Starting phenix.real_space_refine on Tue Jun 25 04:46:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/06_2024/9bkj_44642_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/06_2024/9bkj_44642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/06_2024/9bkj_44642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/06_2024/9bkj_44642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/06_2024/9bkj_44642_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkj_44642/06_2024/9bkj_44642_updated.pdb" } resolution = 2.59 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= 0.005 sd= 0.103 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 4357 2.51 5 N 1150 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 390": "OE1" <-> "OE2" 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: 6795 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2483 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 3, 'ASP:plan': 3, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 396 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2234 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1604 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 200} Chain breaks: 4 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 63 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.30, per 1000 atoms: 0.63 Number of scatterers: 6795 At special positions: 0 Unit cell: (88.4, 88.4, 127.5, 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 1231 8.00 N 1150 7.00 C 4357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.07 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 43.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 39 through 68 Processing helix chain 'R' and resid 75 through 94 removed outlier: 3.528A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 103 removed outlier: 3.975A pdb=" N ILE R 100 " --> pdb=" O PRO R 96 " (cutoff:3.500A) Proline residue: R 101 - end of helix No H-bonds generated for 'chain 'R' and resid 96 through 103' Processing helix chain 'R' and resid 111 through 144 Processing helix chain 'R' and resid 148 through 150 No H-bonds generated for 'chain 'R' and resid 148 through 150' Processing helix chain 'R' and resid 155 through 179 removed outlier: 4.085A pdb=" N THR R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Proline residue: R 175 - end of helix removed outlier: 3.940A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 216 Processing helix chain 'R' and resid 219 through 237 Processing helix chain 'R' and resid 306 through 338 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 340 through 347 Processing helix chain 'R' and resid 350 through 370 removed outlier: 4.214A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS R 364 " --> pdb=" O TYR R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 375 through 384 Processing helix chain 'A' and resid 19 through 39 removed outlier: 4.125A pdb=" N ARG A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.818A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.533A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.904A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 138 through 140 removed outlier: 4.892A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.787A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.101A 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: 6.720A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.297A 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: 6.457A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.145A 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: 6.419A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.406A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.409A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN A 218 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 2.97 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: 1442 1.33 - 1.45: 1594 1.45 - 1.58: 3809 1.58 - 1.70: 1 1.70 - 1.82: 84 Bond restraints: 6930 Sorted by residual: bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.583 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.56e-02 4.11e+03 1.20e+01 bond pdb=" CA ALA B 56 " pdb=" CB ALA B 56 " ideal model delta sigma weight residual 1.533 1.488 0.045 1.35e-02 5.49e+03 1.10e+01 bond pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.34e-02 5.57e+03 9.88e+00 bond pdb=" N ASN R 98 " pdb=" CA ASN R 98 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.29e-02 6.01e+03 9.49e+00 ... (remaining 6925 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.46: 168 106.46 - 113.41: 3826 113.41 - 120.36: 2610 120.36 - 127.31: 2745 127.31 - 134.26: 71 Bond angle restraints: 9420 Sorted by residual: angle pdb=" N CYS R 196 " pdb=" CA CYS R 196 " pdb=" C CYS R 196 " ideal model delta sigma weight residual 110.42 103.21 7.21 1.46e+00 4.69e-01 2.44e+01 angle pdb=" N TRP B 332 " pdb=" CA TRP B 332 " pdb=" C TRP B 332 " ideal model delta sigma weight residual 113.18 107.51 5.67 1.21e+00 6.83e-01 2.20e+01 angle pdb=" C MET P 6 " pdb=" N ASP P 7 " pdb=" CA ASP P 7 " ideal model delta sigma weight residual 120.38 126.24 -5.86 1.37e+00 5.33e-01 1.83e+01 angle pdb=" CA PHE R 185 " pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 121.33 116.84 4.49 1.08e+00 8.57e-01 1.73e+01 angle pdb=" C MET R 173 " pdb=" N THR R 174 " pdb=" CA THR R 174 " ideal model delta sigma weight residual 120.09 125.21 -5.12 1.25e+00 6.40e-01 1.68e+01 ... (remaining 9415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 3766 17.92 - 35.84: 281 35.84 - 53.75: 44 53.75 - 71.67: 6 71.67 - 89.59: 2 Dihedral angle restraints: 4099 sinusoidal: 1496 harmonic: 2603 Sorted by residual: dihedral pdb=" CA CYS R 94 " pdb=" C CYS R 94 " pdb=" N MET R 95 " pdb=" CA MET R 95 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE R 218 " pdb=" C PHE R 218 " pdb=" N LEU R 219 " pdb=" CA LEU R 219 " ideal model delta harmonic sigma weight residual -180.00 -162.89 -17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA LEU R 215 " pdb=" C LEU R 215 " pdb=" N ILE R 216 " pdb=" CA ILE R 216 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 4096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 787 0.042 - 0.084: 225 0.084 - 0.126: 88 0.126 - 0.168: 12 0.168 - 0.210: 2 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA TRP P 5 " pdb=" N TRP P 5 " pdb=" C TRP P 5 " pdb=" CB TRP P 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU R 99 " pdb=" N LEU R 99 " pdb=" C LEU R 99 " pdb=" CB LEU R 99 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET R 72 " pdb=" N MET R 72 " pdb=" C MET R 72 " pdb=" CB MET R 72 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1111 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 329 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C THR B 329 " -0.035 2.00e-02 2.50e+03 pdb=" O THR B 329 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 330 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 184 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C PRO R 184 " -0.034 2.00e-02 2.50e+03 pdb=" O PRO R 184 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE R 185 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 196 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C CYS R 196 " -0.033 2.00e-02 2.50e+03 pdb=" O CYS R 196 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG R 197 " 0.011 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1560 2.79 - 3.32: 6566 3.32 - 3.84: 11423 3.84 - 4.37: 13779 4.37 - 4.90: 23591 Nonbonded interactions: 56919 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.260 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 2.440 nonbonded pdb=" NZ LYS B 280 " pdb=" O ASP B 322 " model vdw 2.296 2.520 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.328 2.440 nonbonded pdb=" OH TYR B 289 " pdb=" NE1 TRP B 297 " model vdw 2.343 2.520 ... (remaining 56914 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: 0.810 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: 3.710 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.850 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 6930 Z= 0.298 Angle : 0.754 7.797 9420 Z= 0.475 Chirality : 0.046 0.210 1114 Planarity : 0.004 0.032 1178 Dihedral : 12.935 89.589 2398 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.96 % Favored : 97.81 % Rotamer: Outliers : 0.71 % Allowed : 1.13 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 869 helix: 2.14 (0.26), residues: 383 sheet: 0.40 (0.39), residues: 171 loop : -1.03 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.006 0.001 HIS B 54 PHE 0.020 0.001 PHE R 185 TYR 0.007 0.001 TYR B 289 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 0.787 Fit side-chains REVERT: B 195 ASP cc_start: 0.6424 (p0) cc_final: 0.6090 (p0) outliers start: 5 outliers final: 1 residues processed: 117 average time/residue: 1.3924 time to fit residues: 170.2120 Evaluate side-chains 98 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6930 Z= 0.199 Angle : 0.553 7.865 9420 Z= 0.284 Chirality : 0.043 0.146 1114 Planarity : 0.004 0.035 1178 Dihedral : 5.081 56.318 950 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.54 % Allowed : 10.33 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 869 helix: 2.60 (0.27), residues: 384 sheet: 0.40 (0.39), residues: 175 loop : -0.89 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 297 HIS 0.004 0.002 HIS B 91 PHE 0.014 0.002 PHE A 212 TYR 0.011 0.001 TYR A 360 ARG 0.005 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.708 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.6401 (pmm) REVERT: A 223 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5956 (p0) outliers start: 25 outliers final: 5 residues processed: 107 average time/residue: 1.4082 time to fit residues: 157.4070 Evaluate side-chains 91 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 0.0470 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 0.0570 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 131 ASN R 202 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6930 Z= 0.133 Angle : 0.503 8.564 9420 Z= 0.253 Chirality : 0.041 0.135 1114 Planarity : 0.003 0.035 1178 Dihedral : 4.737 53.735 949 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.54 % Allowed : 12.73 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 869 helix: 2.83 (0.27), residues: 382 sheet: 0.37 (0.39), residues: 181 loop : -0.84 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR R 48 ARG 0.005 0.000 ARG R 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: G 28 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7165 (pt) REVERT: A 223 ASP cc_start: 0.6240 (OUTLIER) cc_final: 0.5857 (p0) outliers start: 25 outliers final: 6 residues processed: 109 average time/residue: 1.2557 time to fit residues: 144.2353 Evaluate side-chains 95 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 202 ASN A 220 HIS A 236 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6930 Z= 0.156 Angle : 0.502 8.403 9420 Z= 0.257 Chirality : 0.041 0.140 1114 Planarity : 0.003 0.034 1178 Dihedral : 4.742 56.180 949 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.82 % Allowed : 14.14 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.29), residues: 869 helix: 2.86 (0.27), residues: 383 sheet: 0.41 (0.39), residues: 174 loop : -0.78 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 209 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE R 79 TYR 0.013 0.001 TYR R 48 ARG 0.005 0.000 ARG R 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 92 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: G 28 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7228 (pt) REVERT: P 1 ASP cc_start: 0.4566 (OUTLIER) cc_final: 0.3582 (p0) REVERT: R 327 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.6082 (ttp) REVERT: A 223 ASP cc_start: 0.6224 (OUTLIER) cc_final: 0.5836 (p0) REVERT: A 358 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7300 (pt) outliers start: 27 outliers final: 7 residues processed: 107 average time/residue: 1.4441 time to fit residues: 162.2099 Evaluate side-chains 101 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain P residue 1 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 214 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0070 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 0.0050 chunk 20 optimal weight: 7.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6930 Z= 0.126 Angle : 0.480 8.518 9420 Z= 0.245 Chirality : 0.040 0.149 1114 Planarity : 0.003 0.034 1178 Dihedral : 4.612 57.118 949 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.39 % Allowed : 16.12 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.29), residues: 869 helix: 2.96 (0.27), residues: 383 sheet: 0.39 (0.38), residues: 181 loop : -0.77 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6163 (mp0) REVERT: G 28 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7193 (pt) REVERT: P 1 ASP cc_start: 0.4470 (OUTLIER) cc_final: 0.4060 (p0) REVERT: R 327 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6067 (ttp) REVERT: A 223 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5854 (p0) outliers start: 24 outliers final: 8 residues processed: 105 average time/residue: 1.3797 time to fit residues: 151.8064 Evaluate side-chains 101 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain P residue 1 ASP Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0170 chunk 74 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 0.0570 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6930 Z= 0.122 Angle : 0.478 8.533 9420 Z= 0.243 Chirality : 0.041 0.156 1114 Planarity : 0.003 0.034 1178 Dihedral : 4.535 57.873 949 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.25 % Allowed : 16.69 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 869 helix: 3.04 (0.27), residues: 382 sheet: 0.29 (0.38), residues: 183 loop : -0.68 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.010 0.001 TYR A 360 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7206 (pmt) cc_final: 0.6800 (pmt) REVERT: B 226 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: G 28 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7250 (pt) REVERT: P 1 ASP cc_start: 0.4333 (OUTLIER) cc_final: 0.4124 (p0) REVERT: R 327 MET cc_start: 0.6278 (OUTLIER) cc_final: 0.6063 (ttp) REVERT: A 223 ASP cc_start: 0.6170 (OUTLIER) cc_final: 0.5802 (p0) outliers start: 23 outliers final: 9 residues processed: 108 average time/residue: 1.3547 time to fit residues: 153.2622 Evaluate side-chains 101 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain P residue 1 ASP Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6930 Z= 0.144 Angle : 0.503 9.002 9420 Z= 0.255 Chirality : 0.041 0.162 1114 Planarity : 0.003 0.034 1178 Dihedral : 4.596 58.909 949 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.10 % Allowed : 15.56 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.29), residues: 869 helix: 3.02 (0.26), residues: 382 sheet: 0.24 (0.38), residues: 184 loop : -0.58 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.018 0.001 TYR B 59 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6790 (pmt) REVERT: B 226 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: G 28 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7238 (pt) REVERT: R 327 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.6069 (ttp) REVERT: A 223 ASP cc_start: 0.6252 (OUTLIER) cc_final: 0.5855 (p0) REVERT: A 343 LYS cc_start: 0.6071 (tttm) cc_final: 0.5826 (tttm) outliers start: 29 outliers final: 9 residues processed: 112 average time/residue: 1.2518 time to fit residues: 147.1852 Evaluate side-chains 103 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6930 Z= 0.210 Angle : 0.581 9.901 9420 Z= 0.290 Chirality : 0.043 0.171 1114 Planarity : 0.003 0.032 1178 Dihedral : 4.845 58.753 949 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.68 % Allowed : 16.97 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.29), residues: 869 helix: 2.86 (0.27), residues: 382 sheet: 0.37 (0.39), residues: 174 loop : -0.67 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.005 0.002 HIS A 220 PHE 0.014 0.002 PHE B 253 TYR 0.012 0.002 TYR A 360 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: B 226 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: G 28 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7239 (pt) REVERT: R 327 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.6091 (ttp) REVERT: A 223 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5923 (p0) outliers start: 26 outliers final: 9 residues processed: 104 average time/residue: 1.3920 time to fit residues: 151.4919 Evaluate side-chains 100 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 95 MET Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 327 MET Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.0270 chunk 46 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 268 ASN R 202 ASN A 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6930 Z= 0.119 Angle : 0.518 9.811 9420 Z= 0.259 Chirality : 0.042 0.171 1114 Planarity : 0.003 0.033 1178 Dihedral : 4.540 58.383 949 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.40 % Allowed : 17.96 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.29), residues: 869 helix: 3.01 (0.27), residues: 382 sheet: 0.31 (0.39), residues: 182 loop : -0.58 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.018 0.001 TYR B 59 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7304 (pmt) cc_final: 0.6988 (pmt) REVERT: B 226 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: R 327 MET cc_start: 0.6269 (tpp) cc_final: 0.6039 (ttp) REVERT: A 223 ASP cc_start: 0.6076 (OUTLIER) cc_final: 0.5735 (p0) outliers start: 17 outliers final: 7 residues processed: 105 average time/residue: 1.3956 time to fit residues: 153.1566 Evaluate side-chains 95 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 268 ASN A 220 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6930 Z= 0.146 Angle : 0.539 10.154 9420 Z= 0.269 Chirality : 0.042 0.170 1114 Planarity : 0.003 0.034 1178 Dihedral : 4.569 57.884 949 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.98 % Allowed : 18.67 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.29), residues: 869 helix: 3.00 (0.27), residues: 382 sheet: 0.45 (0.39), residues: 174 loop : -0.58 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 209 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE B 253 TYR 0.014 0.001 TYR B 59 ARG 0.007 0.000 ARG R 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 217 MET cc_start: 0.7353 (pmt) cc_final: 0.7010 (pmt) REVERT: B 226 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: A 223 ASP cc_start: 0.6139 (OUTLIER) cc_final: 0.5762 (p0) REVERT: A 343 LYS cc_start: 0.6035 (tttm) cc_final: 0.5811 (tttm) outliers start: 14 outliers final: 8 residues processed: 97 average time/residue: 1.4176 time to fit residues: 144.0522 Evaluate side-chains 98 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 182 LEU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 202 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.187076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.136359 restraints weight = 7036.426| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.10 r_work: 0.3599 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6930 Z= 0.167 Angle : 0.562 11.139 9420 Z= 0.279 Chirality : 0.043 0.175 1114 Planarity : 0.003 0.036 1178 Dihedral : 4.667 56.879 949 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.55 % Allowed : 17.82 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.29), residues: 869 helix: 2.95 (0.27), residues: 382 sheet: 0.41 (0.39), residues: 174 loop : -0.60 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 326 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE B 253 TYR 0.011 0.001 TYR B 59 ARG 0.009 0.000 ARG R 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.46 seconds wall clock time: 57 minutes 26.01 seconds (3446.01 seconds total)