Starting phenix.real_space_refine on Wed Feb 14 08:00:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chb_16659/02_2024/8chb_16659_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chb_16659/02_2024/8chb_16659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chb_16659/02_2024/8chb_16659.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chb_16659/02_2024/8chb_16659.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chb_16659/02_2024/8chb_16659_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8chb_16659/02_2024/8chb_16659_neut.pdb" } resolution = 3.14 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= 0.018 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5716 2.51 5 N 1486 2.21 5 O 1678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 571": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 193": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 484": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 571": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4458 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Chain: "B" Number of atoms: 4458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4458 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 17, 'TRANS': 561} Time building chain proxies: 5.22, per 1000 atoms: 0.59 Number of scatterers: 8916 At special positions: 0 Unit cell: (108.07, 73.83, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1678 8.00 N 1486 7.00 C 5716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS B 582 " distance=1.94 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: 3.44 Conformation dependent library (CDL) restraints added in 2.0 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 63.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.527A pdb=" N ALA A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 44 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 109 removed outlier: 3.879A pdb=" N LYS A 109 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 120 through 140 removed outlier: 4.356A pdb=" N THR A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 164 through 210 Proline residue: A 175 - end of helix Proline residue: A 183 - end of helix Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 222 through 274 removed outlier: 3.635A pdb=" N GLY A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.746A pdb=" N GLN A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET A 295 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 322 removed outlier: 3.517A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.724A pdb=" N PHE A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.832A pdb=" N HIS A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 447 through 454 removed outlier: 4.925A pdb=" N MET A 454 " --> pdb=" O LYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 514 through 525 removed outlier: 4.066A pdb=" N VAL A 523 " --> pdb=" O GLN A 519 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET A 525 " --> pdb=" O LEU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 540 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 569 through 579 removed outlier: 4.118A pdb=" N ALA A 574 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN A 577 " --> pdb=" O PHE A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.527A pdb=" N ALA B 17 " --> pdb=" O LYS B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 64 through 109 removed outlier: 3.880A pdb=" N LYS B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 120 through 140 removed outlier: 4.356A pdb=" N THR B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N MET B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 164 through 210 Proline residue: B 175 - end of helix Proline residue: B 183 - end of helix Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 222 through 274 removed outlier: 3.635A pdb=" N GLY B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.747A pdb=" N GLN B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET B 295 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 322 removed outlier: 3.518A pdb=" N THR B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.724A pdb=" N PHE B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 436 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.832A pdb=" N HIS B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 454 removed outlier: 4.925A pdb=" N MET B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 481 through 495 Processing helix chain 'B' and resid 514 through 525 removed outlier: 4.067A pdb=" N VAL B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET B 525 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 540 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 569 through 579 removed outlier: 4.118A pdb=" N ALA B 574 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLN B 577 " --> pdb=" O PHE B 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 357 through 364 removed outlier: 6.471A pdb=" N LYS B 358 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER B 347 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL B 360 " --> pdb=" O ARG B 345 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 397 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 417 through 421 removed outlier: 6.503A pdb=" N GLY B 418 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ASP B 503 " --> pdb=" O GLY B 418 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL B 420 " --> pdb=" O ASP B 503 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B 500 " --> pdb=" O ILE B 531 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE B 533 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU B 502 " --> pdb=" O ILE B 533 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 369 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N LEU B 547 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA B 371 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL B 549 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL B 373 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 364 removed outlier: 6.470A pdb=" N LYS A 358 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 347 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N VAL A 360 " --> pdb=" O ARG A 345 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 397 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 417 through 421 removed outlier: 6.503A pdb=" N GLY A 418 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ASP A 503 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 420 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 500 " --> pdb=" O ILE A 531 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE A 533 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 502 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 369 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU A 547 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA A 371 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL A 549 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL A 373 " --> pdb=" O VAL A 549 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1584 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: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1600 1.31 - 1.44: 2077 1.44 - 1.56: 5303 1.56 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 9050 Sorted by residual: bond pdb=" CZ ARG A 228 " pdb=" NH2 ARG A 228 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.30e-02 5.92e+03 3.44e+01 bond pdb=" CZ ARG B 228 " pdb=" NH2 ARG B 228 " ideal model delta sigma weight residual 1.330 1.254 0.076 1.30e-02 5.92e+03 3.40e+01 bond pdb=" C THR A 555 " pdb=" O THR A 555 " ideal model delta sigma weight residual 1.235 1.187 0.049 9.00e-03 1.23e+04 2.93e+01 bond pdb=" C THR B 555 " pdb=" O THR B 555 " ideal model delta sigma weight residual 1.235 1.187 0.048 9.00e-03 1.23e+04 2.84e+01 bond pdb=" C ASN A 207 " pdb=" O ASN A 207 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.15e-02 7.56e+03 1.80e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.66: 260 106.66 - 114.23: 5124 114.23 - 121.81: 5243 121.81 - 129.38: 1595 129.38 - 136.96: 24 Bond angle restraints: 12246 Sorted by residual: angle pdb=" N PHE A 304 " pdb=" CA PHE A 304 " pdb=" C PHE A 304 " ideal model delta sigma weight residual 111.36 117.90 -6.54 1.09e+00 8.42e-01 3.60e+01 angle pdb=" N PHE B 304 " pdb=" CA PHE B 304 " pdb=" C PHE B 304 " ideal model delta sigma weight residual 111.36 117.89 -6.53 1.09e+00 8.42e-01 3.59e+01 angle pdb=" N ASN B 207 " pdb=" CA ASN B 207 " pdb=" C ASN B 207 " ideal model delta sigma weight residual 110.97 104.55 6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N ASN A 207 " pdb=" CA ASN A 207 " pdb=" C ASN A 207 " ideal model delta sigma weight residual 110.97 104.59 6.38 1.09e+00 8.42e-01 3.43e+01 angle pdb=" N ARG A 571 " pdb=" CA ARG A 571 " pdb=" C ARG A 571 " ideal model delta sigma weight residual 111.69 104.99 6.70 1.23e+00 6.61e-01 2.97e+01 ... (remaining 12241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4905 17.03 - 34.07: 430 34.07 - 51.10: 98 51.10 - 68.13: 36 68.13 - 85.16: 18 Dihedral angle restraints: 5487 sinusoidal: 2169 harmonic: 3318 Sorted by residual: dihedral pdb=" CA ILE A 364 " pdb=" C ILE A 364 " pdb=" N GLU A 365 " pdb=" CA GLU A 365 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA ILE B 364 " pdb=" C ILE B 364 " pdb=" N GLU B 365 " pdb=" CA GLU B 365 " ideal model delta harmonic sigma weight residual 180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLN A 342 " pdb=" C GLN A 342 " pdb=" N LEU A 343 " pdb=" CA LEU A 343 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 952 0.069 - 0.138: 358 0.138 - 0.207: 120 0.207 - 0.276: 42 0.276 - 0.346: 8 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA SER B 507 " pdb=" N SER B 507 " pdb=" C SER B 507 " pdb=" CB SER B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA SER A 507 " pdb=" N SER A 507 " pdb=" C SER A 507 " pdb=" CB SER A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB THR B 555 " pdb=" CA THR B 555 " pdb=" OG1 THR B 555 " pdb=" CG2 THR B 555 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1477 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 268 " -0.087 2.00e-02 2.50e+03 4.82e-02 4.64e+01 pdb=" CG TYR B 268 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 268 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 268 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR B 268 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR B 268 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR B 268 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 268 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 268 " 0.087 2.00e-02 2.50e+03 4.80e-02 4.61e+01 pdb=" CG TYR A 268 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 268 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 268 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 268 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR A 268 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 268 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 268 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 413 " 0.060 2.00e-02 2.50e+03 3.55e-02 3.14e+01 pdb=" CG TRP B 413 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP B 413 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 413 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP B 413 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 413 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 413 " -0.052 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 413 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 413 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 413 " 0.045 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4447 2.99 - 3.47: 9701 3.47 - 3.94: 13930 3.94 - 4.42: 15782 4.42 - 4.90: 25564 Nonbonded interactions: 69424 Sorted by model distance: nonbonded pdb=" OH TYR A 437 " pdb=" OE2 GLU B 225 " model vdw 2.512 2.440 nonbonded pdb=" OG SER A 428 " pdb=" NE2 GLN B 208 " model vdw 2.521 2.520 nonbonded pdb=" O VAL B 182 " pdb=" CA PRO B 183 " model vdw 2.533 2.776 nonbonded pdb=" O VAL A 182 " pdb=" CA PRO A 183 " model vdw 2.533 2.776 nonbonded pdb=" O GLY B 298 " pdb=" OG1 THR B 301 " model vdw 2.537 2.440 ... (remaining 69419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.760 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: 5.900 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 26.830 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.012 0.105 9050 Z= 0.799 Angle : 1.748 11.960 12246 Z= 1.185 Chirality : 0.088 0.346 1480 Planarity : 0.013 0.157 1540 Dihedral : 15.261 85.163 3352 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.64 % Allowed : 8.18 % Favored : 90.18 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.22), residues: 1154 helix: -0.72 (0.17), residues: 748 sheet: 0.40 (0.74), residues: 54 loop : -1.55 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.014 TRP B 413 HIS 0.012 0.003 HIS B 416 PHE 0.055 0.006 PHE A 286 TYR 0.087 0.012 TYR B 268 ARG 0.040 0.002 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 358 LYS cc_start: 0.7389 (ttpt) cc_final: 0.7066 (mtmm) REVERT: A 390 PHE cc_start: 0.7410 (t80) cc_final: 0.6989 (t80) REVERT: A 391 TYR cc_start: 0.7864 (m-80) cc_final: 0.7606 (m-10) REVERT: A 427 MET cc_start: 0.8154 (mmt) cc_final: 0.7682 (mmt) REVERT: B 358 LYS cc_start: 0.7436 (ttpt) cc_final: 0.7140 (mtmm) REVERT: B 390 PHE cc_start: 0.7384 (t80) cc_final: 0.7046 (t80) REVERT: B 391 TYR cc_start: 0.7907 (m-10) cc_final: 0.7648 (m-10) REVERT: B 427 MET cc_start: 0.8100 (mmt) cc_final: 0.7724 (mmt) outliers start: 16 outliers final: 6 residues processed: 143 average time/residue: 0.2588 time to fit residues: 49.5967 Evaluate side-chains 87 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 571 ARG Chi-restraints excluded: chain B residue 319 GLU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 571 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 GLN A 208 GLN A 292 GLN B 52 GLN B 66 GLN B 208 GLN B 292 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.229 Angle : 0.668 5.972 12246 Z= 0.355 Chirality : 0.043 0.181 1480 Planarity : 0.004 0.044 1540 Dihedral : 5.999 50.943 1256 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.23 % Allowed : 10.53 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1154 helix: 1.28 (0.19), residues: 746 sheet: 0.97 (0.70), residues: 54 loop : -1.15 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 164 HIS 0.004 0.002 HIS B 141 PHE 0.017 0.002 PHE A 390 TYR 0.014 0.002 TYR B 456 ARG 0.004 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7882 (tmm) cc_final: 0.7473 (tmm) REVERT: A 529 THR cc_start: 0.7663 (m) cc_final: 0.6587 (p) REVERT: B 188 MET cc_start: 0.7958 (tmm) cc_final: 0.7541 (tmm) REVERT: B 368 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6816 (ttmm) REVERT: B 529 THR cc_start: 0.7643 (m) cc_final: 0.6593 (p) outliers start: 12 outliers final: 10 residues processed: 98 average time/residue: 0.2119 time to fit residues: 29.6775 Evaluate side-chains 83 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 368 LYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 GLN B 52 GLN B 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9050 Z= 0.286 Angle : 0.623 7.397 12246 Z= 0.326 Chirality : 0.042 0.156 1480 Planarity : 0.004 0.032 1540 Dihedral : 4.896 24.233 1240 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.45 % Allowed : 12.99 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1154 helix: 1.82 (0.19), residues: 746 sheet: 1.69 (0.70), residues: 54 loop : -0.94 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 164 HIS 0.003 0.001 HIS B 141 PHE 0.024 0.002 PHE B 390 TYR 0.012 0.002 TYR B 456 ARG 0.003 0.001 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7985 (tmm) cc_final: 0.7646 (tmm) REVERT: B 188 MET cc_start: 0.7948 (tmm) cc_final: 0.7619 (tmm) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.1803 time to fit residues: 25.3899 Evaluate side-chains 84 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.206 Angle : 0.567 8.781 12246 Z= 0.292 Chirality : 0.040 0.153 1480 Planarity : 0.003 0.032 1540 Dihedral : 4.650 24.486 1240 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.64 % Allowed : 14.42 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.25), residues: 1154 helix: 2.14 (0.20), residues: 732 sheet: 1.89 (0.73), residues: 54 loop : -0.78 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 164 HIS 0.003 0.001 HIS B 141 PHE 0.014 0.001 PHE A 390 TYR 0.007 0.001 TYR B 456 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 MET cc_start: 0.7940 (tmm) cc_final: 0.7594 (tmm) outliers start: 16 outliers final: 10 residues processed: 84 average time/residue: 0.1848 time to fit residues: 22.9007 Evaluate side-chains 77 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9050 Z= 0.263 Angle : 0.600 8.218 12246 Z= 0.307 Chirality : 0.041 0.163 1480 Planarity : 0.003 0.033 1540 Dihedral : 4.623 25.276 1240 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.35 % Allowed : 15.13 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1154 helix: 2.19 (0.20), residues: 730 sheet: 1.83 (0.74), residues: 54 loop : -0.68 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 164 HIS 0.003 0.001 HIS A 561 PHE 0.014 0.001 PHE A 390 TYR 0.009 0.001 TYR A 456 ARG 0.002 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 70 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 580 MET cc_start: 0.5320 (ttt) cc_final: 0.5081 (ppp) REVERT: B 529 THR cc_start: 0.7587 (m) cc_final: 0.7135 (m) outliers start: 23 outliers final: 18 residues processed: 89 average time/residue: 0.1850 time to fit residues: 24.4771 Evaluate side-chains 83 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9050 Z= 0.200 Angle : 0.564 7.892 12246 Z= 0.289 Chirality : 0.040 0.150 1480 Planarity : 0.003 0.031 1540 Dihedral : 4.523 23.473 1240 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.56 % Allowed : 16.36 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.26), residues: 1154 helix: 2.31 (0.20), residues: 730 sheet: 2.02 (0.75), residues: 54 loop : -0.72 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 164 HIS 0.003 0.001 HIS B 141 PHE 0.012 0.001 PHE B 390 TYR 0.010 0.001 TYR A 350 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 88 average time/residue: 0.1872 time to fit residues: 24.4969 Evaluate side-chains 82 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.232 Angle : 0.578 11.008 12246 Z= 0.291 Chirality : 0.040 0.152 1480 Planarity : 0.003 0.032 1540 Dihedral : 4.498 23.193 1240 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.56 % Allowed : 17.28 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.26), residues: 1154 helix: 2.29 (0.20), residues: 734 sheet: 1.22 (0.68), residues: 72 loop : -0.96 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 164 HIS 0.003 0.001 HIS B 561 PHE 0.015 0.001 PHE B 390 TYR 0.008 0.001 TYR A 456 ARG 0.001 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 21 residues processed: 85 average time/residue: 0.1873 time to fit residues: 23.6976 Evaluate side-chains 84 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 63 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 33 optimal weight: 0.0170 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9050 Z= 0.146 Angle : 0.539 9.710 12246 Z= 0.271 Chirality : 0.038 0.155 1480 Planarity : 0.003 0.029 1540 Dihedral : 4.309 19.818 1240 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.74 % Allowed : 17.89 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.26), residues: 1154 helix: 2.61 (0.20), residues: 726 sheet: 1.14 (0.65), residues: 82 loop : -0.84 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 164 HIS 0.003 0.001 HIS A 141 PHE 0.009 0.001 PHE B 390 TYR 0.006 0.001 TYR A 90 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: B 222 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7103 (mm-30) outliers start: 17 outliers final: 10 residues processed: 83 average time/residue: 0.1928 time to fit residues: 23.5887 Evaluate side-chains 76 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.0770 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9050 Z= 0.186 Angle : 0.553 9.050 12246 Z= 0.276 Chirality : 0.039 0.154 1480 Planarity : 0.003 0.028 1540 Dihedral : 4.262 19.197 1240 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.25 % Allowed : 17.48 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.26), residues: 1154 helix: 2.59 (0.20), residues: 730 sheet: 0.59 (0.76), residues: 62 loop : -0.73 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 164 HIS 0.002 0.001 HIS B 561 PHE 0.027 0.001 PHE B 390 TYR 0.007 0.001 TYR B 456 ARG 0.001 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: B 222 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7140 (mm-30) outliers start: 22 outliers final: 15 residues processed: 83 average time/residue: 0.1950 time to fit residues: 23.9056 Evaluate side-chains 84 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 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 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9050 Z= 0.206 Angle : 0.575 11.928 12246 Z= 0.285 Chirality : 0.039 0.154 1480 Planarity : 0.003 0.029 1540 Dihedral : 4.259 18.318 1239 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.94 % Allowed : 17.69 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.26), residues: 1154 helix: 2.56 (0.20), residues: 736 sheet: 0.74 (0.81), residues: 44 loop : -0.63 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 164 HIS 0.003 0.001 HIS A 567 PHE 0.024 0.001 PHE A 468 TYR 0.007 0.001 TYR A 456 ARG 0.001 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 67 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 222 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: B 222 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7145 (mm-30) outliers start: 19 outliers final: 16 residues processed: 83 average time/residue: 0.1933 time to fit residues: 23.7482 Evaluate side-chains 85 residues out of total 978 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 67 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 567 HIS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 ASN ** 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 = 0.4239 r_free = 0.4239 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.127470 restraints weight = 13429.448| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.46 r_work: 0.3570 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9050 Z= 0.196 Angle : 0.565 11.616 12246 Z= 0.280 Chirality : 0.039 0.154 1480 Planarity : 0.003 0.030 1540 Dihedral : 4.198 18.564 1238 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.35 % Allowed : 17.59 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.26), residues: 1154 helix: 2.60 (0.19), residues: 734 sheet: 0.39 (0.76), residues: 44 loop : -0.60 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 164 HIS 0.003 0.001 HIS A 567 PHE 0.024 0.001 PHE A 468 TYR 0.006 0.001 TYR B 350 ARG 0.001 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1857.86 seconds wall clock time: 34 minutes 42.26 seconds (2082.26 seconds total)