 (tmm) cc_final: 0.5523 (tmm) REVERT: R 138 HIS cc_start: 0.6156 (OUTLIER) cc_final: 0.3959 (m170) outliers start: 16 outliers final: 13 residues processed: 75 average time/residue: 0.1931 time to fit residues: 21.3495 Evaluate side-chains 77 residues out of total 925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 138 HIS Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 387 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0270 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.242457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.212730 restraints weight = 11329.711| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.51 r_work: 0.4319 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2365 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 8582 Z= 0.158 Angle : 0.588 9.592 11634 Z= 0.296 Chirality : 0.041 0.162 1331 Planarity : 0.004 0.058 1468 Dihedral : 5.051 71.968 1170 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.00 % Allowed : 17.31 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1061 helix: 1.69 (0.28), residues: 353 sheet: -1.21 (0.35), residues: 214 loop : -1.75 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.010 0.002 HIS R 138 PHE 0.013 0.001 PHE B 241 TYR 0.011 0.001 TYR H 60 ARG 0.010 0.000 ARG B 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.12 seconds wall clock time: 37 minutes 39.52 seconds (2259.52 seconds total)