Starting phenix.real_space_refine on Wed Feb 14 01:30:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z24_14457/02_2024/7z24_14457_updated.pdb" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 35 5.49 5 S 13 5.16 5 C 5266 2.51 5 N 1378 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 6": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8303 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4260 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 490} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3303 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 371} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.62 Number of scatterers: 8303 At special positions: 0 Unit cell: (97, 109.61, 101.85, 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 13 16.00 P 35 15.00 O 1611 8.00 N 1378 7.00 C 5266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 10 sheets defined 34.1% alpha, 14.7% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.931A pdb=" N VAL A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.340A pdb=" N LYS A 126 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 174 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 195 through 211 removed outlier: 3.580A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 254 through 269 removed outlier: 4.640A pdb=" N GLN A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.917A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 Processing helix chain 'A' and resid 364 through 383 Processing helix chain 'A' and resid 395 through 404 Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.006A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.891A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.602A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.528A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 5.925A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 125 through 128 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 156 through 172 removed outlier: 5.231A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 195 through 211 removed outlier: 3.524A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 270 removed outlier: 4.251A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 311 removed outlier: 3.765A pdb=" N GLU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 382 Processing helix chain 'B' and resid 395 through 404 removed outlier: 5.568A pdb=" N THR B 403 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLU B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 47 through 50 removed outlier: 4.605A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 105 through 110 Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 Processing sheet with id= D, first strand: chain 'A' and resid 414 through 416 removed outlier: 6.626A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 438 through 441 removed outlier: 7.050A pdb=" N LYS A 530 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE A 495 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TYR A 532 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR A 497 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 534 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.772A pdb=" N LEU A 452 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 465 " --> pdb=" O TYR A 457 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 60 through 64 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 110 Processing sheet with id= I, first strand: chain 'B' and resid 130 through 132 Processing sheet with id= J, first strand: chain 'B' and resid 413 through 416 removed outlier: 3.607A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) 268 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1472 1.33 - 1.45: 2307 1.45 - 1.57: 4721 1.57 - 1.69: 71 1.69 - 1.81: 23 Bond restraints: 8594 Sorted by residual: bond pdb=" C2 OMC E 2 " pdb=" N3 OMC E 2 " ideal model delta sigma weight residual 1.491 1.347 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C2 OMC E 4 " pdb=" N3 OMC E 4 " ideal model delta sigma weight residual 1.491 1.352 0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" N1 OMC E 4 " pdb=" C6 OMC E 4 " ideal model delta sigma weight residual 1.455 1.333 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" N1 OMC E 2 " pdb=" C6 OMC E 2 " ideal model delta sigma weight residual 1.455 1.335 0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C5 OMC E 4 " pdb=" C6 OMC E 4 " ideal model delta sigma weight residual 1.488 1.381 0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 8589 not shown) Histogram of bond angle deviations from ideal: 59.64 - 74.68: 3 74.68 - 89.73: 0 89.73 - 104.77: 322 104.77 - 119.81: 7679 119.81 - 134.85: 3830 Bond angle restraints: 11834 Sorted by residual: angle pdb=" C5' DG E 12 " pdb=" C4' DG E 12 " pdb=" O4' DG E 12 " ideal model delta sigma weight residual 109.40 123.17 -13.77 1.50e+00 4.44e-01 8.43e+01 angle pdb=" C5' DT E 13 " pdb=" C4' DT E 13 " pdb=" O4' DT E 13 " ideal model delta sigma weight residual 109.40 122.69 -13.29 1.50e+00 4.44e-01 7.85e+01 angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.40 120.19 -10.79 1.50e+00 4.44e-01 5.17e+01 angle pdb=" C HIS B 235 " pdb=" CA HIS B 235 " pdb=" CB HIS B 235 " ideal model delta sigma weight residual 110.08 117.91 -7.83 1.15e+00 7.56e-01 4.63e+01 angle pdb=" C3' OMC E 2 " pdb=" C2' OMC E 2 " pdb=" C1' OMC E 2 " ideal model delta sigma weight residual 101.30 106.98 -5.68 1.00e+00 1.00e+00 3.22e+01 ... (remaining 11829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 4364 19.40 - 38.80: 498 38.80 - 58.20: 141 58.20 - 77.59: 33 77.59 - 96.99: 9 Dihedral angle restraints: 5045 sinusoidal: 2333 harmonic: 2712 Sorted by residual: dihedral pdb=" C PHE B 346 " pdb=" N PHE B 346 " pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " ideal model delta harmonic sigma weight residual -122.60 -133.18 10.58 0 2.50e+00 1.60e-01 1.79e+01 dihedral pdb=" C GLU B 291 " pdb=" N GLU B 291 " pdb=" CA GLU B 291 " pdb=" CB GLU B 291 " ideal model delta harmonic sigma weight residual -122.60 -132.67 10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CD ARG A 277 " pdb=" NE ARG A 277 " pdb=" CZ ARG A 277 " pdb=" NH1 ARG A 277 " ideal model delta sinusoidal sigma weight residual 0.00 32.46 -32.46 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 5042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1137 0.109 - 0.217: 120 0.217 - 0.326: 23 0.326 - 0.434: 2 0.434 - 0.543: 2 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C4' DG E 12 " pdb=" C5' DG E 12 " pdb=" O4' DG E 12 " pdb=" C3' DG E 12 " both_signs ideal model delta sigma weight residual False -2.53 -1.98 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C4' DT E 13 " pdb=" C5' DT E 13 " pdb=" O4' DT E 13 " pdb=" C3' DT E 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C4' DC E 20 " pdb=" C5' DC E 20 " pdb=" O4' DC E 20 " pdb=" C3' DC E 20 " both_signs ideal model delta sigma weight residual False -2.53 -2.17 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1281 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 4 " -0.086 2.00e-02 2.50e+03 5.33e-01 6.40e+03 pdb=" C4' OMC E 4 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMC E 4 " 0.698 2.00e-02 2.50e+03 pdb=" C3' OMC E 4 " -0.585 2.00e-02 2.50e+03 pdb=" O3' OMC E 4 " -0.419 2.00e-02 2.50e+03 pdb=" C2' OMC E 4 " -0.259 2.00e-02 2.50e+03 pdb=" O2' OMC E 4 " 0.752 2.00e-02 2.50e+03 pdb=" C1' OMC E 4 " 0.278 2.00e-02 2.50e+03 pdb=" N1 OMC E 4 " -0.808 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC E 2 " 0.291 2.00e-02 2.50e+03 3.83e-01 3.30e+03 pdb=" C4' OMC E 2 " -0.354 2.00e-02 2.50e+03 pdb=" O4' OMC E 2 " -0.572 2.00e-02 2.50e+03 pdb=" C3' OMC E 2 " 0.485 2.00e-02 2.50e+03 pdb=" O3' OMC E 2 " -0.068 2.00e-02 2.50e+03 pdb=" C2' OMC E 2 " 0.399 2.00e-02 2.50e+03 pdb=" O2' OMC E 2 " -0.293 2.00e-02 2.50e+03 pdb=" C1' OMC E 2 " -0.326 2.00e-02 2.50e+03 pdb=" N1 OMC E 2 " 0.438 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 277 " 0.582 9.50e-02 1.11e+02 2.61e-01 4.16e+01 pdb=" NE ARG A 277 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 277 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 277 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 277 " 0.019 2.00e-02 2.50e+03 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 3015 2.89 - 3.39: 7474 3.39 - 3.89: 13926 3.89 - 4.40: 15973 4.40 - 4.90: 26070 Nonbonded interactions: 66458 Sorted by model distance: nonbonded pdb=" O VAL A 276 " pdb=" OG SER A 280 " model vdw 2.387 2.440 nonbonded pdb=" OG1 THR A 286 " pdb=" OE2 GLU A 291 " model vdw 2.390 2.440 nonbonded pdb=" O TYR B 56 " pdb=" NH2 ARG B 143 " model vdw 2.417 2.520 nonbonded pdb=" O ILE A 341 " pdb=" N LEU A 349 " model vdw 2.438 2.520 nonbonded pdb=" O GLU A 194 " pdb=" N HIS A 198 " model vdw 2.445 2.520 ... (remaining 66453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.990 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.030 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 0.144 8594 Z= 0.551 Angle : 1.039 13.772 11834 Z= 0.705 Chirality : 0.075 0.543 1284 Planarity : 0.020 0.533 1369 Dihedral : 18.281 96.992 3295 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.07 % Allowed : 3.04 % Favored : 94.89 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 917 helix: 1.09 (0.30), residues: 311 sheet: -0.29 (0.40), residues: 177 loop : -0.90 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 414 HIS 0.006 0.001 HIS A 315 PHE 0.021 0.002 PHE A 124 TYR 0.020 0.002 TYR A 532 ARG 0.004 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 498 ASN cc_start: 0.6968 (t0) cc_final: 0.6588 (t0) REVERT: B 280 SER cc_start: 0.7756 (p) cc_final: 0.7080 (t) outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.2053 time to fit residues: 37.9408 Evaluate side-chains 105 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 255 ASN A 332 GLN B 207 GLN B 242 GLN B 278 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8594 Z= 0.264 Angle : 0.750 14.142 11834 Z= 0.432 Chirality : 0.044 0.137 1284 Planarity : 0.007 0.114 1369 Dihedral : 17.581 82.172 1380 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.19 % Allowed : 9.85 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.28), residues: 917 helix: 1.01 (0.30), residues: 316 sheet: -0.13 (0.40), residues: 170 loop : -0.86 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 414 HIS 0.004 0.001 HIS A 315 PHE 0.018 0.002 PHE B 87 TYR 0.015 0.002 TYR A 501 ARG 0.003 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 1.031 Fit side-chains REVERT: A 78 ARG cc_start: 0.6628 (mmp80) cc_final: 0.5624 (mmt-90) REVERT: A 184 MET cc_start: 0.6389 (mtp) cc_final: 0.6188 (mtm) REVERT: A 375 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8126 (mp) REVERT: A 498 ASN cc_start: 0.7085 (t0) cc_final: 0.6760 (t0) REVERT: B 280 SER cc_start: 0.7820 (p) cc_final: 0.7165 (t) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.2000 time to fit residues: 32.4269 Evaluate side-chains 111 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 0.1980 chunk 23 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8594 Z= 0.326 Angle : 0.765 13.294 11834 Z= 0.438 Chirality : 0.044 0.143 1284 Planarity : 0.007 0.113 1369 Dihedral : 17.698 82.282 1378 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.04 % Allowed : 12.53 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 917 helix: 0.77 (0.30), residues: 319 sheet: -0.20 (0.40), residues: 168 loop : -0.91 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 402 HIS 0.007 0.001 HIS A 315 PHE 0.024 0.002 PHE A 124 TYR 0.016 0.002 TYR A 501 ARG 0.004 0.001 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 95 time to evaluate : 0.989 Fit side-chains REVERT: A 78 ARG cc_start: 0.6446 (mmp80) cc_final: 0.6186 (mmp80) REVERT: A 91 GLN cc_start: 0.6475 (mm110) cc_final: 0.6224 (tp40) REVERT: A 375 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 498 ASN cc_start: 0.7278 (t0) cc_final: 0.6918 (t0) REVERT: B 280 SER cc_start: 0.7811 (p) cc_final: 0.7121 (t) outliers start: 25 outliers final: 20 residues processed: 115 average time/residue: 0.2065 time to fit residues: 33.2730 Evaluate side-chains 116 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.0170 chunk 45 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8594 Z= 0.184 Angle : 0.675 13.485 11834 Z= 0.396 Chirality : 0.041 0.140 1284 Planarity : 0.006 0.111 1369 Dihedral : 17.320 81.772 1374 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.31 % Allowed : 14.60 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 917 helix: 1.19 (0.31), residues: 317 sheet: -0.14 (0.39), residues: 174 loop : -0.77 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 410 HIS 0.009 0.001 HIS B 208 PHE 0.016 0.001 PHE B 87 TYR 0.013 0.001 TYR A 501 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.880 Fit side-chains REVERT: A 78 ARG cc_start: 0.6396 (mmp80) cc_final: 0.6158 (mmp80) REVERT: A 375 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 498 ASN cc_start: 0.7123 (t0) cc_final: 0.6757 (t0) REVERT: B 206 ARG cc_start: 0.6628 (ttp80) cc_final: 0.6206 (ttp-170) REVERT: B 280 SER cc_start: 0.7754 (p) cc_final: 0.7078 (t) outliers start: 19 outliers final: 12 residues processed: 122 average time/residue: 0.1894 time to fit residues: 32.3491 Evaluate side-chains 114 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 0.0770 chunk 78 optimal weight: 40.0000 chunk 63 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 overall best weight: 6.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8594 Z= 0.332 Angle : 0.760 13.018 11834 Z= 0.432 Chirality : 0.044 0.159 1284 Planarity : 0.007 0.114 1369 Dihedral : 17.687 85.038 1373 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.77 % Allowed : 14.84 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.28), residues: 917 helix: 0.91 (0.30), residues: 318 sheet: -0.27 (0.40), residues: 170 loop : -0.85 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 402 HIS 0.007 0.002 HIS B 208 PHE 0.022 0.002 PHE A 124 TYR 0.017 0.002 TYR A 501 ARG 0.004 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 0.916 Fit side-chains REVERT: A 91 GLN cc_start: 0.6420 (mm110) cc_final: 0.6157 (tp40) REVERT: A 375 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8116 (mt) REVERT: A 498 ASN cc_start: 0.7273 (t0) cc_final: 0.6992 (t0) REVERT: B 280 SER cc_start: 0.7885 (p) cc_final: 0.7222 (t) outliers start: 31 outliers final: 22 residues processed: 125 average time/residue: 0.1868 time to fit residues: 33.2673 Evaluate side-chains 121 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 overall best weight: 2.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8594 Z= 0.200 Angle : 0.689 13.044 11834 Z= 0.400 Chirality : 0.042 0.192 1284 Planarity : 0.007 0.113 1369 Dihedral : 17.550 89.043 1373 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.43 % Allowed : 16.79 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 917 helix: 1.14 (0.31), residues: 317 sheet: -0.24 (0.39), residues: 177 loop : -0.73 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.011 0.001 HIS B 208 PHE 0.014 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.005 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.989 Fit side-chains REVERT: A 91 GLN cc_start: 0.6317 (mm110) cc_final: 0.6079 (tp40) REVERT: A 375 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8107 (mt) REVERT: A 498 ASN cc_start: 0.7242 (t0) cc_final: 0.6901 (t0) REVERT: B 206 ARG cc_start: 0.6498 (ttp80) cc_final: 0.6126 (ttp-170) REVERT: B 280 SER cc_start: 0.7860 (p) cc_final: 0.7195 (t) outliers start: 20 outliers final: 17 residues processed: 115 average time/residue: 0.1949 time to fit residues: 32.0210 Evaluate side-chains 115 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.3980 chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8594 Z= 0.223 Angle : 0.695 12.911 11834 Z= 0.402 Chirality : 0.042 0.176 1284 Planarity : 0.007 0.113 1369 Dihedral : 17.513 91.883 1373 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.41 % Allowed : 16.79 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.28), residues: 917 helix: 1.13 (0.31), residues: 317 sheet: -0.07 (0.40), residues: 169 loop : -0.78 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 402 HIS 0.010 0.001 HIS B 208 PHE 0.015 0.001 PHE A 124 TYR 0.015 0.002 TYR A 501 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.899 Fit side-chains REVERT: A 331 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.7069 (tttp) REVERT: A 375 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 498 ASN cc_start: 0.7267 (t0) cc_final: 0.6947 (t0) REVERT: B 280 SER cc_start: 0.7847 (p) cc_final: 0.7178 (t) outliers start: 28 outliers final: 25 residues processed: 117 average time/residue: 0.1928 time to fit residues: 32.2246 Evaluate side-chains 121 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 17 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN B 373 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8594 Z= 0.180 Angle : 0.676 12.872 11834 Z= 0.393 Chirality : 0.041 0.170 1284 Planarity : 0.006 0.113 1369 Dihedral : 17.394 92.604 1373 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.04 % Allowed : 17.52 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 917 helix: 1.29 (0.31), residues: 317 sheet: 0.07 (0.40), residues: 168 loop : -0.72 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 402 HIS 0.009 0.001 HIS B 208 PHE 0.013 0.001 PHE B 87 TYR 0.014 0.001 TYR A 501 ARG 0.007 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.949 Fit side-chains REVERT: A 331 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7080 (tttp) REVERT: A 375 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 498 ASN cc_start: 0.7235 (t0) cc_final: 0.6903 (t0) REVERT: B 280 SER cc_start: 0.7845 (p) cc_final: 0.7176 (t) outliers start: 25 outliers final: 20 residues processed: 117 average time/residue: 0.2068 time to fit residues: 33.9429 Evaluate side-chains 119 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 545 ASN B 373 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8594 Z= 0.250 Angle : 0.707 12.821 11834 Z= 0.407 Chirality : 0.043 0.172 1284 Planarity : 0.007 0.113 1369 Dihedral : 17.468 93.435 1373 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.65 % Allowed : 17.52 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 917 helix: 1.18 (0.31), residues: 317 sheet: -0.03 (0.39), residues: 169 loop : -0.76 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 402 HIS 0.008 0.001 HIS B 208 PHE 0.016 0.002 PHE A 124 TYR 0.044 0.002 TYR A 319 ARG 0.006 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.940 Fit side-chains REVERT: A 331 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.7075 (tttp) REVERT: A 375 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8101 (mt) REVERT: A 498 ASN cc_start: 0.7307 (t0) cc_final: 0.7001 (t0) REVERT: B 280 SER cc_start: 0.7846 (p) cc_final: 0.7189 (t) REVERT: B 405 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7310 (m-80) outliers start: 30 outliers final: 26 residues processed: 122 average time/residue: 0.1956 time to fit residues: 33.7042 Evaluate side-chains 128 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8594 Z= 0.369 Angle : 0.786 14.012 11834 Z= 0.444 Chirality : 0.046 0.176 1284 Planarity : 0.007 0.113 1369 Dihedral : 17.757 95.012 1373 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.53 % Allowed : 17.76 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.28), residues: 917 helix: 0.87 (0.30), residues: 318 sheet: -0.09 (0.40), residues: 168 loop : -0.87 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 410 HIS 0.014 0.002 HIS B 208 PHE 0.025 0.002 PHE A 124 TYR 0.047 0.003 TYR A 319 ARG 0.005 0.001 ARG A 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1834 Ramachandran restraints generated. 917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 0.971 Fit side-chains REVERT: A 91 GLN cc_start: 0.6469 (mm110) cc_final: 0.6199 (tp40) REVERT: A 331 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.7043 (tttp) REVERT: A 375 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 498 ASN cc_start: 0.7235 (t0) cc_final: 0.6897 (t0) REVERT: B 280 SER cc_start: 0.7838 (p) cc_final: 0.7207 (t) REVERT: B 405 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7381 (m-80) outliers start: 29 outliers final: 25 residues processed: 120 average time/residue: 0.1994 time to fit residues: 33.5008 Evaluate side-chains 128 residues out of total 836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 410 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.213482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173961 restraints weight = 8616.095| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.71 r_work: 0.3700 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8594 Z= 0.232 Angle : 0.708 12.946 11834 Z= 0.408 Chirality : 0.042 0.174 1284 Planarity : 0.007 0.113 1369 Dihedral : 17.619 93.355 1373 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.41 % Allowed : 18.37 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.28), residues: 917 helix: 1.07 (0.30), residues: 319 sheet: -0.20 (0.39), residues: 169 loop : -0.79 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 402 HIS 0.014 0.001 HIS B 208 PHE 0.017 0.002 PHE A 124 TYR 0.040 0.002 TYR A 319 ARG 0.006 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1790.75 seconds wall clock time: 33 minutes 24.46 seconds (2004.46 seconds total)