Starting phenix.real_space_refine on Mon Mar 11 12:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/03_2024/6jt2_9885_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/03_2024/6jt2_9885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/03_2024/6jt2_9885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/03_2024/6jt2_9885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/03_2024/6jt2_9885_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jt2_9885/03_2024/6jt2_9885_updated.pdb" } resolution = 3.8 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= 0.004 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8191 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3742 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 8 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 4372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 4452 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 Time building chain proxies: 7.15, per 1000 atoms: 0.87 Number of scatterers: 8191 At special positions: 0 Unit cell: (147.345, 87.78, 98.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 56 16.00 P 3 15.00 Mg 2 11.99 O 1475 8.00 N 1392 7.00 C 5262 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: 3.23 Conformation dependent library (CDL) restraints added in 2.6 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 9 sheets defined 44.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 148 removed outlier: 3.730A pdb=" N GLU A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 154 No H-bonds generated for 'chain 'A' and resid 151 through 154' Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.800A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.762A pdb=" N LEU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.643A pdb=" N LYS A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 409 through 457 Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.517A pdb=" N GLN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 4.084A pdb=" N GLU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.642A pdb=" N ASN A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.732A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 156 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.892A pdb=" N SER B 270 " --> pdb=" O HIS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 348 through 397 removed outlier: 4.349A pdb=" N VAL B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU B 357 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 492 through 508 removed outlier: 4.412A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 201 through 204 Processing sheet with id= B, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.649A pdb=" N GLN A 300 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 523 through 525 removed outlier: 4.409A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 615 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU A 577 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN A 617 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N SER A 579 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 634 through 636 Processing sheet with id= F, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.896A pdb=" N GLN B 168 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU B 180 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL B 166 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLU B 182 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N MET B 164 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.754A pdb=" N ARG B 258 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG B 279 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU B 256 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.532A pdb=" N GLY B 531 " --> pdb=" O CYS B 541 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 469 through 474 removed outlier: 7.068A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR B 474 " --> pdb=" O LYS B 478 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1062 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: 2.41 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3335 1.39 - 1.56: 4924 1.56 - 1.73: 6 1.73 - 1.90: 86 1.90 - 2.07: 4 Bond restraints: 8355 Sorted by residual: bond pdb=" O3B G2P A1001 " pdb=" PG G2P A1001 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" O1A G2P A1001 " pdb=" PA G2P A1001 " ideal model delta sigma weight residual 1.507 1.610 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O1B G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 1.510 1.609 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C4 G2P A1001 " pdb=" C5 G2P A1001 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C5 G2P A1001 " pdb=" C6 G2P A1001 " ideal model delta sigma weight residual 1.420 1.483 -0.063 2.00e-02 2.50e+03 9.79e+00 ... (remaining 8350 not shown) Histogram of bond angle deviations from ideal: 88.58 - 106.57: 253 106.57 - 124.57: 10970 124.57 - 142.56: 142 142.56 - 160.55: 0 160.55 - 178.54: 2 Bond angle restraints: 11367 Sorted by residual: angle pdb=" PA G2P A1001 " pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 120.83 109.47 11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " pdb=" O3B G2P A1001 " ideal model delta sigma weight residual 99.71 109.82 -10.11 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C5 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N3 G2P A1001 " ideal model delta sigma weight residual 128.08 118.69 9.39 3.00e+00 1.11e-01 9.79e+00 angle pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.28e+00 angle pdb=" C3A G2P A1001 " pdb=" PA G2P A1001 " pdb=" O5' G2P A1001 " ideal model delta sigma weight residual 99.14 108.27 -9.13 3.00e+00 1.11e-01 9.26e+00 ... (remaining 11362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 4668 16.26 - 32.52: 249 32.52 - 48.78: 56 48.78 - 65.03: 15 65.03 - 81.29: 4 Dihedral angle restraints: 4992 sinusoidal: 1869 harmonic: 3123 Sorted by residual: dihedral pdb=" CA ASP B 262 " pdb=" C ASP B 262 " pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N LEU B 340 " pdb=" CA LEU B 340 " ideal model delta harmonic sigma weight residual 180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE A 301 " pdb=" C PHE A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1106 0.055 - 0.111: 213 0.111 - 0.166: 22 0.166 - 0.221: 0 0.221 - 0.276: 1 Chirality restraints: 1342 Sorted by residual: chirality pdb=" CB VAL A 462 " pdb=" CA VAL A 462 " pdb=" CG1 VAL A 462 " pdb=" CG2 VAL A 462 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA VAL A 462 " pdb=" N VAL A 462 " pdb=" C VAL A 462 " pdb=" CB VAL A 462 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C2' G2P A1001 " pdb=" C1' G2P A1001 " pdb=" C3' G2P A1001 " pdb=" O2' G2P A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1339 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 462 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C VAL A 462 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL A 462 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 463 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 258 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 259 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 209 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO B 210 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " 0.031 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 50 2.56 - 3.15: 6549 3.15 - 3.73: 12636 3.73 - 4.32: 16594 4.32 - 4.90: 27833 Nonbonded interactions: 63662 Sorted by model distance: nonbonded pdb=" O2B G2P A1001 " pdb="MG MG A1002 " model vdw 1.980 2.170 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1002 " model vdw 2.095 2.170 nonbonded pdb=" OD2 ASP A 486 " pdb="MG MG A1002 " model vdw 2.101 2.170 nonbonded pdb=" O5' G2P A1001 " pdb="MG MG A1003 " model vdw 2.172 2.170 nonbonded pdb=" O LEU A 520 " pdb=" NE2 GLN A 548 " model vdw 2.259 2.520 ... (remaining 63657 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=0.30 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.260 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 29.280 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.004 0.106 8355 Z= 0.290 Angle : 0.738 11.357 11367 Z= 0.377 Chirality : 0.042 0.276 1342 Planarity : 0.005 0.058 1431 Dihedral : 11.363 81.292 2966 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.00 % Favored : 95.71 % Rotamer: Outliers : 3.54 % Allowed : 5.19 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.54 (0.23), residues: 1049 helix: -1.24 (0.20), residues: 478 sheet: -1.17 (0.35), residues: 192 loop : -2.34 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 602 HIS 0.005 0.001 HIS B 105 PHE 0.016 0.002 PHE A 292 TYR 0.013 0.001 TYR B 479 ARG 0.003 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 CYS cc_start: 0.8998 (t) cc_final: 0.8778 (m) REVERT: A 455 CYS cc_start: 0.8971 (m) cc_final: 0.8406 (t) REVERT: A 479 ASN cc_start: 0.7920 (m110) cc_final: 0.7647 (p0) REVERT: A 514 ASP cc_start: 0.9019 (m-30) cc_final: 0.8740 (m-30) REVERT: A 516 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8498 (mm-40) REVERT: A 543 ASP cc_start: 0.8435 (m-30) cc_final: 0.7491 (p0) REVERT: A 554 VAL cc_start: 0.9375 (t) cc_final: 0.9168 (t) REVERT: A 556 MET cc_start: 0.9443 (tpp) cc_final: 0.8926 (mmm) REVERT: A 583 PHE cc_start: 0.8186 (m-80) cc_final: 0.7859 (m-10) REVERT: B 73 MET cc_start: 0.8564 (tpp) cc_final: 0.8300 (tpp) REVERT: B 106 ASP cc_start: 0.9202 (t0) cc_final: 0.8917 (t0) REVERT: B 119 SER cc_start: 0.9177 (m) cc_final: 0.8363 (p) REVERT: B 160 THR cc_start: 0.8562 (m) cc_final: 0.8351 (p) REVERT: B 211 TYR cc_start: 0.8649 (t80) cc_final: 0.8372 (t80) REVERT: B 228 VAL cc_start: 0.8802 (t) cc_final: 0.8571 (p) REVERT: B 320 LEU cc_start: 0.8545 (tt) cc_final: 0.8089 (tp) REVERT: B 323 CYS cc_start: 0.8540 (p) cc_final: 0.8244 (p) REVERT: B 394 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8711 (tt) REVERT: B 491 HIS cc_start: 0.8482 (p90) cc_final: 0.7513 (t-170) REVERT: B 537 MET cc_start: 0.8659 (ttm) cc_final: 0.8425 (ttt) outliers start: 30 outliers final: 11 residues processed: 212 average time/residue: 0.1899 time to fit residues: 54.9775 Evaluate side-chains 123 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 96 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 408 HIS B 548 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8355 Z= 0.203 Angle : 0.668 9.474 11367 Z= 0.330 Chirality : 0.043 0.208 1342 Planarity : 0.005 0.049 1431 Dihedral : 7.781 67.223 1203 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.01 % Allowed : 12.63 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.24), residues: 1049 helix: -0.12 (0.22), residues: 488 sheet: -0.93 (0.35), residues: 204 loop : -2.04 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP A 467 HIS 0.010 0.001 HIS B 266 PHE 0.023 0.002 PHE A 335 TYR 0.027 0.002 TYR B 237 ARG 0.007 0.001 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6092 (t80) REVERT: A 341 MET cc_start: 0.7917 (tpt) cc_final: 0.7617 (tpp) REVERT: A 455 CYS cc_start: 0.9025 (m) cc_final: 0.8354 (t) REVERT: A 479 ASN cc_start: 0.7760 (m110) cc_final: 0.7448 (p0) REVERT: A 514 ASP cc_start: 0.8997 (m-30) cc_final: 0.8750 (m-30) REVERT: A 516 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8511 (tp-100) REVERT: A 543 ASP cc_start: 0.8439 (m-30) cc_final: 0.7498 (p0) REVERT: A 583 PHE cc_start: 0.8258 (m-80) cc_final: 0.8046 (m-80) REVERT: A 622 THR cc_start: 0.9334 (m) cc_final: 0.9119 (p) REVERT: B 69 MET cc_start: 0.8591 (ttm) cc_final: 0.8388 (mtm) REVERT: B 73 MET cc_start: 0.8648 (tpp) cc_final: 0.8343 (tpp) REVERT: B 106 ASP cc_start: 0.9205 (t0) cc_final: 0.8918 (t0) REVERT: B 119 SER cc_start: 0.9194 (m) cc_final: 0.8290 (p) REVERT: B 211 TYR cc_start: 0.8624 (t80) cc_final: 0.8423 (t80) REVERT: B 320 LEU cc_start: 0.8561 (tt) cc_final: 0.8354 (tp) REVERT: B 339 TYR cc_start: 0.8190 (m-10) cc_final: 0.7614 (m-10) REVERT: B 342 ASP cc_start: 0.8335 (m-30) cc_final: 0.7940 (m-30) REVERT: B 375 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8213 (ttm170) REVERT: B 480 MET cc_start: 0.9295 (ttm) cc_final: 0.9072 (ttm) REVERT: B 491 HIS cc_start: 0.8435 (p90) cc_final: 0.7607 (t-170) REVERT: B 537 MET cc_start: 0.8704 (ttm) cc_final: 0.8263 (ttt) outliers start: 34 outliers final: 20 residues processed: 149 average time/residue: 0.1623 time to fit residues: 35.2813 Evaluate side-chains 122 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 346 HIS B 408 HIS B 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8355 Z= 0.199 Angle : 0.630 8.990 11367 Z= 0.313 Chirality : 0.042 0.257 1342 Planarity : 0.004 0.048 1431 Dihedral : 7.409 65.521 1198 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 4.13 % Allowed : 13.81 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1049 helix: 0.21 (0.23), residues: 492 sheet: -0.65 (0.36), residues: 204 loop : -1.92 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 22 HIS 0.015 0.001 HIS B 266 PHE 0.023 0.002 PHE A 141 TYR 0.017 0.001 TYR B 569 ARG 0.004 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9231 (pp) REVERT: A 203 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.6170 (t80) REVERT: A 455 CYS cc_start: 0.9020 (m) cc_final: 0.8401 (t) REVERT: A 479 ASN cc_start: 0.7694 (m110) cc_final: 0.7405 (p0) REVERT: A 514 ASP cc_start: 0.9060 (m-30) cc_final: 0.8778 (m-30) REVERT: A 516 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8595 (tp-100) REVERT: A 543 ASP cc_start: 0.8516 (m-30) cc_final: 0.7587 (p0) REVERT: B 1 MET cc_start: 0.8543 (tpp) cc_final: 0.8242 (ttm) REVERT: B 73 MET cc_start: 0.8701 (tpp) cc_final: 0.8409 (tpp) REVERT: B 106 ASP cc_start: 0.9213 (t0) cc_final: 0.8871 (t0) REVERT: B 119 SER cc_start: 0.9235 (m) cc_final: 0.8382 (p) REVERT: B 328 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8288 (mmm) REVERT: B 342 ASP cc_start: 0.8395 (m-30) cc_final: 0.8025 (m-30) REVERT: B 491 HIS cc_start: 0.8552 (p90) cc_final: 0.7656 (t-170) REVERT: B 503 MET cc_start: 0.9161 (mtp) cc_final: 0.8831 (mmm) REVERT: B 537 MET cc_start: 0.8718 (ttm) cc_final: 0.8359 (ttt) outliers start: 35 outliers final: 25 residues processed: 131 average time/residue: 0.1593 time to fit residues: 30.7903 Evaluate side-chains 124 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0170 chunk 72 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 422 GLN B 171 ASN B 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8355 Z= 0.189 Angle : 0.590 8.928 11367 Z= 0.291 Chirality : 0.040 0.141 1342 Planarity : 0.004 0.047 1431 Dihedral : 6.828 64.254 1196 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.84 % Allowed : 13.81 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.74 (0.25), residues: 1049 helix: 0.46 (0.23), residues: 492 sheet: -0.41 (0.37), residues: 203 loop : -1.81 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 22 HIS 0.004 0.001 HIS B 266 PHE 0.019 0.002 PHE B 433 TYR 0.014 0.001 TYR B 569 ARG 0.004 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 111 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.6404 (t80) REVERT: A 341 MET cc_start: 0.7843 (tpt) cc_final: 0.7642 (mmm) REVERT: A 479 ASN cc_start: 0.7624 (m110) cc_final: 0.7187 (p0) REVERT: A 514 ASP cc_start: 0.9119 (m-30) cc_final: 0.8867 (m-30) REVERT: A 516 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8574 (tp-100) REVERT: A 543 ASP cc_start: 0.8555 (m-30) cc_final: 0.7570 (p0) REVERT: A 556 MET cc_start: 0.9297 (tpp) cc_final: 0.9033 (mmm) REVERT: A 573 MET cc_start: 0.8785 (tpt) cc_final: 0.8514 (tpt) REVERT: A 607 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 73 MET cc_start: 0.8775 (tpp) cc_final: 0.8464 (tpp) REVERT: B 106 ASP cc_start: 0.9195 (t0) cc_final: 0.8825 (t0) REVERT: B 119 SER cc_start: 0.9265 (m) cc_final: 0.8385 (p) REVERT: B 328 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8515 (mmm) REVERT: B 342 ASP cc_start: 0.8303 (m-30) cc_final: 0.7924 (m-30) REVERT: B 491 HIS cc_start: 0.8567 (p90) cc_final: 0.7640 (t-170) REVERT: B 503 MET cc_start: 0.9254 (mtp) cc_final: 0.8762 (mmm) outliers start: 41 outliers final: 24 residues processed: 141 average time/residue: 0.1647 time to fit residues: 34.6832 Evaluate side-chains 124 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 87 optimal weight: 0.0040 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 GLN A 422 GLN B 266 HIS B 448 ASN B 563 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8355 Z= 0.190 Angle : 0.579 8.442 11367 Z= 0.286 Chirality : 0.040 0.136 1342 Planarity : 0.004 0.048 1431 Dihedral : 6.772 63.297 1196 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.37 % Allowed : 14.88 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.59 (0.26), residues: 1049 helix: 0.58 (0.23), residues: 493 sheet: -0.38 (0.37), residues: 203 loop : -1.71 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 22 HIS 0.009 0.001 HIS B 266 PHE 0.014 0.001 PHE A 458 TYR 0.016 0.001 TYR B 569 ARG 0.004 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6428 (t80) REVERT: A 291 MET cc_start: 0.8694 (mtp) cc_final: 0.8015 (mtp) REVERT: A 479 ASN cc_start: 0.7618 (m110) cc_final: 0.7174 (p0) REVERT: A 514 ASP cc_start: 0.9150 (m-30) cc_final: 0.8909 (m-30) REVERT: A 516 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8596 (tp-100) REVERT: A 543 ASP cc_start: 0.8561 (m-30) cc_final: 0.7624 (p0) REVERT: A 607 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 73 MET cc_start: 0.8847 (tpp) cc_final: 0.8546 (tpp) REVERT: B 106 ASP cc_start: 0.9208 (t0) cc_final: 0.8831 (t0) REVERT: B 328 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: B 342 ASP cc_start: 0.8268 (m-30) cc_final: 0.7895 (m-30) REVERT: B 491 HIS cc_start: 0.8563 (p90) cc_final: 0.7627 (t-170) REVERT: B 503 MET cc_start: 0.9301 (mtp) cc_final: 0.8722 (mmm) REVERT: B 592 MET cc_start: 0.7228 (ppp) cc_final: 0.6882 (ppp) outliers start: 37 outliers final: 27 residues processed: 125 average time/residue: 0.1540 time to fit residues: 29.4950 Evaluate side-chains 122 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8355 Z= 0.194 Angle : 0.576 7.895 11367 Z= 0.284 Chirality : 0.040 0.258 1342 Planarity : 0.004 0.048 1431 Dihedral : 6.666 62.169 1196 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.01 % Allowed : 15.35 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.49 (0.26), residues: 1049 helix: 0.63 (0.23), residues: 493 sheet: -0.34 (0.36), residues: 208 loop : -1.61 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 22 HIS 0.003 0.001 HIS A 406 PHE 0.014 0.001 PHE A 458 TYR 0.015 0.001 TYR B 569 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.6380 (t80) REVERT: A 399 TYR cc_start: 0.7817 (m-80) cc_final: 0.7322 (m-80) REVERT: A 479 ASN cc_start: 0.7604 (m110) cc_final: 0.7176 (p0) REVERT: A 514 ASP cc_start: 0.9167 (m-30) cc_final: 0.8919 (m-30) REVERT: A 543 ASP cc_start: 0.8578 (m-30) cc_final: 0.7648 (p0) REVERT: A 607 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7881 (t80) REVERT: B 73 MET cc_start: 0.8920 (tpp) cc_final: 0.8617 (tpp) REVERT: B 106 ASP cc_start: 0.9197 (t0) cc_final: 0.8810 (t0) REVERT: B 491 HIS cc_start: 0.8564 (p90) cc_final: 0.7633 (t-170) REVERT: B 592 MET cc_start: 0.7203 (ppp) cc_final: 0.6941 (ppp) outliers start: 34 outliers final: 26 residues processed: 117 average time/residue: 0.1538 time to fit residues: 27.0398 Evaluate side-chains 118 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.0170 chunk 57 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8355 Z= 0.186 Angle : 0.572 10.293 11367 Z= 0.282 Chirality : 0.040 0.186 1342 Planarity : 0.004 0.049 1431 Dihedral : 6.453 61.699 1194 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.60 % Allowed : 15.23 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.41 (0.26), residues: 1049 helix: 0.67 (0.23), residues: 493 sheet: -0.28 (0.36), residues: 208 loop : -1.54 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 22 HIS 0.003 0.001 HIS A 406 PHE 0.013 0.001 PHE B 223 TYR 0.014 0.001 TYR B 569 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 97 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6981 (OUTLIER) cc_final: 0.6382 (t80) REVERT: A 291 MET cc_start: 0.8600 (mtp) cc_final: 0.7911 (mtp) REVERT: A 341 MET cc_start: 0.8105 (mmm) cc_final: 0.7761 (tpt) REVERT: A 399 TYR cc_start: 0.7851 (m-80) cc_final: 0.7370 (m-80) REVERT: A 479 ASN cc_start: 0.7603 (m110) cc_final: 0.7172 (p0) REVERT: A 514 ASP cc_start: 0.9168 (m-30) cc_final: 0.8939 (m-30) REVERT: A 543 ASP cc_start: 0.8567 (m-30) cc_final: 0.7624 (p0) REVERT: A 607 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 73 MET cc_start: 0.8931 (tpp) cc_final: 0.8619 (tpp) REVERT: B 106 ASP cc_start: 0.9179 (t0) cc_final: 0.8912 (t0) REVERT: B 423 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8851 (pp) REVERT: B 491 HIS cc_start: 0.8551 (p90) cc_final: 0.7629 (t-170) REVERT: B 592 MET cc_start: 0.7182 (ppp) cc_final: 0.6926 (ppp) outliers start: 39 outliers final: 27 residues processed: 125 average time/residue: 0.1501 time to fit residues: 28.3796 Evaluate side-chains 121 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 69 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8355 Z= 0.159 Angle : 0.575 11.215 11367 Z= 0.283 Chirality : 0.040 0.213 1342 Planarity : 0.004 0.050 1431 Dihedral : 6.396 61.979 1194 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.54 % Allowed : 15.94 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.34 (0.26), residues: 1049 helix: 0.71 (0.23), residues: 492 sheet: -0.23 (0.36), residues: 210 loop : -1.48 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 22 HIS 0.003 0.001 HIS A 406 PHE 0.013 0.001 PHE B 223 TYR 0.014 0.001 TYR A 372 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 91 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6960 (OUTLIER) cc_final: 0.6368 (t80) REVERT: A 291 MET cc_start: 0.8588 (mtp) cc_final: 0.7974 (mtp) REVERT: A 399 TYR cc_start: 0.8104 (m-80) cc_final: 0.7518 (m-80) REVERT: A 479 ASN cc_start: 0.7597 (m110) cc_final: 0.7164 (p0) REVERT: A 514 ASP cc_start: 0.9144 (m-30) cc_final: 0.8900 (m-30) REVERT: A 543 ASP cc_start: 0.8600 (m-30) cc_final: 0.7725 (p0) REVERT: A 607 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7835 (t80) REVERT: B 73 MET cc_start: 0.8918 (tpp) cc_final: 0.8591 (tpp) REVERT: B 106 ASP cc_start: 0.9273 (t0) cc_final: 0.8932 (t0) REVERT: B 124 ASP cc_start: 0.8828 (m-30) cc_final: 0.8281 (t0) REVERT: B 491 HIS cc_start: 0.8560 (p90) cc_final: 0.7720 (t-170) REVERT: B 592 MET cc_start: 0.7204 (ppp) cc_final: 0.6912 (ppp) outliers start: 30 outliers final: 24 residues processed: 115 average time/residue: 0.1540 time to fit residues: 26.5483 Evaluate side-chains 115 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.6980 chunk 97 optimal weight: 0.0010 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8355 Z= 0.169 Angle : 0.581 12.035 11367 Z= 0.284 Chirality : 0.040 0.197 1342 Planarity : 0.004 0.050 1431 Dihedral : 6.317 61.996 1192 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.42 % Allowed : 15.82 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.25 (0.26), residues: 1049 helix: 0.77 (0.23), residues: 492 sheet: -0.12 (0.36), residues: 208 loop : -1.46 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 22 HIS 0.004 0.001 HIS B 586 PHE 0.013 0.001 PHE A 141 TYR 0.015 0.001 TYR B 569 ARG 0.003 0.000 ARG B 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6945 (OUTLIER) cc_final: 0.6351 (t80) REVERT: A 291 MET cc_start: 0.8568 (mtp) cc_final: 0.7995 (mtp) REVERT: A 341 MET cc_start: 0.7684 (mmm) cc_final: 0.7321 (tpt) REVERT: A 399 TYR cc_start: 0.8165 (m-80) cc_final: 0.7618 (m-80) REVERT: A 479 ASN cc_start: 0.7575 (m110) cc_final: 0.7138 (p0) REVERT: A 514 ASP cc_start: 0.9150 (m-30) cc_final: 0.8931 (m-30) REVERT: A 543 ASP cc_start: 0.8600 (m-30) cc_final: 0.7737 (p0) REVERT: A 556 MET cc_start: 0.9443 (tpp) cc_final: 0.8966 (mmm) REVERT: A 607 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7893 (t80) REVERT: B 73 MET cc_start: 0.8931 (tpp) cc_final: 0.8609 (tpp) REVERT: B 106 ASP cc_start: 0.9274 (t0) cc_final: 0.8948 (t0) REVERT: B 124 ASP cc_start: 0.8809 (m-30) cc_final: 0.8293 (t0) REVERT: B 162 ILE cc_start: 0.9132 (pt) cc_final: 0.8714 (tp) REVERT: B 491 HIS cc_start: 0.8544 (p90) cc_final: 0.7717 (t-170) REVERT: B 592 MET cc_start: 0.7236 (ppp) cc_final: 0.6959 (ppp) outliers start: 29 outliers final: 26 residues processed: 113 average time/residue: 0.1532 time to fit residues: 26.2322 Evaluate side-chains 114 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 86 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 69 optimal weight: 0.1980 chunk 105 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 89 optimal weight: 0.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8355 Z= 0.158 Angle : 0.588 12.339 11367 Z= 0.284 Chirality : 0.040 0.154 1342 Planarity : 0.004 0.050 1431 Dihedral : 6.214 61.938 1192 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.31 % Allowed : 16.17 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.21 (0.26), residues: 1049 helix: 0.80 (0.23), residues: 492 sheet: -0.06 (0.36), residues: 206 loop : -1.45 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 22 HIS 0.003 0.001 HIS B 586 PHE 0.020 0.001 PHE B 457 TYR 0.014 0.001 TYR B 569 ARG 0.003 0.000 ARG B 381 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6396 (t80) REVERT: A 291 MET cc_start: 0.8562 (mtp) cc_final: 0.8032 (mtp) REVERT: A 341 MET cc_start: 0.7598 (mmm) cc_final: 0.7350 (tpt) REVERT: A 479 ASN cc_start: 0.7647 (m110) cc_final: 0.7171 (p0) REVERT: A 514 ASP cc_start: 0.9107 (m-30) cc_final: 0.8906 (m-30) REVERT: A 543 ASP cc_start: 0.8627 (m-30) cc_final: 0.7784 (p0) REVERT: A 556 MET cc_start: 0.9447 (tpp) cc_final: 0.8977 (mmm) REVERT: A 607 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7825 (t80) REVERT: B 73 MET cc_start: 0.8930 (tpp) cc_final: 0.8596 (tpp) REVERT: B 106 ASP cc_start: 0.9289 (t0) cc_final: 0.8987 (t0) REVERT: B 124 ASP cc_start: 0.8792 (m-30) cc_final: 0.8301 (t0) REVERT: B 162 ILE cc_start: 0.8996 (pt) cc_final: 0.8660 (tp) REVERT: B 491 HIS cc_start: 0.8549 (p90) cc_final: 0.7735 (t-170) REVERT: B 592 MET cc_start: 0.7300 (ppp) cc_final: 0.6949 (ppp) outliers start: 28 outliers final: 25 residues processed: 112 average time/residue: 0.1550 time to fit residues: 26.2298 Evaluate side-chains 114 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 87 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 370 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.0070 chunk 77 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.082601 restraints weight = 22580.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085217 restraints weight = 13640.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087003 restraints weight = 9671.056| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8355 Z= 0.170 Angle : 0.593 12.297 11367 Z= 0.285 Chirality : 0.040 0.187 1342 Planarity : 0.004 0.050 1431 Dihedral : 6.142 61.042 1192 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.31 % Allowed : 16.17 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1049 helix: 0.84 (0.23), residues: 492 sheet: -0.01 (0.36), residues: 209 loop : -1.39 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 22 HIS 0.003 0.001 HIS A 406 PHE 0.020 0.001 PHE B 457 TYR 0.013 0.001 TYR B 569 ARG 0.003 0.000 ARG B 381 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.64 seconds wall clock time: 34 minutes 25.06 seconds (2065.06 seconds total)