Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 08:55:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/04_2023/5tv4_8469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/04_2023/5tv4_8469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/04_2023/5tv4_8469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/04_2023/5tv4_8469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/04_2023/5tv4_8469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/04_2023/5tv4_8469_updated.pdb" } resolution = 4.2 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 16 5.16 5 C 4040 2.51 5 N 1234 2.21 5 O 1254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 78": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6548 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3205 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 375} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555} Unresolved chain links: 1 Unresolved chain link angles: 11 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1255 Unresolved non-hydrogen angles: 1592 Unresolved non-hydrogen dihedrals: 1004 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 11, 'ASN:plan1': 19, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 13, 'GLU:plan': 28, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 654 Chain: "B" Number of atoms: 3180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 3180 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 386} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 555} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1279 Unresolved non-hydrogen angles: 1619 Unresolved non-hydrogen dihedrals: 1021 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 17, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 16, 'GLU:plan': 28, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 640 Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 91 Unusual residues: {'GMH': 3, 'KDO': 2, 'PA1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 60 Unusual residues: {'DAO': 1, 'FTT': 4, 'MYR': 1, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'DAO:plan-1': 1, 'FTT:plan-1': 4, 'MYR:plan-1': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 4.45, per 1000 atoms: 0.68 Number of scatterers: 6548 At special positions: 0 Unit cell: (91.02, 84.87, 134.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 4 15.00 O 1254 8.00 N 1234 7.00 C 4040 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=8, symmetry=0 Links applied ?1-6 " PA1 C 1 " - " PA1 C 2 " ALPHA1-3 " GMH C 4 " - " GMH C 5 " ALPHA1-5 " KDO C 3 " - " GMH C 4 " ALPHA1-7 " GMH C 5 " - " GMH C 6 " ALPHA2-6 " PA1 C 2 " - " KDO C 3 " Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 3 sheets defined 62.8% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.772A pdb=" N LEU A 16 " --> pdb=" O PHE A 13 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP A 17 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Proline residue: A 18 - end of helix Processing helix chain 'A' and resid 24 through 53 Proline residue: A 50 - end of helix removed outlier: 3.860A pdb=" N ASP A 53 " --> pdb=" O PRO A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 67 through 109 removed outlier: 3.615A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 121 through 163 removed outlier: 3.736A pdb=" N ALA A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.642A pdb=" N ILE A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 192 removed outlier: 4.374A pdb=" N LEU A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.931A pdb=" N HIS A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LYS A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 249 removed outlier: 3.894A pdb=" N LYS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 257 through 267 removed outlier: 4.455A pdb=" N ALA A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 265 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 281 through 322 removed outlier: 3.603A pdb=" N SER A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Proline residue: A 297 - end of helix removed outlier: 4.091A pdb=" N THR A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.867A pdb=" N ILE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 412 through 418 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.817A pdb=" N ILE A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 513 through 527 Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 571 through 578 Processing helix chain 'B' and resid 12 through 54 removed outlier: 4.059A pdb=" N TRP B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix Proline residue: B 22 - end of helix removed outlier: 5.687A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 26 " --> pdb=" O PRO B 22 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU B 27 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 61 through 108 Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 121 through 162 Processing helix chain 'B' and resid 165 through 212 removed outlier: 5.014A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Proline residue: B 176 - end of helix Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 223 through 275 removed outlier: 3.706A pdb=" N PHE B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 233 " --> pdb=" O ARG B 229 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B 247 " --> pdb=" O LYS B 243 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Proline residue: B 253 - end of helix removed outlier: 4.102A pdb=" N LEU B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE B 258 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 281 through 307 removed outlier: 4.084A pdb=" N PHE B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Proline residue: B 297 - end of helix removed outlier: 3.764A pdb=" N ASN B 303 " --> pdb=" O LYS B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 447 through 455 Processing helix chain 'B' and resid 459 through 462 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 513 through 526 Processing helix chain 'B' and resid 541 through 544 No H-bonds generated for 'chain 'B' and resid 541 through 544' Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 571 through 578 Processing sheet with id= A, first strand: chain 'A' and resid 364 through 367 Processing sheet with id= B, first strand: chain 'A' and resid 532 through 535 removed outlier: 7.332A pdb=" N GLU A 547 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 347 through 349 removed outlier: 6.575A pdb=" N PHE A 349 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG A 360 " --> pdb=" O PHE A 349 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1338 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: 1.83 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2305 1.34 - 1.46: 775 1.46 - 1.57: 3475 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 6586 Sorted by residual: bond pdb=" C5 PA1 C 2 " pdb=" O5 PA1 C 2 " ideal model delta sigma weight residual 1.417 1.533 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" O3 PO4 A 608 " pdb=" P PO4 A 608 " ideal model delta sigma weight residual 1.569 1.464 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O3 PO4 A 610 " pdb=" P PO4 A 610 " ideal model delta sigma weight residual 1.569 1.466 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" O1 PO4 A 610 " pdb=" P PO4 A 610 " ideal model delta sigma weight residual 1.565 1.464 0.101 2.00e-02 2.50e+03 2.58e+01 bond pdb=" O3 PO4 A 609 " pdb=" P PO4 A 609 " ideal model delta sigma weight residual 1.569 1.468 0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 6581 not shown) Histogram of bond angle deviations from ideal: 91.04 - 99.63: 6 99.63 - 108.22: 255 108.22 - 116.82: 4343 116.82 - 125.41: 4414 125.41 - 134.00: 56 Bond angle restraints: 9074 Sorted by residual: angle pdb=" N GLN B 309 " pdb=" CA GLN B 309 " pdb=" C GLN B 309 " ideal model delta sigma weight residual 113.88 106.52 7.36 1.23e+00 6.61e-01 3.58e+01 angle pdb=" C6 PA1 C 2 " pdb=" C5 PA1 C 2 " pdb=" O5 PA1 C 2 " ideal model delta sigma weight residual 107.26 91.04 16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" CA SER A 300 " pdb=" C SER A 300 " pdb=" N LEU A 301 " ideal model delta sigma weight residual 118.17 125.27 -7.10 1.33e+00 5.65e-01 2.85e+01 angle pdb=" N GLY B 311 " pdb=" CA GLY B 311 " pdb=" C GLY B 311 " ideal model delta sigma weight residual 113.24 106.46 6.78 1.31e+00 5.83e-01 2.68e+01 angle pdb=" C ARG A 333 " pdb=" N VAL A 334 " pdb=" CA VAL A 334 " ideal model delta sigma weight residual 121.70 131.00 -9.30 1.80e+00 3.09e-01 2.67e+01 ... (remaining 9069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3593 17.53 - 35.07: 139 35.07 - 52.60: 30 52.60 - 70.14: 6 70.14 - 87.67: 6 Dihedral angle restraints: 3774 sinusoidal: 500 harmonic: 3274 Sorted by residual: dihedral pdb=" CA TYR B 351 " pdb=" C TYR B 351 " pdb=" N PRO B 352 " pdb=" CA PRO B 352 " ideal model delta harmonic sigma weight residual 180.00 139.03 40.97 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA ASP B 498 " pdb=" C ASP B 498 " pdb=" N SER B 499 " pdb=" CA SER B 499 " ideal model delta harmonic sigma weight residual -180.00 -141.68 -38.32 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA SER B 278 " pdb=" C SER B 278 " pdb=" N LEU B 279 " pdb=" CA LEU B 279 " ideal model delta harmonic sigma weight residual -180.00 -142.85 -37.15 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 3771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 1164 0.141 - 0.283: 38 0.283 - 0.424: 0 0.424 - 0.566: 0 0.566 - 0.707: 1 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C1 GMH C 6 " pdb=" O7 GMH C 5 " pdb=" C2 GMH C 6 " pdb=" O5 GMH C 6 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.64e+01 chirality pdb=" C1 GMH C 5 " pdb=" O3 GMH C 4 " pdb=" C2 GMH C 5 " pdb=" O5 GMH C 5 " both_signs ideal model delta sigma weight residual False 2.40 2.48 -0.08 2.00e-02 2.50e+03 1.55e+01 chirality pdb=" C5 PA1 C 2 " pdb=" C4 PA1 C 2 " pdb=" C6 PA1 C 2 " pdb=" O5 PA1 C 2 " both_signs ideal model delta sigma weight residual False -2.49 -3.20 0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 1200 not shown) Planarity restraints: 1225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 414 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C SER B 414 " -0.063 2.00e-02 2.50e+03 pdb=" O SER B 414 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU B 415 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 97 " -0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C VAL A 97 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL A 97 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 98 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 519 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C ILE A 519 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 519 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 520 " 0.013 2.00e-02 2.50e+03 ... (remaining 1222 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 33 2.19 - 2.87: 3085 2.87 - 3.54: 10263 3.54 - 4.22: 13898 4.22 - 4.90: 21668 Nonbonded interactions: 48947 Sorted by model distance: nonbonded pdb=" O LEU A 77 " pdb=" CG2 THR A 81 " model vdw 1.511 3.460 nonbonded pdb=" O4 PA1 C 2 " pdb=" P PO4 B 601 " model vdw 1.577 3.400 nonbonded pdb=" O4 GMH C 5 " pdb=" P PO4 A 610 " model vdw 1.580 3.400 nonbonded pdb=" O1 PA1 C 1 " pdb=" P PO4 A 608 " model vdw 1.591 3.400 nonbonded pdb=" O4 GMH C 4 " pdb=" P PO4 A 609 " model vdw 1.600 3.400 ... (remaining 48942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 31 or (resid 32 through 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 through 40 or (res \ id 41 and (name N or name CA or name C or name O or name CB )) or resid 42 or (r \ esid 43 through 44 and (name N or name CA or name C or name O or name CB )) or r \ esid 45 through 48 or (resid 49 and (name N or name CA or name C or name O or na \ me CB )) or resid 50 or (resid 51 through 54 and (name N or name CA or name C or \ name O or name CB )) or (resid 55 through 65 and (name N or name CA or name C o \ r name O or name CB )) or resid 66 through 79 or (resid 80 and (name N or name C \ A or name C or name O or name CB )) or resid 81 through 83 or (resid 84 through \ 86 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resi \ d 88 through 90 and (name N or name CA or name C or name O or name CB )) or resi \ d 91 through 94 or (resid 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 100 or (resid 101 and (name N or name CA or name C or \ name O or name CB )) or resid 102 through 103 or (resid 104 and (name N or name \ CA or name C or name O or name CB )) or resid 105 through 112 or (resid 113 thro \ ugh 121 and (name N or name CA or name C or name O or name CB )) or resid 122 or \ (resid 123 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 4 through 144 or (resid 145 through 147 and (name N or name CA or name C or name \ O or name CB )) or resid 148 through 152 or (resid 153 through 154 and (name N \ or name CA or name C or name O or name CB )) or resid 155 or (resid 156 through \ 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throug \ h 171 or (resid 172 through 175 and (name N or name CA or name C or name O or na \ me CB )) or resid 176 through 179 or (resid 180 through 187 and (name N or name \ CA or name C or name O or name CB )) or resid 188 through 191 or (resid 192 thro \ ugh 200 and (name N or name CA or name C or name O or name CB )) or resid 201 th \ rough 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) \ or resid 221 through 232 or (resid 233 through 236 and (name N or name CA or na \ me C or name O or name CB )) or resid 237 through 239 or (resid 240 and (name N \ or name CA or name C or name O or name CB )) or resid 241 or (resid 242 through \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 throug \ h 252 or (resid 253 and (name N or name CA or name C or name O or name CB )) or \ resid 254 or (resid 255 and (name N or name CA or name C or name O or name CB )) \ or resid 256 or (resid 257 through 262 and (name N or name CA or name C or name \ O or name CB )) or resid 263 through 264 or (resid 265 through 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 274 or (resid \ 275 through 281 and (name N or name CA or name C or name O or name CB )) or resi \ d 282 through 302 or (resid 303 through 306 and (name N or name CA or name C or \ name O or name CB )) or resid 307 through 311 or (resid 312 through 318 and (nam \ e N or name CA or name C or name O or name CB )) or resid 319 through 321 or (re \ sid 322 through 330 and (name N or name CA or name C or name O or name CB )) or \ resid 331 through 580 or resid 608)) selection = (chain 'B' and (resid 11 through 17 or (resid 18 through 19 and (name N or name \ CA or name C or name O or name CB )) or resid 20 through 21 or (resid 22 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 36 or (resid 37 through 41 and (name N or name CA or name C or name O or name C \ B )) or resid 42 through 81 or (resid 82 and (name N or name CA or name C or nam \ e O or name CB )) or resid 83 through 84 or (resid 85 through 86 and (name N or \ name CA or name C or name O or name CB )) or resid 87 through 96 or (resid 97 th \ rough 99 and (name N or name CA or name C or name O or name CB )) or resid 100 t \ hrough 102 or (resid 103 through 104 and (name N or name CA or name C or name O \ or name CB )) or resid 105 through 108 or (resid 109 and (name N or name CA or n \ ame C or name O or name CB )) or resid 110 through 129 or (resid 130 through 133 \ and (name N or name CA or name C or name O or name CB )) or resid 134 or (resid \ 135 through 140 and (name N or name CA or name C or name O or name CB )) or res \ id 141 through 143 or (resid 144 through 147 and (name N or name CA or name C or \ name O or name CB )) or resid 148 or (resid 149 and (name CA or name C or name \ O or name CB )) or (resid 150 through 154 and (name N or name CA or name C or na \ me O or name CB )) or resid 155 through 161 or (resid 162 through 165 and (name \ N or name CA or name C or name O or name CB )) or resid 166 through 181 or (resi \ d 182 through 187 and (name N or name CA or name C or name O or name CB )) or re \ sid 188 through 196 or (resid 197 through 200 and (name N or name CA or name C o \ r name O or name CB )) or resid 201 through 208 or (resid 209 through 212 and (n \ ame N or name CA or name C or name O or name CB )) or resid 213 through 216 or ( \ resid 217 through 220 and (name N or name CA or name C or name O or name CB )) o \ r resid 221 through 224 or (resid 225 through 236 and (name N or name CA or name \ C or name O or name CB )) or resid 237 through 238 or (resid 239 through 240 an \ d (name N or name CA or name C or name O or name CB )) or resid 241 through 251 \ or (resid 252 through 253 and (name N or name CA or name C or name O or name CB \ )) or resid 254 through 266 or (resid 267 through 271 and (name N or name CA or \ name C or name O or name CB )) or resid 272 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 through 287 or (resi \ d 288 through 291 and (name N or name CA or name C or name O or name CB )) or re \ sid 292 through 294 or (resid 295 and (name N or name CA or name C or name O or \ name CB )) or resid 296 through 304 or (resid 305 through 306 and (name N or nam \ e CA or name C or name O or name CB )) or resid 307 through 309 or (resid 310 an \ d (name N or name CA or name C or name O or name CB )) or (resid 311 through 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 3 \ 20 or (resid 321 through 330 and (name N or name CA or name C or name O or name \ CB )) or resid 331 through 580 or resid 601)) } 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 group one per residue 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: 0.300 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.120 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.630 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5888 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 : 0.008 0.116 6586 Z= 0.604 Angle : 1.264 16.223 9074 Z= 0.748 Chirality : 0.064 0.707 1203 Planarity : 0.005 0.045 1225 Dihedral : 12.843 87.669 1644 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 46.46 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.14 % Favored : 86.16 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 7.69 % Twisted General : 0.72 % 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: -5.82 (0.16), residues: 1134 helix: -3.92 (0.11), residues: 718 sheet: -3.39 (0.83), residues: 23 loop : -3.35 (0.23), residues: 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1844 time to fit residues: 33.0195 Evaluate side-chains 90 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 40.0000 chunk 89 optimal weight: 0.0170 chunk 34 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 6586 Z= 0.239 Angle : 0.775 9.580 9074 Z= 0.418 Chirality : 0.048 0.300 1203 Planarity : 0.005 0.048 1225 Dihedral : 8.326 86.717 1189 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -2.95 (0.22), residues: 1134 helix: -1.50 (0.17), residues: 727 sheet: -3.32 (0.58), residues: 39 loop : -2.44 (0.29), residues: 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1620 time to fit residues: 25.7431 Evaluate side-chains 87 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 40.0000 chunk 112 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 6586 Z= 0.186 Angle : 0.641 9.061 9074 Z= 0.341 Chirality : 0.044 0.227 1203 Planarity : 0.004 0.037 1225 Dihedral : 7.152 84.759 1189 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -1.33 (0.24), residues: 1134 helix: -0.07 (0.19), residues: 738 sheet: -3.27 (0.59), residues: 41 loop : -2.18 (0.30), residues: 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1629 time to fit residues: 23.7838 Evaluate side-chains 86 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 40.0000 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 50.0000 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 0.0270 chunk 98 optimal weight: 50.0000 chunk 29 optimal weight: 2.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6010 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.103 6586 Z= 0.251 Angle : 0.648 9.798 9074 Z= 0.348 Chirality : 0.045 0.234 1203 Planarity : 0.004 0.035 1225 Dihedral : 6.815 68.995 1189 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1134 helix: 0.43 (0.19), residues: 744 sheet: -2.85 (0.62), residues: 51 loop : -2.16 (0.31), residues: 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.776 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1532 time to fit residues: 21.6178 Evaluate side-chains 87 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.747 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 40.0000 chunk 62 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 6586 Z= 0.182 Angle : 0.580 9.113 9074 Z= 0.309 Chirality : 0.043 0.243 1203 Planarity : 0.003 0.030 1225 Dihedral : 6.109 74.433 1189 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.13 (0.25), residues: 1134 helix: 0.96 (0.19), residues: 736 sheet: -2.47 (0.75), residues: 44 loop : -1.98 (0.32), residues: 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.781 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1524 time to fit residues: 22.1745 Evaluate side-chains 83 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 30.0000 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 50.0000 chunk 91 optimal weight: 30.0000 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 40.0000 chunk 57 optimal weight: 8.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 6586 Z= 0.197 Angle : 0.594 9.395 9074 Z= 0.316 Chirality : 0.043 0.234 1203 Planarity : 0.004 0.028 1225 Dihedral : 6.107 66.484 1189 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.06 (0.25), residues: 1134 helix: 1.12 (0.19), residues: 741 sheet: -2.60 (0.72), residues: 44 loop : -1.98 (0.32), residues: 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1405 time to fit residues: 19.3113 Evaluate side-chains 80 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 50.0000 chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 40.0000 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 30.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6586 Z= 0.181 Angle : 0.569 8.898 9074 Z= 0.301 Chirality : 0.042 0.231 1203 Planarity : 0.004 0.038 1225 Dihedral : 5.903 77.518 1189 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1134 helix: 1.22 (0.20), residues: 749 sheet: -2.78 (0.70), residues: 44 loop : -1.92 (0.33), residues: 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1393 time to fit residues: 20.3016 Evaluate side-chains 84 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 10 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 30.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 6586 Z= 0.213 Angle : 0.585 9.312 9074 Z= 0.311 Chirality : 0.043 0.234 1203 Planarity : 0.003 0.030 1225 Dihedral : 5.950 64.263 1189 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: 0.14 (0.26), residues: 1134 helix: 1.19 (0.19), residues: 743 sheet: -3.00 (0.62), residues: 51 loop : -1.85 (0.33), residues: 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1363 time to fit residues: 19.9697 Evaluate side-chains 82 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 40.0000 chunk 102 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 50.0000 chunk 67 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 6586 Z= 0.244 Angle : 0.651 9.787 9074 Z= 0.348 Chirality : 0.045 0.236 1203 Planarity : 0.004 0.034 1225 Dihedral : 6.190 65.941 1189 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.11 (0.25), residues: 1134 helix: 0.98 (0.19), residues: 745 sheet: -3.14 (0.63), residues: 40 loop : -1.98 (0.33), residues: 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.731 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1107 time to fit residues: 16.4624 Evaluate side-chains 84 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.734 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 0.0970 chunk 104 optimal weight: 8.9990 chunk 90 optimal weight: 50.0000 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.6709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 6586 Z= 0.249 Angle : 0.644 9.816 9074 Z= 0.343 Chirality : 0.044 0.240 1203 Planarity : 0.004 0.047 1225 Dihedral : 6.230 63.970 1189 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.31 (0.25), residues: 1134 helix: 0.91 (0.19), residues: 733 sheet: -3.15 (0.72), residues: 31 loop : -2.24 (0.30), residues: 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1181 time to fit residues: 17.9206 Evaluate side-chains 84 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0670 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 30.0000 chunk 90 optimal weight: 50.0000 chunk 37 optimal weight: 30.0000 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 overall best weight: 2.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.102817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.090894 restraints weight = 32038.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088987 restraints weight = 43790.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088420 restraints weight = 40634.528| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.6930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6586 Z= 0.180 Angle : 0.589 9.197 9074 Z= 0.311 Chirality : 0.043 0.246 1203 Planarity : 0.003 0.031 1225 Dihedral : 5.954 68.337 1189 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % 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: -0.02 (0.26), residues: 1134 helix: 1.16 (0.20), residues: 734 sheet: -3.13 (0.64), residues: 41 loop : -2.14 (0.31), residues: 359 =============================================================================== Job complete usr+sys time: 1288.65 seconds wall clock time: 23 minutes 57.61 seconds (1437.61 seconds total)