Starting phenix.real_space_refine on Mon Mar 11 01:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/03_2024/5tv4_8469_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/03_2024/5tv4_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_8469/03_2024/5tv4_8469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/03_2024/5tv4_8469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/03_2024/5tv4_8469_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tv4_8469/03_2024/5tv4_8469_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-dev-5265/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 dihedrals: 22 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: 4.74, per 1000 atoms: 0.72 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=7, symmetry=0 Links applied ?1-6 " PA1 C 1 " - " PA1 C 2 " ?2-4 " KDO C 3 " - " KDO C 7 " ?2-6 " PA1 C 2 " - " KDO C 3 " ALPHA1-3 " GMH C 4 " - " GMH C 5 " ALPHA1-5 " KDO C 3 " - " GMH C 4 " ALPHA1-7 " GMH C 5 " - " GMH C 6 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 1.6 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: 1.69 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: 2.18 Time building geometry restraints manager: 3.60 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 - 25.23: 3780 25.23 - 50.45: 108 50.45 - 75.68: 27 75.68 - 100.90: 15 100.90 - 126.13: 20 Dihedral angle restraints: 3950 sinusoidal: 676 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 3947 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: 0.460 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: 1.940 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.750 Find NCS groups from input model: 0.710 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.810 ------------------------------------------------------------------------------- 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 : 20.358 126.129 1820 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 % Allowed : 11.06 % Favored : 88.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 17 HIS 0.021 0.006 HIS B 214 PHE 0.036 0.003 PHE A 220 TYR 0.028 0.002 TYR B 268 ARG 0.007 0.001 ARG A 238 *********************** 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 : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 LEU cc_start: 0.7112 (tt) cc_final: 0.6893 (tt) REVERT: A 302 THR cc_start: 0.7128 (p) cc_final: 0.6890 (p) REVERT: B 75 MET cc_start: 0.5168 (mmp) cc_final: 0.4866 (mmp) REVERT: B 98 MET cc_start: 0.7031 (mmt) cc_final: 0.6799 (mmm) outliers start: 1 outliers final: 0 residues processed: 136 average time/residue: 0.1809 time to fit residues: 32.2907 Evaluate side-chains 91 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.9980 chunk 103 optimal weight: 9.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- 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: 0.5848 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6586 Z= 0.243 Angle : 0.806 9.846 9074 Z= 0.427 Chirality : 0.047 0.259 1203 Planarity : 0.005 0.044 1225 Dihedral : 16.607 121.430 1365 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % 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: -2.98 (0.22), residues: 1134 helix: -1.54 (0.17), residues: 723 sheet: -3.39 (0.57), residues: 39 loop : -2.40 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 17 HIS 0.002 0.001 HIS A 107 PHE 0.035 0.003 PHE A 157 TYR 0.010 0.002 TYR B 130 ARG 0.013 0.001 ARG B 238 *********************** 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 113 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 302 THR cc_start: 0.6813 (p) cc_final: 0.6566 (p) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1545 time to fit residues: 24.2248 Evaluate side-chains 88 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 0.0470 chunk 86 optimal weight: 0.0070 chunk 70 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 overall best weight: 2.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6586 Z= 0.188 Angle : 0.671 8.270 9074 Z= 0.349 Chirality : 0.043 0.149 1203 Planarity : 0.004 0.039 1225 Dihedral : 13.074 103.989 1365 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -1.30 (0.24), residues: 1134 helix: -0.05 (0.18), residues: 741 sheet: -3.26 (0.60), residues: 41 loop : -2.18 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 17 HIS 0.004 0.001 HIS A 214 PHE 0.024 0.002 PHE A 157 TYR 0.011 0.001 TYR B 268 ARG 0.006 0.001 ARG A 238 *********************** 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 106 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 THR cc_start: 0.6853 (p) cc_final: 0.6631 (p) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1526 time to fit residues: 22.5539 Evaluate side-chains 86 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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: 0.0270 chunk 53 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 98 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 overall best weight: 0.7046 ------------------------------------------------------------------------------- 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: 0.5800 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6586 Z= 0.168 Angle : 0.620 10.309 9074 Z= 0.317 Chirality : 0.042 0.162 1203 Planarity : 0.003 0.030 1225 Dihedral : 11.970 106.138 1365 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.49 (0.25), residues: 1134 helix: 0.62 (0.19), residues: 737 sheet: -2.91 (0.59), residues: 53 loop : -1.88 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 91 HIS 0.001 0.001 HIS B 214 PHE 0.018 0.002 PHE A 105 TYR 0.011 0.001 TYR B 83 ARG 0.008 0.001 ARG A 148 *********************** 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 102 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.711 Fit side-chains REVERT: A 302 THR cc_start: 0.6902 (p) cc_final: 0.6690 (p) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.1457 time to fit residues: 20.9377 Evaluate side-chains 89 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.0570 chunk 98 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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: 0.5795 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6586 Z= 0.152 Angle : 0.579 8.144 9074 Z= 0.294 Chirality : 0.041 0.160 1203 Planarity : 0.003 0.028 1225 Dihedral : 11.226 107.419 1365 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % 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: 0.01 (0.26), residues: 1134 helix: 1.01 (0.20), residues: 738 sheet: -2.65 (0.60), residues: 63 loop : -1.66 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 66 HIS 0.001 0.000 HIS A 214 PHE 0.012 0.001 PHE A 157 TYR 0.006 0.001 TYR B 162 ARG 0.003 0.001 ARG B 296 *********************** 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 107 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6146 (tt) cc_final: 0.5875 (tt) REVERT: A 312 MET cc_start: 0.4926 (tpt) cc_final: 0.4654 (tpt) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1541 time to fit residues: 22.9152 Evaluate side-chains 90 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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: 20.0000 chunk 99 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 40.0000 chunk 57 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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: 0.5934 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6586 Z= 0.195 Angle : 0.615 8.283 9074 Z= 0.318 Chirality : 0.042 0.153 1203 Planarity : 0.004 0.032 1225 Dihedral : 10.938 108.372 1365 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % 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: 1.13 (0.20), residues: 736 sheet: -2.52 (0.64), residues: 61 loop : -1.68 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 17 HIS 0.003 0.001 HIS A 107 PHE 0.013 0.001 PHE B 161 TYR 0.015 0.001 TYR B 83 ARG 0.008 0.001 ARG A 238 *********************** 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 103 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ILE cc_start: 0.8831 (mt) cc_final: 0.8543 (mt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1627 time to fit residues: 22.9832 Evaluate side-chains 85 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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: 0.0170 chunk 80 optimal weight: 7.9990 chunk 92 optimal weight: 50.0000 chunk 61 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 0.0770 overall best weight: 1.5578 ------------------------------------------------------------------------------- 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: 0.5884 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6586 Z= 0.171 Angle : 0.586 9.351 9074 Z= 0.299 Chirality : 0.042 0.155 1203 Planarity : 0.003 0.030 1225 Dihedral : 10.771 110.025 1365 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.41 (0.26), residues: 1134 helix: 1.39 (0.20), residues: 731 sheet: -2.30 (0.72), residues: 54 loop : -1.71 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 66 HIS 0.002 0.001 HIS A 214 PHE 0.027 0.001 PHE B 288 TYR 0.007 0.001 TYR B 162 ARG 0.005 0.001 ARG A 238 *********************** 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 113 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 35 ILE cc_start: 0.8709 (mt) cc_final: 0.8496 (mt) REVERT: A 74 LEU cc_start: 0.6457 (tt) cc_final: 0.6130 (tt) REVERT: A 157 PHE cc_start: 0.6128 (m-80) cc_final: 0.5752 (m-80) REVERT: B 20 ILE cc_start: 0.5911 (mm) cc_final: 0.4795 (mm) REVERT: B 98 MET cc_start: 0.7034 (ttm) cc_final: 0.6492 (tpp) REVERT: B 285 THR cc_start: 0.7603 (p) cc_final: 0.7270 (m) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1732 time to fit residues: 27.5879 Evaluate side-chains 90 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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: 40.0000 chunk 65 optimal weight: 6.9990 chunk 33 optimal weight: 50.0000 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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: 0.5957 moved from start: 0.5717 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= 0.184 Angle : 0.596 9.406 9074 Z= 0.304 Chirality : 0.042 0.168 1203 Planarity : 0.003 0.038 1225 Dihedral : 10.805 110.780 1365 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 0.51 (0.26), residues: 1134 helix: 1.49 (0.20), residues: 732 sheet: -2.35 (0.69), residues: 54 loop : -1.74 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 17 HIS 0.003 0.001 HIS A 214 PHE 0.019 0.001 PHE B 288 TYR 0.006 0.001 TYR A 87 ARG 0.011 0.001 ARG A 78 *********************** 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 101 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6579 (tt) cc_final: 0.6335 (tt) REVERT: A 78 ARG cc_start: 0.7656 (mmm160) cc_final: 0.7299 (tpp80) REVERT: B 98 MET cc_start: 0.7210 (ttm) cc_final: 0.6545 (tpp) REVERT: B 295 MET cc_start: 0.7895 (tmm) cc_final: 0.7485 (tmm) REVERT: B 296 ARG cc_start: 0.6795 (tmt170) cc_final: 0.6037 (tmt170) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1264 time to fit residues: 18.8376 Evaluate side-chains 87 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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: 0.9980 chunk 102 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 92 optimal weight: 40.0000 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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: 0.6035 moved from start: 0.5996 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= 0.203 Angle : 0.617 8.821 9074 Z= 0.320 Chirality : 0.043 0.194 1203 Planarity : 0.004 0.035 1225 Dihedral : 10.855 112.331 1365 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.43 (0.26), residues: 1134 helix: 1.41 (0.20), residues: 741 sheet: -2.50 (0.68), residues: 54 loop : -1.77 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 66 HIS 0.005 0.001 HIS A 214 PHE 0.015 0.001 PHE A 161 TYR 0.008 0.001 TYR A 87 ARG 0.005 0.001 ARG A 78 *********************** 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 : 0.749 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7851 (mmm160) cc_final: 0.7415 (tpp80) REVERT: B 98 MET cc_start: 0.7043 (ttm) cc_final: 0.6575 (tpp) REVERT: B 295 MET cc_start: 0.7792 (tmm) cc_final: 0.7449 (tmm) REVERT: B 296 ARG cc_start: 0.7013 (tmt170) cc_final: 0.6241 (tmt170) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1349 time to fit residues: 18.8085 Evaluate side-chains 83 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 0.5980 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 71 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 overall best weight: 3.1324 ------------------------------------------------------------------------------- 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: 0.6033 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6586 Z= 0.184 Angle : 0.594 8.745 9074 Z= 0.304 Chirality : 0.042 0.181 1203 Planarity : 0.003 0.031 1225 Dihedral : 10.760 112.489 1365 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.52 (0.26), residues: 1134 helix: 1.49 (0.20), residues: 743 sheet: -2.62 (0.60), residues: 60 loop : -1.70 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 17 HIS 0.006 0.001 HIS A 214 PHE 0.012 0.001 PHE B 23 TYR 0.006 0.001 TYR B 162 ARG 0.007 0.001 ARG A 78 ********************** 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 103 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.696 Fit side-chains REVERT: A 78 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7251 (tpp80) REVERT: B 97 VAL cc_start: 0.7942 (p) cc_final: 0.7510 (p) REVERT: B 98 MET cc_start: 0.7276 (ttm) cc_final: 0.6563 (tpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1442 time to fit residues: 21.3643 Evaluate side-chains 85 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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: 7.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 90 optimal weight: 50.0000 chunk 37 optimal weight: 20.0000 chunk 93 optimal weight: 50.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.104316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094416 restraints weight = 31821.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.091828 restraints weight = 46982.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.090536 restraints weight = 49537.797| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6586 Z= 0.215 Angle : 0.611 8.682 9074 Z= 0.318 Chirality : 0.043 0.196 1203 Planarity : 0.003 0.034 1225 Dihedral : 10.721 112.598 1365 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.46 (0.26), residues: 1134 helix: 1.43 (0.20), residues: 745 sheet: -2.78 (0.58), residues: 59 loop : -1.69 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 17 HIS 0.005 0.002 HIS A 214 PHE 0.014 0.001 PHE B 308 TYR 0.009 0.001 TYR A 87 ARG 0.006 0.001 ARG A 78 =============================================================================== Job complete usr+sys time: 1393.13 seconds wall clock time: 26 minutes 10.85 seconds (1570.85 seconds total)