Starting phenix.real_space_refine on Tue Jun 25 18:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trs_26102/06_2024/7trs_26102_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trs_26102/06_2024/7trs_26102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trs_26102/06_2024/7trs_26102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trs_26102/06_2024/7trs_26102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trs_26102/06_2024/7trs_26102_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7trs_26102/06_2024/7trs_26102_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 62 5.16 5 C 5471 2.51 5 N 1443 2.21 5 O 1595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8571 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2549 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 391 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1768 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1748 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2115 Unusual residues: {'ACH': 1} Classifications: {'peptide': 270, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 259, None: 1} Not linked: pdbres="HIS R 466 " pdbres="ACH R 501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 5.19, per 1000 atoms: 0.61 Number of scatterers: 8571 At special positions: 0 Unit cell: (90.47, 119.52, 121.18, 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 62 16.00 O 1595 8.00 N 1443 7.00 C 5471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " 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 1.8 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: 2102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 33.8% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.587A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.053A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 5.007A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'R' and resid 34 through 59 Processing helix chain 'R' and resid 61 through 63 No H-bonds generated for 'chain 'R' and resid 61 through 63' Processing helix chain 'R' and resid 66 through 83 removed outlier: 4.123A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 Processing helix chain 'R' and resid 102 through 135 Processing helix chain 'R' and resid 140 through 143 No H-bonds generated for 'chain 'R' and resid 140 through 143' Processing helix chain 'R' and resid 146 through 175 Proline residue: R 166 - end of helix removed outlier: 5.249A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 190 No H-bonds generated for 'chain 'R' and resid 188 through 190' Processing helix chain 'R' and resid 193 through 203 Processing helix chain 'R' and resid 205 through 220 Processing helix chain 'R' and resid 393 through 423 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 427 through 429 No H-bonds generated for 'chain 'R' and resid 427 through 429' Processing helix chain 'R' and resid 432 through 447 removed outlier: 3.974A pdb=" N CYS R 442 " --> pdb=" O GLY R 438 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR R 443 " --> pdb=" O TYR R 439 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL R 444 " --> pdb=" O TRP R 440 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN R 445 " --> pdb=" O LEU R 441 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR R 447 " --> pdb=" O TYR R 443 " (cutoff:3.500A) Processing helix chain 'R' and resid 449 through 453 Processing helix chain 'R' and resid 458 through 465 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.931A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.914A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.805A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.998A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.521A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.481A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 327 through 330 Processing sheet with id= H, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.520A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.531A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 155 through 160 Processing sheet with id= L, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.409A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1104 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: 2.42 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2677 1.34 - 1.46: 1799 1.46 - 1.58: 4188 1.58 - 1.69: 0 1.69 - 1.81: 89 Bond restraints: 8753 Sorted by residual: bond pdb=" C5 ACH R 501 " pdb=" O4 ACH R 501 " ideal model delta sigma weight residual 1.335 1.455 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" C THR R 414 " pdb=" N PRO R 415 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.38e-02 5.25e+03 8.16e+00 bond pdb=" CA THR R 414 " pdb=" C THR R 414 " ideal model delta sigma weight residual 1.522 1.544 -0.022 1.26e-02 6.30e+03 3.03e+00 bond pdb=" CB PRO R 415 " pdb=" CG PRO R 415 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.82e+00 bond pdb=" C2 ACH R 501 " pdb=" N1 ACH R 501 " ideal model delta sigma weight residual 1.506 1.473 0.033 2.00e-02 2.50e+03 2.74e+00 ... (remaining 8748 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.49: 179 106.49 - 113.37: 4826 113.37 - 120.25: 3116 120.25 - 127.13: 3693 127.13 - 134.01: 87 Bond angle restraints: 11901 Sorted by residual: angle pdb=" CA PRO R 415 " pdb=" N PRO R 415 " pdb=" CD PRO R 415 " ideal model delta sigma weight residual 112.00 107.57 4.43 1.40e+00 5.10e-01 1.00e+01 angle pdb=" CA ARG B 150 " pdb=" CB ARG B 150 " pdb=" CG ARG B 150 " ideal model delta sigma weight residual 114.10 120.36 -6.26 2.00e+00 2.50e-01 9.80e+00 angle pdb=" CA THR R 414 " pdb=" CB THR R 414 " pdb=" CG2 THR R 414 " ideal model delta sigma weight residual 110.50 115.78 -5.28 1.70e+00 3.46e-01 9.64e+00 angle pdb=" C ARG B 19 " pdb=" N ASP B 20 " pdb=" CA ASP B 20 " ideal model delta sigma weight residual 122.06 116.30 5.76 1.86e+00 2.89e-01 9.58e+00 angle pdb=" C PHE A 307 " pdb=" N GLU A 308 " pdb=" CA GLU A 308 " ideal model delta sigma weight residual 121.58 115.58 6.00 1.95e+00 2.63e-01 9.46e+00 ... (remaining 11896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4765 17.18 - 34.35: 312 34.35 - 51.53: 57 51.53 - 68.71: 6 68.71 - 85.88: 8 Dihedral angle restraints: 5148 sinusoidal: 1891 harmonic: 3257 Sorted by residual: dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 51.52 41.48 1 1.00e+01 1.00e-02 2.41e+01 dihedral pdb=" CA TYR H 101 " pdb=" C TYR H 101 " pdb=" N TYR H 102 " pdb=" CA TYR H 102 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+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 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1068 0.060 - 0.121: 264 0.121 - 0.181: 44 0.181 - 0.241: 4 0.241 - 0.302: 1 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA THR R 414 " pdb=" N THR R 414 " pdb=" C THR R 414 " pdb=" CB THR R 414 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB VAL R 33 " pdb=" CA VAL R 33 " pdb=" CG1 VAL R 33 " pdb=" CG2 VAL R 33 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.14e-01 ... (remaining 1378 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 199 " 0.047 5.00e-02 4.00e+02 7.22e-02 8.34e+00 pdb=" N PRO H 200 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO H 200 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 200 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO B 236 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 40 " 0.039 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO H 41 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " 0.033 5.00e-02 4.00e+02 ... (remaining 1493 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1754 2.77 - 3.31: 7708 3.31 - 3.84: 14748 3.84 - 4.37: 17214 4.37 - 4.90: 30188 Nonbonded interactions: 71612 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.243 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.273 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.304 2.440 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.321 2.440 ... (remaining 71607 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 3.760 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.720 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.006 0.120 8753 Z= 0.384 Angle : 0.775 8.943 11901 Z= 0.425 Chirality : 0.054 0.302 1381 Planarity : 0.006 0.072 1496 Dihedral : 12.246 85.881 3034 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.09 (0.23), residues: 1105 helix: -1.01 (0.22), residues: 388 sheet: -0.23 (0.29), residues: 302 loop : -0.54 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 164 HIS 0.008 0.001 HIS B 142 PHE 0.023 0.002 PHE R 204 TYR 0.016 0.002 TYR A 302 ARG 0.006 0.001 ARG R 178 *********************** 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 188 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ASN cc_start: 0.8948 (m-40) cc_final: 0.8741 (m-40) REVERT: B 23 LYS cc_start: 0.9285 (tptp) cc_final: 0.9084 (tptp) REVERT: H 46 GLU cc_start: 0.7958 (tt0) cc_final: 0.7727 (tt0) REVERT: A 208 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8135 (ttt90) REVERT: A 306 GLN cc_start: 0.8949 (mm110) cc_final: 0.8479 (mp10) REVERT: A 345 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8315 (ttmt) REVERT: R 106 ASP cc_start: 0.7081 (m-30) cc_final: 0.6767 (t0) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 1.4609 time to fit residues: 289.1618 Evaluate side-chains 131 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 0.0020 overall best weight: 1.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 340 ASN G 18 GLN H 3 GLN H 231 GLN A 331 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8753 Z= 0.200 Angle : 0.580 8.821 11901 Z= 0.299 Chirality : 0.042 0.175 1381 Planarity : 0.005 0.056 1496 Dihedral : 4.319 26.024 1207 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.42 % Allowed : 11.45 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.03 (0.24), residues: 1105 helix: 0.71 (0.26), residues: 383 sheet: -0.05 (0.29), residues: 282 loop : -0.51 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE R 84 TYR 0.010 0.001 TYR R 215 ARG 0.006 0.000 ARG H 160 *********************** 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 161 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8023 (tt0) cc_final: 0.7800 (tt0) REVERT: H 76 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8540 (mtmm) REVERT: A 208 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.8161 (ttt90) REVERT: A 296 TYR cc_start: 0.7509 (t80) cc_final: 0.7196 (t80) REVERT: A 306 GLN cc_start: 0.8910 (mm110) cc_final: 0.8495 (mp10) REVERT: A 345 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8300 (ttmt) REVERT: R 152 MET cc_start: 0.7558 (mmp) cc_final: 0.7189 (mmt) outliers start: 22 outliers final: 8 residues processed: 150 average time/residue: 1.4932 time to fit residues: 235.6719 Evaluate side-chains 129 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 129 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN H 231 GLN R 122 ASN R 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8753 Z= 0.316 Angle : 0.606 8.803 11901 Z= 0.314 Chirality : 0.042 0.162 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.304 28.776 1207 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.64 % Allowed : 15.64 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1105 helix: 1.56 (0.27), residues: 377 sheet: -0.05 (0.29), residues: 289 loop : -0.46 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.001 PHE B 253 TYR 0.015 0.002 TYR H 227 ARG 0.006 0.001 ARG H 160 *********************** 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 144 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 19 LEU cc_start: 0.9750 (mm) cc_final: 0.9529 (mm) REVERT: H 46 GLU cc_start: 0.8012 (tt0) cc_final: 0.7791 (tt0) REVERT: H 76 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8465 (mtmm) REVERT: A 306 GLN cc_start: 0.8908 (mm110) cc_final: 0.8508 (mp10) REVERT: A 345 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8277 (ttmt) REVERT: A 349 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8234 (tptp) REVERT: R 152 MET cc_start: 0.7583 (mmp) cc_final: 0.7229 (mmt) REVERT: R 188 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 24 outliers final: 12 residues processed: 134 average time/residue: 1.4599 time to fit residues: 206.4238 Evaluate side-chains 122 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 234 GLU Chi-restraints excluded: chain H residue 247 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 45 VAL Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 188 GLN Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 219 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 51 optimal weight: 50.0000 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 110 ASN H 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8753 Z= 0.300 Angle : 0.586 7.825 11901 Z= 0.303 Chirality : 0.042 0.155 1381 Planarity : 0.004 0.047 1496 Dihedral : 4.276 29.942 1207 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.75 % Allowed : 17.07 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1105 helix: 1.75 (0.28), residues: 376 sheet: -0.04 (0.29), residues: 287 loop : -0.35 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 98 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE B 253 TYR 0.012 0.001 TYR H 227 ARG 0.007 0.001 ARG H 160 *********************** 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 144 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8034 (tt0) cc_final: 0.7811 (tt0) REVERT: H 76 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8310 (mtmm) REVERT: H 244 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8805 (ttpp) REVERT: A 306 GLN cc_start: 0.8905 (mm110) cc_final: 0.8503 (mp10) REVERT: A 345 LYS cc_start: 0.8583 (ttmt) cc_final: 0.8300 (ttmt) REVERT: A 349 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8288 (tptp) REVERT: R 86 MET cc_start: 0.7155 (mmt) cc_final: 0.6829 (tmt) REVERT: R 98 TRP cc_start: 0.7214 (t-100) cc_final: 0.6899 (t60) REVERT: R 136 LYS cc_start: 0.7541 (mmmm) cc_final: 0.7246 (mmtp) REVERT: R 152 MET cc_start: 0.7683 (mmp) cc_final: 0.7317 (mmt) outliers start: 25 outliers final: 14 residues processed: 132 average time/residue: 1.4605 time to fit residues: 203.4688 Evaluate side-chains 127 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 73 optimal weight: 0.1980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.4980 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8753 Z= 0.212 Angle : 0.556 8.843 11901 Z= 0.285 Chirality : 0.041 0.160 1381 Planarity : 0.004 0.048 1496 Dihedral : 4.123 32.587 1207 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.64 % Allowed : 17.62 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.79 (0.25), residues: 1105 helix: 2.04 (0.28), residues: 365 sheet: -0.04 (0.29), residues: 287 loop : -0.27 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.011 0.001 PHE B 253 TYR 0.013 0.001 TYR H 190 ARG 0.008 0.000 ARG H 160 *********************** 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 142 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: G 19 LEU cc_start: 0.9740 (mm) cc_final: 0.9504 (mm) REVERT: H 46 GLU cc_start: 0.8082 (tt0) cc_final: 0.7872 (tt0) REVERT: H 76 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8342 (mtmm) REVERT: H 244 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8817 (ttpp) REVERT: A 306 GLN cc_start: 0.8874 (mm110) cc_final: 0.8536 (mp10) REVERT: A 345 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8279 (ttmt) REVERT: A 349 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8274 (tptp) REVERT: R 86 MET cc_start: 0.7196 (mmt) cc_final: 0.6817 (tmt) REVERT: R 136 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7294 (mmtp) REVERT: R 152 MET cc_start: 0.7710 (mmp) cc_final: 0.7385 (mmt) outliers start: 24 outliers final: 13 residues processed: 133 average time/residue: 1.3728 time to fit residues: 193.1342 Evaluate side-chains 125 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 122 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8753 Z= 0.205 Angle : 0.566 9.040 11901 Z= 0.291 Chirality : 0.040 0.158 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.083 34.039 1207 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.53 % Allowed : 19.16 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.84 (0.25), residues: 1105 helix: 2.04 (0.28), residues: 363 sheet: 0.05 (0.30), residues: 285 loop : -0.23 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 98 HIS 0.003 0.001 HIS B 225 PHE 0.010 0.001 PHE B 253 TYR 0.013 0.001 TYR H 190 ARG 0.007 0.000 ARG H 160 *********************** 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 139 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8078 (tt0) cc_final: 0.7866 (tt0) REVERT: H 76 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8331 (mtmm) REVERT: H 244 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8830 (ttpp) REVERT: A 306 GLN cc_start: 0.8868 (mm110) cc_final: 0.8515 (mp10) REVERT: A 345 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8262 (ttmt) REVERT: A 349 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8272 (tptp) REVERT: R 86 MET cc_start: 0.7172 (mmt) cc_final: 0.6791 (tmt) REVERT: R 136 LYS cc_start: 0.7590 (mmmm) cc_final: 0.7357 (mmtm) REVERT: R 152 MET cc_start: 0.7734 (mmp) cc_final: 0.7426 (mmt) outliers start: 23 outliers final: 12 residues processed: 130 average time/residue: 1.4213 time to fit residues: 195.2413 Evaluate side-chains 125 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 47 ASN Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 0.0980 chunk 65 optimal weight: 0.4980 chunk 42 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8753 Z= 0.152 Angle : 0.548 11.094 11901 Z= 0.279 Chirality : 0.040 0.157 1381 Planarity : 0.004 0.052 1496 Dihedral : 3.947 37.491 1207 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.43 % Allowed : 21.04 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1105 helix: 1.80 (0.28), residues: 377 sheet: 0.23 (0.30), residues: 270 loop : -0.18 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 98 HIS 0.003 0.000 HIS B 225 PHE 0.008 0.001 PHE R 186 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.001 ARG H 160 *********************** 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 131 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8053 (tt0) cc_final: 0.7852 (tt0) REVERT: H 244 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8805 (ttpp) REVERT: A 38 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7533 (mt) REVERT: A 306 GLN cc_start: 0.8845 (mm110) cc_final: 0.8538 (mp10) REVERT: A 345 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8186 (ttmt) REVERT: A 349 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8311 (tptp) REVERT: R 86 MET cc_start: 0.7021 (mmt) cc_final: 0.6747 (tmt) REVERT: R 129 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7879 (t0) REVERT: R 136 LYS cc_start: 0.7580 (mmmm) cc_final: 0.7368 (mmtm) REVERT: R 152 MET cc_start: 0.7773 (mmp) cc_final: 0.7487 (mmt) REVERT: R 444 VAL cc_start: 0.8658 (t) cc_final: 0.8456 (m) outliers start: 13 outliers final: 4 residues processed: 128 average time/residue: 1.4341 time to fit residues: 193.8021 Evaluate side-chains 116 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8753 Z= 0.241 Angle : 0.600 13.224 11901 Z= 0.303 Chirality : 0.041 0.157 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.065 34.896 1207 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.31 % Allowed : 20.37 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.80 (0.26), residues: 1105 helix: 1.81 (0.28), residues: 377 sheet: 0.12 (0.30), residues: 279 loop : -0.22 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 440 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 253 TYR 0.020 0.001 TYR A 296 ARG 0.011 0.001 ARG A 205 *********************** 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 131 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8066 (tt0) cc_final: 0.7856 (tt0) REVERT: H 244 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8831 (ttpp) REVERT: A 38 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7668 (mt) REVERT: A 306 GLN cc_start: 0.8866 (mm110) cc_final: 0.8599 (mp10) REVERT: A 345 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8217 (ttmt) REVERT: A 349 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8318 (tptp) REVERT: R 86 MET cc_start: 0.7092 (mmt) cc_final: 0.6815 (tmt) REVERT: R 136 LYS cc_start: 0.7562 (mmmm) cc_final: 0.7356 (mmtm) REVERT: R 152 MET cc_start: 0.7725 (mmp) cc_final: 0.7412 (mmt) outliers start: 21 outliers final: 11 residues processed: 124 average time/residue: 1.4637 time to fit residues: 191.4642 Evaluate side-chains 119 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8753 Z= 0.339 Angle : 0.657 13.365 11901 Z= 0.332 Chirality : 0.043 0.157 1381 Planarity : 0.004 0.049 1496 Dihedral : 4.341 29.906 1207 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.75 % Allowed : 20.48 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1105 helix: 1.88 (0.28), residues: 364 sheet: 0.02 (0.30), residues: 283 loop : -0.20 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 440 HIS 0.005 0.001 HIS B 225 PHE 0.015 0.001 PHE B 253 TYR 0.012 0.002 TYR H 190 ARG 0.009 0.001 ARG H 160 *********************** 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 134 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 244 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8857 (ttpp) REVERT: A 38 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 306 GLN cc_start: 0.8892 (mm110) cc_final: 0.8591 (mp10) REVERT: A 345 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8278 (ttmt) REVERT: A 349 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8335 (tptp) REVERT: R 86 MET cc_start: 0.7153 (mmt) cc_final: 0.6742 (tmt) REVERT: R 136 LYS cc_start: 0.7602 (mmmm) cc_final: 0.7402 (mmtm) REVERT: R 152 MET cc_start: 0.7763 (mmp) cc_final: 0.7423 (mmt) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 1.4274 time to fit residues: 188.7656 Evaluate side-chains 119 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 199 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8753 Z= 0.275 Angle : 0.646 13.805 11901 Z= 0.322 Chirality : 0.042 0.157 1381 Planarity : 0.004 0.062 1496 Dihedral : 4.295 30.932 1207 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.31 % Allowed : 20.93 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.73 (0.26), residues: 1105 helix: 1.76 (0.28), residues: 372 sheet: 0.06 (0.30), residues: 276 loop : -0.21 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 253 TYR 0.012 0.001 TYR H 190 ARG 0.012 0.001 ARG A 205 ********************** 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 129 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 244 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8838 (ttpp) REVERT: A 306 GLN cc_start: 0.8891 (mm110) cc_final: 0.8576 (mp10) REVERT: A 345 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8267 (ttmt) REVERT: A 349 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8337 (tptp) REVERT: R 86 MET cc_start: 0.7176 (mmt) cc_final: 0.6756 (tmt) REVERT: R 136 LYS cc_start: 0.7564 (mmmm) cc_final: 0.7352 (mmtm) REVERT: R 152 MET cc_start: 0.7795 (mmp) cc_final: 0.7463 (mmt) outliers start: 21 outliers final: 14 residues processed: 123 average time/residue: 1.4423 time to fit residues: 187.8440 Evaluate side-chains 119 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain H residue 137 ASP Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 244 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain R residue 219 SER Chi-restraints excluded: chain R residue 421 LEU Chi-restraints excluded: chain R residue 463 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN H 231 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.090695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063946 restraints weight = 19811.162| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.99 r_work: 0.2941 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8753 Z= 0.231 Angle : 0.629 13.576 11901 Z= 0.314 Chirality : 0.042 0.179 1381 Planarity : 0.004 0.050 1496 Dihedral : 4.212 31.921 1207 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.20 % Allowed : 21.37 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.83 (0.26), residues: 1105 helix: 1.93 (0.28), residues: 366 sheet: -0.01 (0.30), residues: 284 loop : -0.12 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 440 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 253 TYR 0.013 0.001 TYR H 190 ARG 0.010 0.001 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3965.71 seconds wall clock time: 69 minutes 55.95 seconds (4195.95 seconds total)