Starting phenix.real_space_refine (version: dev) on Sun Feb 19 13:38:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmh_13533/02_2023/7pmh_13533_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmh_13533/02_2023/7pmh_13533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmh_13533/02_2023/7pmh_13533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmh_13533/02_2023/7pmh_13533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmh_13533/02_2023/7pmh_13533_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmh_13533/02_2023/7pmh_13533_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 Process input model Symmetric amino acids flipped Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 666": "OD1" <-> "OD2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10154 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 6070 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 26, 'TRANS': 715} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.84, per 1000 atoms: 0.58 Number of scatterers: 10154 At special positions: 0 Unit cell: (102.3, 128.7, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1898 8.00 N 1724 7.00 C 6461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.3 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 48.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'B' and resid 6 through 19 Processing helix chain 'B' and resid 29 through 38 removed outlier: 4.287A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 67 through 78 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.326A pdb=" N PHE B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.783A pdb=" N GLN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 183 removed outlier: 3.733A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.584A pdb=" N SER A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 260 through 270 removed outlier: 5.036A pdb=" N ALA A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 277 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.864A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLY A 291 " --> pdb=" O TYR A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 291' Processing helix chain 'A' and resid 301 through 314 removed outlier: 4.203A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 337 removed outlier: 3.624A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.242A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 423 Processing helix chain 'A' and resid 449 through 480 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.821A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.525A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 568 Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 636 through 652 Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.612A pdb=" N VAL A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 755 through 791 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 92 removed outlier: 3.577A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.667A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 183 through 196 removed outlier: 4.090A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.529A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 261 Proline residue: C 258 - end of helix removed outlier: 4.799A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.610A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 No H-bonds generated for 'chain 'C' and resid 290 through 293' Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.242A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.574A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 367 through 373 removed outlier: 3.694A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 12 through 16 removed outlier: 7.066A pdb=" N GLN A 39 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 100 through 103 removed outlier: 3.941A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 377 through 382 Processing sheet with id= F, first strand: chain 'A' and resid 547 through 551 Processing sheet with id= G, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.671A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 8 through 11 Processing sheet with id= I, first strand: chain 'C' and resid 65 through 69 Processing sheet with id= J, first strand: chain 'C' and resid 103 through 107 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.458A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 442 hydrogen bonds defined for protein. 1233 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: 3.83 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1695 1.31 - 1.44: 2739 1.44 - 1.56: 5823 1.56 - 1.69: 8 1.69 - 1.81: 103 Bond restraints: 10368 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.439 0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.571 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.196 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 10363 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.68: 195 104.68 - 112.46: 5204 112.46 - 120.24: 4599 120.24 - 128.02: 3919 128.02 - 135.80: 91 Bond angle restraints: 14008 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 110.78 10.92 1.80e+00 3.09e-01 3.68e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 101.96 9.54 1.70e+00 3.46e-01 3.15e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 110.70 16.25 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.10 99.89 10.21 1.90e+00 2.77e-01 2.89e+01 angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 121.71 -7.85 1.50e+00 4.44e-01 2.74e+01 ... (remaining 14003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.34: 5988 26.34 - 52.68: 192 52.68 - 79.02: 35 79.02 - 105.36: 14 105.36 - 131.70: 3 Dihedral angle restraints: 6232 sinusoidal: 2552 harmonic: 3680 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 168.30 131.70 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 67.81 -127.82 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 64.63 -124.63 1 2.00e+01 2.50e-03 3.76e+01 ... (remaining 6229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1000 0.052 - 0.105: 415 0.105 - 0.157: 99 0.157 - 0.209: 13 0.209 - 0.261: 3 Chirality restraints: 1530 Sorted by residual: chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU C 226 " pdb=" N GLU C 226 " pdb=" C GLU C 226 " pdb=" CB GLU C 226 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1527 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.006 2.00e-02 2.50e+03 3.77e-02 2.85e+01 pdb=" CG TYR C 306 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.053 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 147 " -0.129 9.50e-02 1.11e+02 7.14e-02 2.41e+01 pdb=" NE ARG C 147 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG C 147 " -0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG C 147 " 0.028 2.00e-02 2.50e+03 pdb=" NH2 ARG C 147 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.040 2.00e-02 2.50e+03 3.64e-02 2.32e+01 pdb=" CG PHE A 564 " 0.084 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.009 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 5 2.03 - 2.75: 1313 2.75 - 3.46: 14302 3.46 - 4.18: 23526 4.18 - 4.90: 42758 Nonbonded interactions: 81904 Sorted by model distance: nonbonded pdb=" N TRP H 1 " pdb=" C ALA H 7 " model vdw 1.310 3.350 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" O3G ANP A1901 " pdb="MG MG A1902 " model vdw 2.000 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 2.020 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.024 2.170 ... (remaining 81899 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6461 2.51 5 N 1724 2.21 5 O 1898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.590 Check model and map are aligned: 0.160 Process input model: 28.190 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.009 0.149 10368 Z= 0.611 Angle : 1.006 16.253 14008 Z= 0.576 Chirality : 0.058 0.261 1530 Planarity : 0.008 0.089 1786 Dihedral : 14.970 131.704 3858 Min Nonbonded Distance : 1.310 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.25 % 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: -1.51 (0.20), residues: 1230 helix: -1.62 (0.17), residues: 599 sheet: 0.02 (0.36), residues: 166 loop : -0.16 (0.26), residues: 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.3127 time to fit residues: 39.1043 Evaluate side-chains 54 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0897 time to fit residues: 1.8055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 chunk 97 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN A 264 GLN A 290 GLN A 410 ASN A 455 ASN A 466 ASN A 775 GLN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 296 ASN C 371 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 10368 Z= 0.185 Angle : 0.594 9.159 14008 Z= 0.313 Chirality : 0.043 0.213 1530 Planarity : 0.004 0.050 1786 Dihedral : 8.867 132.373 1386 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1230 helix: 0.66 (0.21), residues: 609 sheet: 0.38 (0.36), residues: 166 loop : 0.43 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 0.3442 time to fit residues: 33.6666 Evaluate side-chains 62 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1123 time to fit residues: 2.9398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 0.0370 chunk 90 optimal weight: 3.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 560 GLN C 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 10368 Z= 0.161 Angle : 0.540 8.690 14008 Z= 0.276 Chirality : 0.041 0.164 1530 Planarity : 0.003 0.049 1786 Dihedral : 8.305 131.819 1386 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.08 % 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: 1.31 (0.24), residues: 1230 helix: 1.29 (0.21), residues: 609 sheet: 0.65 (0.37), residues: 175 loop : 0.59 (0.31), residues: 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 62 average time/residue: 0.2460 time to fit residues: 22.4680 Evaluate side-chains 53 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0991 time to fit residues: 1.8280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN A 373 HIS A 497 ASN C 121 GLN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 10368 Z= 0.330 Angle : 0.582 5.987 14008 Z= 0.298 Chirality : 0.042 0.177 1530 Planarity : 0.004 0.049 1786 Dihedral : 8.207 132.462 1386 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.08 % 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: 1.47 (0.24), residues: 1230 helix: 1.48 (0.21), residues: 609 sheet: 0.75 (0.39), residues: 166 loop : 0.54 (0.30), residues: 455 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 57 average time/residue: 0.2598 time to fit residues: 21.9219 Evaluate side-chains 52 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1098 time to fit residues: 2.3034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 10368 Z= 0.321 Angle : 0.573 8.640 14008 Z= 0.293 Chirality : 0.042 0.179 1530 Planarity : 0.003 0.044 1786 Dihedral : 8.079 129.688 1386 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.08 % 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: 1.35 (0.24), residues: 1230 helix: 1.48 (0.21), residues: 610 sheet: 0.68 (0.39), residues: 166 loop : 0.34 (0.30), residues: 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.2643 time to fit residues: 20.1675 Evaluate side-chains 50 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1051 time to fit residues: 1.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10368 Z= 0.185 Angle : 0.510 6.754 14008 Z= 0.259 Chirality : 0.040 0.174 1530 Planarity : 0.003 0.043 1786 Dihedral : 7.684 125.969 1386 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.08 % 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: 1.63 (0.24), residues: 1230 helix: 1.75 (0.22), residues: 609 sheet: 0.67 (0.38), residues: 166 loop : 0.48 (0.30), residues: 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 1.185 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 57 average time/residue: 0.2379 time to fit residues: 20.6110 Evaluate side-chains 49 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.210 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0919 time to fit residues: 1.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 4.9990 chunk 13 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10368 Z= 0.248 Angle : 0.560 14.097 14008 Z= 0.277 Chirality : 0.041 0.183 1530 Planarity : 0.003 0.044 1786 Dihedral : 7.529 121.976 1386 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.08 % 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 (0.25), residues: 1230 helix: 1.79 (0.22), residues: 603 sheet: 0.66 (0.38), residues: 167 loop : 0.48 (0.30), residues: 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 0.2392 time to fit residues: 19.3801 Evaluate side-chains 48 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 1.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1030 time to fit residues: 1.9028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 10368 Z= 0.150 Angle : 0.525 9.806 14008 Z= 0.262 Chirality : 0.040 0.184 1530 Planarity : 0.003 0.044 1786 Dihedral : 7.145 114.664 1386 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.08 % 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: 1.75 (0.25), residues: 1230 helix: 1.88 (0.22), residues: 595 sheet: 0.66 (0.38), residues: 169 loop : 0.55 (0.30), residues: 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.2456 time to fit residues: 20.6525 Evaluate side-chains 50 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0998 time to fit residues: 2.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 GLN A 730 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 10368 Z= 0.174 Angle : 0.561 12.686 14008 Z= 0.273 Chirality : 0.040 0.187 1530 Planarity : 0.003 0.044 1786 Dihedral : 6.926 112.670 1386 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % 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: 1.75 (0.25), residues: 1230 helix: 1.90 (0.22), residues: 597 sheet: 0.65 (0.38), residues: 169 loop : 0.52 (0.30), residues: 464 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2709 time to fit residues: 21.0930 Evaluate side-chains 48 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 0.0010 chunk 113 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 10368 Z= 0.148 Angle : 0.534 9.248 14008 Z= 0.263 Chirality : 0.040 0.204 1530 Planarity : 0.003 0.043 1786 Dihedral : 6.626 105.735 1386 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.08 % 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 (0.25), residues: 1230 helix: 1.86 (0.22), residues: 600 sheet: 0.79 (0.37), residues: 181 loop : 0.47 (0.31), residues: 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.264 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.2630 time to fit residues: 20.0150 Evaluate side-chains 49 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1002 time to fit residues: 1.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.0010 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.048740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035264 restraints weight = 57956.004| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 4.03 r_work: 0.2636 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 10368 Z= 0.136 Angle : 0.549 12.312 14008 Z= 0.266 Chirality : 0.039 0.192 1530 Planarity : 0.003 0.043 1786 Dihedral : 6.353 101.696 1386 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.08 % 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: 1.79 (0.25), residues: 1230 helix: 1.93 (0.22), residues: 598 sheet: 0.86 (0.39), residues: 174 loop : 0.44 (0.31), residues: 458 =============================================================================== Job complete usr+sys time: 1997.85 seconds wall clock time: 37 minutes 41.64 seconds (2261.64 seconds total)