Starting phenix.real_space_refine on Fri Mar 15 15:01:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlu_7957/03_2024/6dlu_7957_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlu_7957/03_2024/6dlu_7957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlu_7957/03_2024/6dlu_7957.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlu_7957/03_2024/6dlu_7957.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlu_7957/03_2024/6dlu_7957_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dlu_7957/03_2024/6dlu_7957_neut_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 66 5.16 5 C 7512 2.51 5 N 2105 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 601": "NH1" <-> "NH2" Residue "P ARG 59": "NH1" <-> "NH2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P ARG 266": "NH1" <-> "NH2" Residue "P ARG 318": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 361": "NH1" <-> "NH2" Residue "P ARG 364": "NH1" <-> "NH2" Residue "P ARG 399": "NH1" <-> "NH2" Residue "P ARG 594": "NH1" <-> "NH2" Residue "P ARG 601": "NH1" <-> "NH2" Residue "P ARG 663": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11991 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5918 Classifications: {'peptide': 734} Link IDs: {'CIS': 13, 'PTRANS': 26, 'TRANS': 694} Chain breaks: 1 Chain: "P" Number of atoms: 6007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6007 Classifications: {'peptide': 747} Link IDs: {'CIS': 12, 'PTRANS': 26, 'TRANS': 708} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.49, per 1000 atoms: 0.54 Number of scatterers: 11991 At special positions: 0 Unit cell: (216.14, 199.02, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 6 15.00 Mg 2 11.99 O 2300 8.00 N 2105 7.00 C 7512 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.12 Conformation dependent library (CDL) restraints added in 2.2 seconds 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 7 sheets defined 46.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'B' and resid 9 through 18 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 94 through 108 Processing helix chain 'B' and resid 152 through 164 removed outlier: 3.992A pdb=" N PHE B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 217 through 220 No H-bonds generated for 'chain 'B' and resid 217 through 220' Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 293 through 308 removed outlier: 3.710A pdb=" N LEU B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 344 Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.873A pdb=" N PHE B 366 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 407 through 416 Processing helix chain 'B' and resid 418 through 441 removed outlier: 3.745A pdb=" N ARG B 421 " --> pdb=" O LYS B 418 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 422 " --> pdb=" O LYS B 419 " (cutoff:3.500A) Proline residue: B 423 - end of helix removed outlier: 3.642A pdb=" N GLU B 434 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE B 436 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 437 " --> pdb=" O GLU B 434 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL B 439 " --> pdb=" O ILE B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 483 removed outlier: 3.894A pdb=" N GLY B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 470 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 4.688A pdb=" N LYS B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 623 removed outlier: 3.733A pdb=" N ASP B 614 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 656 through 688 Proline residue: B 682 - end of helix removed outlier: 3.714A pdb=" N LEU B 688 " --> pdb=" O THR B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.820A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 747 Processing helix chain 'P' and resid 5 through 22 Proline residue: P 11 - end of helix Processing helix chain 'P' and resid 44 through 52 Processing helix chain 'P' and resid 94 through 108 Processing helix chain 'P' and resid 152 through 164 removed outlier: 4.194A pdb=" N PHE P 163 " --> pdb=" O MET P 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 183 No H-bonds generated for 'chain 'P' and resid 181 through 183' Processing helix chain 'P' and resid 185 through 193 Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 217 through 220 No H-bonds generated for 'chain 'P' and resid 217 through 220' Processing helix chain 'P' and resid 239 through 244 Processing helix chain 'P' and resid 248 through 261 Processing helix chain 'P' and resid 274 through 314 Proline residue: P 294 - end of helix removed outlier: 3.798A pdb=" N SER P 306 " --> pdb=" O SER P 302 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE P 307 " --> pdb=" O GLN P 303 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS P 309 " --> pdb=" O LEU P 305 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU P 310 " --> pdb=" O SER P 306 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU P 313 " --> pdb=" O LYS P 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR P 314 " --> pdb=" O GLU P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 322 through 344 Processing helix chain 'P' and resid 360 through 369 removed outlier: 3.815A pdb=" N GLU P 368 " --> pdb=" O ARG P 364 " (cutoff:3.500A) Processing helix chain 'P' and resid 372 through 375 No H-bonds generated for 'chain 'P' and resid 372 through 375' Processing helix chain 'P' and resid 384 through 395 Processing helix chain 'P' and resid 407 through 446 removed outlier: 3.555A pdb=" N LYS P 418 " --> pdb=" O LYS P 414 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS P 419 " --> pdb=" O LYS P 415 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE P 420 " --> pdb=" O GLN P 416 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG P 421 " --> pdb=" O VAL P 417 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU P 422 " --> pdb=" O LYS P 418 " (cutoff:3.500A) Proline residue: P 423 - end of helix removed outlier: 3.536A pdb=" N SER P 437 " --> pdb=" O SER P 433 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG P 440 " --> pdb=" O ILE P 436 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR P 443 " --> pdb=" O VAL P 439 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS P 444 " --> pdb=" O ARG P 440 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS P 445 " --> pdb=" O GLN P 441 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU P 446 " --> pdb=" O CYS P 442 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 483 removed outlier: 4.300A pdb=" N GLY P 469 " --> pdb=" O ARG P 465 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG P 470 " --> pdb=" O GLU P 466 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU P 482 " --> pdb=" O LEU P 478 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU P 483 " --> pdb=" O ILE P 479 " (cutoff:3.500A) Processing helix chain 'P' and resid 503 through 507 Processing helix chain 'P' and resid 512 through 515 No H-bonds generated for 'chain 'P' and resid 512 through 515' Processing helix chain 'P' and resid 610 through 623 Processing helix chain 'P' and resid 655 through 688 Proline residue: P 682 - end of helix Processing helix chain 'P' and resid 691 through 698 Processing helix chain 'P' and resid 701 through 707 Processing helix chain 'P' and resid 711 through 714 No H-bonds generated for 'chain 'P' and resid 711 through 714' Processing helix chain 'P' and resid 719 through 746 Processing sheet with id= A, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.653A pdb=" N ILE B 34 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 73 through 75 removed outlier: 7.861A pdb=" N VAL B 74 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 124 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 522 through 528 removed outlier: 3.825A pdb=" N LYS B 539 " --> pdb=" O ILE B 528 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 584 through 588 removed outlier: 4.536A pdb=" N LEU B 603 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'P' and resid 80 through 83 removed outlier: 6.586A pdb=" N ILE P 34 " --> pdb=" O VAL P 135 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL P 174 " --> pdb=" O VAL P 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'P' and resid 522 through 528 removed outlier: 3.700A pdb=" N LYS P 539 " --> pdb=" O ILE P 528 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'P' and resid 585 through 587 507 hydrogen bonds defined for protein. 1461 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: 3.53 Time building geometry restraints manager: 4.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2082 1.28 - 1.42: 2843 1.42 - 1.56: 7123 1.56 - 1.70: 10 1.70 - 1.84: 122 Bond restraints: 12180 Sorted by residual: bond pdb=" C3' GCP B 801 " pdb=" C4' GCP B 801 " ideal model delta sigma weight residual 1.526 1.292 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C3' GCP P 801 " pdb=" C4' GCP P 801 " ideal model delta sigma weight residual 1.526 1.293 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C4' GCP P 801 " pdb=" O4' GCP P 801 " ideal model delta sigma weight residual 1.429 1.620 -0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C4' GCP B 801 " pdb=" O4' GCP B 801 " ideal model delta sigma weight residual 1.429 1.619 -0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" C3' GCP P 801 " pdb=" O3' GCP P 801 " ideal model delta sigma weight residual 1.401 1.562 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 12175 not shown) Histogram of bond angle deviations from ideal: 96.35 - 103.88: 165 103.88 - 111.41: 5196 111.41 - 118.94: 4816 118.94 - 126.47: 6114 126.47 - 134.00: 125 Bond angle restraints: 16416 Sorted by residual: angle pdb=" C SER B 582 " pdb=" N LYS B 583 " pdb=" CA LYS B 583 " ideal model delta sigma weight residual 121.70 133.09 -11.39 1.80e+00 3.09e-01 4.00e+01 angle pdb=" C SER P 582 " pdb=" N LYS P 583 " pdb=" CA LYS P 583 " ideal model delta sigma weight residual 121.70 132.97 -11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" C GLU P 717 " pdb=" N SER P 718 " pdb=" CA SER P 718 " ideal model delta sigma weight residual 121.70 131.71 -10.01 1.80e+00 3.09e-01 3.09e+01 angle pdb=" C GLU B 717 " pdb=" N SER B 718 " pdb=" CA SER B 718 " ideal model delta sigma weight residual 121.70 131.04 -9.34 1.80e+00 3.09e-01 2.69e+01 angle pdb=" C PHE B 317 " pdb=" N ARG B 318 " pdb=" CA ARG B 318 " ideal model delta sigma weight residual 121.70 130.04 -8.34 1.80e+00 3.09e-01 2.15e+01 ... (remaining 16411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 7170 16.47 - 32.94: 311 32.94 - 49.42: 70 49.42 - 65.89: 22 65.89 - 82.36: 13 Dihedral angle restraints: 7586 sinusoidal: 3266 harmonic: 4320 Sorted by residual: dihedral pdb=" CA ARG P 364 " pdb=" C ARG P 364 " pdb=" N ILE P 365 " pdb=" CA ILE P 365 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLU B 368 " pdb=" C GLU B 368 " pdb=" N ARG B 369 " pdb=" CA ARG B 369 " ideal model delta harmonic sigma weight residual 180.00 158.99 21.01 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ARG B 290 " pdb=" C ARG B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 7583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1082 0.038 - 0.077: 539 0.077 - 0.115: 167 0.115 - 0.153: 38 0.153 - 0.191: 4 Chirality restraints: 1830 Sorted by residual: chirality pdb=" C2' GCP B 801 " pdb=" C1' GCP B 801 " pdb=" C3' GCP B 801 " pdb=" O2' GCP B 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" C2' GCP P 801 " pdb=" C1' GCP P 801 " pdb=" C3' GCP P 801 " pdb=" O2' GCP P 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA VAL B 544 " pdb=" N VAL B 544 " pdb=" C VAL B 544 " pdb=" CB VAL B 544 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1827 not shown) Planarity restraints: 2135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 432 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE B 432 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 432 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 433 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 330 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.66e+00 pdb=" C LEU P 330 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU P 330 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN P 331 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 430 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C MET B 430 " -0.032 2.00e-02 2.50e+03 pdb=" O MET B 430 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL B 431 " 0.011 2.00e-02 2.50e+03 ... (remaining 2132 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 63 2.54 - 3.13: 9613 3.13 - 3.72: 17729 3.72 - 4.31: 24069 4.31 - 4.90: 39494 Nonbonded interactions: 90968 Sorted by model distance: nonbonded pdb=" O1B GCP B 801 " pdb="MG MG B 802 " model vdw 1.944 2.170 nonbonded pdb=" OG1 THR B 65 " pdb="MG MG B 802 " model vdw 1.963 2.170 nonbonded pdb=" OG1 THR P 65 " pdb="MG MG P 802 " model vdw 2.002 2.170 nonbonded pdb=" OE2 GLU B 104 " pdb=" NH2 ARG B 107 " model vdw 2.025 2.520 nonbonded pdb=" O2G GCP B 801 " pdb="MG MG B 802 " model vdw 2.035 2.170 ... (remaining 90963 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 'B' and (resid 7 through 747 or resid 801 through 802)) selection = (chain 'P' and (resid 7 through 20 or resid 29 through 747 or resid 801 through \ 802)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.770 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: 0.020 Extract box with map and model: 35.910 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.210 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 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 : 0.009 0.234 12180 Z= 0.589 Angle : 0.945 14.147 16416 Z= 0.488 Chirality : 0.048 0.191 1830 Planarity : 0.004 0.031 2135 Dihedral : 11.137 82.361 4782 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.23 % Allowed : 3.10 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -2.78 (0.19), residues: 1475 helix: -0.90 (0.18), residues: 695 sheet: -1.67 (0.34), residues: 184 loop : -3.02 (0.19), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 616 HIS 0.009 0.002 HIS P 396 PHE 0.022 0.002 PHE B 366 TYR 0.022 0.002 TYR B 669 ARG 0.009 0.001 ARG B 724 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 361 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6722 (tpp-160) REVERT: B 434 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 480 ASP cc_start: 0.8008 (m-30) cc_final: 0.7681 (m-30) REVERT: B 648 MET cc_start: 0.4195 (mpp) cc_final: 0.3877 (mpp) REVERT: B 681 MET cc_start: 0.7568 (ppp) cc_final: 0.7262 (tmm) REVERT: P 1 MET cc_start: 0.7218 (mtt) cc_final: 0.7014 (mtp) REVERT: P 181 LEU cc_start: 0.8820 (tp) cc_final: 0.8592 (tt) REVERT: P 297 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7642 (ttm-80) REVERT: P 356 LEU cc_start: 0.7181 (tt) cc_final: 0.6587 (mt) REVERT: P 376 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7659 (ttpp) REVERT: P 489 ASN cc_start: 0.7964 (t0) cc_final: 0.7252 (p0) REVERT: P 506 MET cc_start: -0.0395 (tpt) cc_final: -0.0913 (tpp) outliers start: 3 outliers final: 0 residues processed: 229 average time/residue: 0.2719 time to fit residues: 86.6626 Evaluate side-chains 124 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 8.9990 chunk 111 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 59 optimal weight: 30.0000 chunk 115 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 133 optimal weight: 30.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 ASN B 284 GLN B 288 HIS ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 HIS P 50 ASN P 155 GLN ** P 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 530 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12180 Z= 0.205 Angle : 0.639 12.054 16416 Z= 0.331 Chirality : 0.042 0.201 1830 Planarity : 0.003 0.033 2135 Dihedral : 7.011 84.076 1679 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.81 % Allowed : 7.48 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -1.54 (0.21), residues: 1475 helix: 0.26 (0.19), residues: 699 sheet: -1.27 (0.36), residues: 182 loop : -2.53 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 616 HIS 0.008 0.001 HIS P 367 PHE 0.017 0.001 PHE P 83 TYR 0.016 0.001 TYR P 314 ARG 0.008 0.000 ARG B 657 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: B 434 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7904 (tm-30) REVERT: B 648 MET cc_start: 0.4180 (mpp) cc_final: 0.3730 (mpp) REVERT: B 681 MET cc_start: 0.7666 (ppp) cc_final: 0.7431 (tmm) REVERT: P 297 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7742 (ttm-80) REVERT: P 361 ARG cc_start: 0.5398 (ttt90) cc_final: 0.4424 (ttt90) REVERT: P 376 LYS cc_start: 0.7740 (ttpt) cc_final: 0.7528 (ttpp) REVERT: P 506 MET cc_start: -0.0395 (tpt) cc_final: -0.0843 (tpp) REVERT: P 670 MET cc_start: 0.8303 (mmm) cc_final: 0.7995 (mmt) outliers start: 24 outliers final: 13 residues processed: 153 average time/residue: 0.2660 time to fit residues: 57.2088 Evaluate side-chains 114 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 305 LEU Chi-restraints excluded: chain P residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 ASN P 50 ASN P 367 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12180 Z= 0.296 Angle : 0.693 11.174 16416 Z= 0.361 Chirality : 0.044 0.169 1830 Planarity : 0.004 0.029 2135 Dihedral : 6.160 73.407 1679 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.02 % Allowed : 9.37 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -1.15 (0.21), residues: 1475 helix: 0.51 (0.20), residues: 698 sheet: -1.07 (0.38), residues: 182 loop : -2.23 (0.22), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 616 HIS 0.010 0.002 HIS P 396 PHE 0.018 0.002 PHE B 409 TYR 0.017 0.002 TYR P 354 ARG 0.007 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 1.308 Fit side-chains REVERT: B 434 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7844 (tm-30) REVERT: B 486 MET cc_start: 0.7539 (tmm) cc_final: 0.7223 (tmm) REVERT: B 648 MET cc_start: 0.4453 (mpp) cc_final: 0.3988 (mpp) REVERT: B 681 MET cc_start: 0.7650 (ppp) cc_final: 0.7345 (tmm) REVERT: P 304 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7663 (tt) REVERT: P 361 ARG cc_start: 0.5478 (ttt90) cc_final: 0.3968 (ttt90) outliers start: 40 outliers final: 18 residues processed: 135 average time/residue: 0.2488 time to fit residues: 48.7247 Evaluate side-chains 109 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 708 CYS Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 304 LEU Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 459 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 132 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 127 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12180 Z= 0.231 Angle : 0.610 11.277 16416 Z= 0.317 Chirality : 0.041 0.140 1830 Planarity : 0.003 0.028 2135 Dihedral : 6.012 82.266 1679 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.64 % Allowed : 11.40 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 0.87 (0.20), residues: 700 sheet: -1.08 (0.38), residues: 180 loop : -2.07 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 616 HIS 0.004 0.001 HIS P 396 PHE 0.012 0.001 PHE B 409 TYR 0.011 0.001 TYR P 314 ARG 0.005 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.284 Fit side-chains REVERT: B 361 ARG cc_start: 0.7633 (tpt-90) cc_final: 0.6914 (tpt-90) REVERT: B 434 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7945 (tm-30) REVERT: B 486 MET cc_start: 0.7453 (tmm) cc_final: 0.7206 (tmm) REVERT: B 648 MET cc_start: 0.4679 (mpp) cc_final: 0.4209 (mpp) REVERT: B 657 ARG cc_start: 0.6943 (ptt-90) cc_final: 0.6741 (ptp90) REVERT: P 361 ARG cc_start: 0.5692 (ttt90) cc_final: 0.3896 (ttt90) REVERT: P 476 MET cc_start: 0.7688 (tpt) cc_final: 0.7483 (tpp) REVERT: P 564 MET cc_start: 0.4128 (tmm) cc_final: 0.3319 (tpp) REVERT: P 670 MET cc_start: 0.8766 (mmm) cc_final: 0.8533 (mmt) REVERT: P 715 MET cc_start: 0.8835 (mtp) cc_final: 0.8597 (mtp) outliers start: 35 outliers final: 20 residues processed: 124 average time/residue: 0.2582 time to fit residues: 45.6907 Evaluate side-chains 109 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 305 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 494 ILE Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 697 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 118 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 127 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 ASN ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12180 Z= 0.267 Angle : 0.625 11.308 16416 Z= 0.324 Chirality : 0.042 0.142 1830 Planarity : 0.003 0.032 2135 Dihedral : 6.059 81.652 1679 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 2.34 % Allowed : 12.92 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -0.65 (0.22), residues: 1475 helix: 0.99 (0.20), residues: 698 sheet: -1.00 (0.38), residues: 181 loop : -2.01 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 616 HIS 0.007 0.001 HIS P 396 PHE 0.013 0.001 PHE B 409 TYR 0.011 0.002 TYR B 125 ARG 0.006 0.000 ARG P 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 1.381 Fit side-chains REVERT: B 361 ARG cc_start: 0.7655 (tpt-90) cc_final: 0.6901 (tpt-90) REVERT: B 434 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 486 MET cc_start: 0.7626 (tmm) cc_final: 0.7355 (tmm) REVERT: B 648 MET cc_start: 0.4553 (mpp) cc_final: 0.4075 (mpp) REVERT: B 679 ASP cc_start: 0.7860 (t0) cc_final: 0.7653 (t0) REVERT: P 6 MET cc_start: 0.8543 (tpp) cc_final: 0.8303 (tpp) REVERT: P 272 MET cc_start: 0.9060 (mmt) cc_final: 0.8654 (mmt) REVERT: P 399 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.5173 (tpp-160) REVERT: P 564 MET cc_start: 0.4371 (tmm) cc_final: 0.3508 (tpp) outliers start: 31 outliers final: 20 residues processed: 116 average time/residue: 0.2421 time to fit residues: 42.0486 Evaluate side-chains 109 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 713 THR Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 417 VAL Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 697 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 47 optimal weight: 0.0060 chunk 127 optimal weight: 30.0000 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 288 HIS ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12180 Z= 0.153 Angle : 0.560 11.313 16416 Z= 0.291 Chirality : 0.039 0.142 1830 Planarity : 0.003 0.030 2135 Dihedral : 5.711 82.306 1679 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.44 % Allowed : 13.90 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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 (0.22), residues: 1475 helix: 1.28 (0.21), residues: 703 sheet: -0.99 (0.38), residues: 180 loop : -1.87 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.003 0.000 HIS P 288 PHE 0.010 0.001 PHE B 409 TYR 0.008 0.001 TYR B 80 ARG 0.007 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.424 Fit side-chains REVERT: B 161 MET cc_start: 0.8503 (tpp) cc_final: 0.8031 (tpp) REVERT: B 361 ARG cc_start: 0.7622 (tpt-90) cc_final: 0.6900 (tpt-90) REVERT: B 434 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7644 (tp30) REVERT: B 521 ILE cc_start: -0.2219 (OUTLIER) cc_final: -0.2427 (mt) REVERT: B 648 MET cc_start: 0.4546 (mpp) cc_final: 0.4029 (mpp) REVERT: B 679 ASP cc_start: 0.7801 (t0) cc_final: 0.7577 (t0) REVERT: P 6 MET cc_start: 0.8588 (tpp) cc_final: 0.8337 (tpp) REVERT: P 364 ARG cc_start: 0.6755 (ptm160) cc_final: 0.4973 (mtt90) REVERT: P 564 MET cc_start: 0.4105 (tmm) cc_final: 0.3330 (tpp) REVERT: P 689 MET cc_start: 0.8630 (tpp) cc_final: 0.8045 (tpp) outliers start: 19 outliers final: 12 residues processed: 111 average time/residue: 0.2613 time to fit residues: 41.9549 Evaluate side-chains 102 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 29 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 697 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 16 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 chunk 141 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12180 Z= 0.147 Angle : 0.561 11.323 16416 Z= 0.288 Chirality : 0.039 0.144 1830 Planarity : 0.003 0.030 2135 Dihedral : 5.593 82.990 1679 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.44 % Allowed : 14.27 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1475 helix: 1.49 (0.21), residues: 703 sheet: -0.90 (0.39), residues: 180 loop : -1.76 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.003 0.000 HIS P 396 PHE 0.008 0.001 PHE B 94 TYR 0.010 0.001 TYR P 669 ARG 0.007 0.000 ARG P 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: B 161 MET cc_start: 0.8521 (tpp) cc_final: 0.8086 (tpp) REVERT: B 365 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8330 (tt) REVERT: B 434 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7661 (tp30) REVERT: B 521 ILE cc_start: -0.2147 (OUTLIER) cc_final: -0.2365 (mt) REVERT: B 648 MET cc_start: 0.4435 (mpp) cc_final: 0.3913 (mpp) REVERT: B 679 ASP cc_start: 0.7732 (t0) cc_final: 0.7465 (t0) REVERT: P 6 MET cc_start: 0.8666 (tpp) cc_final: 0.8424 (tpp) REVERT: P 364 ARG cc_start: 0.6486 (ptm160) cc_final: 0.4968 (mtt90) REVERT: P 564 MET cc_start: 0.4316 (tmm) cc_final: 0.3408 (tpp) REVERT: P 689 MET cc_start: 0.8614 (tpp) cc_final: 0.8086 (tpp) outliers start: 19 outliers final: 13 residues processed: 109 average time/residue: 0.2470 time to fit residues: 39.5125 Evaluate side-chains 107 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 436 ILE Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 697 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 584 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12180 Z= 0.214 Angle : 0.589 11.331 16416 Z= 0.304 Chirality : 0.041 0.145 1830 Planarity : 0.003 0.032 2135 Dihedral : 5.703 82.444 1679 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.11 % Allowed : 13.97 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -0.10 (0.22), residues: 1475 helix: 1.46 (0.20), residues: 704 sheet: -0.84 (0.39), residues: 178 loop : -1.73 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 616 HIS 0.005 0.001 HIS P 396 PHE 0.009 0.001 PHE P 647 TYR 0.011 0.001 TYR P 669 ARG 0.007 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.396 Fit side-chains revert: symmetry clash REVERT: B 161 MET cc_start: 0.8592 (tpp) cc_final: 0.8123 (tpp) REVERT: B 365 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 434 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7730 (tp30) REVERT: B 521 ILE cc_start: -0.2066 (OUTLIER) cc_final: -0.2285 (mt) REVERT: B 648 MET cc_start: 0.4624 (mpp) cc_final: 0.4068 (mpp) REVERT: B 679 ASP cc_start: 0.7672 (t0) cc_final: 0.7401 (t0) REVERT: B 689 MET cc_start: 0.8224 (tpp) cc_final: 0.7896 (ttt) REVERT: P 6 MET cc_start: 0.8704 (tpp) cc_final: 0.8457 (tpp) REVERT: P 364 ARG cc_start: 0.6608 (ptm160) cc_final: 0.5207 (mtt90) REVERT: P 476 MET cc_start: 0.7746 (tpt) cc_final: 0.7475 (tpp) REVERT: P 564 MET cc_start: 0.4306 (tmm) cc_final: 0.3391 (tpp) REVERT: P 689 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7693 (ttm) outliers start: 28 outliers final: 17 residues processed: 110 average time/residue: 0.2472 time to fit residues: 40.8059 Evaluate side-chains 109 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 670 MET Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 689 MET Chi-restraints excluded: chain P residue 697 ILE Chi-restraints excluded: chain P residue 715 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 135 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 30.0000 chunk 103 optimal weight: 7.9990 chunk 40 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 85 HIS ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12180 Z= 0.146 Angle : 0.567 11.334 16416 Z= 0.291 Chirality : 0.040 0.147 1830 Planarity : 0.003 0.031 2135 Dihedral : 5.493 82.344 1679 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.51 % Allowed : 14.12 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1475 helix: 1.61 (0.21), residues: 704 sheet: -0.80 (0.39), residues: 178 loop : -1.67 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.003 0.000 HIS P 396 PHE 0.008 0.001 PHE B 94 TYR 0.009 0.001 TYR P 669 ARG 0.006 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.527 Fit side-chains revert: symmetry clash REVERT: B 161 MET cc_start: 0.8507 (tpp) cc_final: 0.8221 (tpp) REVERT: B 365 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8368 (tt) REVERT: B 434 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7591 (tp30) REVERT: B 521 ILE cc_start: -0.2275 (OUTLIER) cc_final: -0.2506 (mt) REVERT: B 648 MET cc_start: 0.4673 (mpp) cc_final: 0.4142 (mpp) REVERT: B 679 ASP cc_start: 0.7684 (t0) cc_final: 0.7406 (t0) REVERT: B 689 MET cc_start: 0.8175 (tpp) cc_final: 0.7951 (ttm) REVERT: P 6 MET cc_start: 0.8750 (tpp) cc_final: 0.8550 (tpp) REVERT: P 364 ARG cc_start: 0.6332 (ptm160) cc_final: 0.4895 (mtt90) REVERT: P 476 MET cc_start: 0.7710 (tpt) cc_final: 0.7433 (tpp) REVERT: P 564 MET cc_start: 0.4184 (tmm) cc_final: 0.3487 (tpp) REVERT: P 648 MET cc_start: 0.0222 (mtp) cc_final: 0.0000 (mtt) REVERT: P 689 MET cc_start: 0.8466 (tpp) cc_final: 0.7632 (ttt) outliers start: 20 outliers final: 12 residues processed: 111 average time/residue: 0.2502 time to fit residues: 41.2861 Evaluate side-chains 105 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 494 ILE Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 697 ILE Chi-restraints excluded: chain P residue 715 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 139 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12180 Z= 0.304 Angle : 0.666 11.371 16416 Z= 0.340 Chirality : 0.043 0.153 1830 Planarity : 0.003 0.034 2135 Dihedral : 5.896 83.416 1679 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.51 % Allowed : 14.43 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % 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: -0.15 (0.22), residues: 1475 helix: 1.39 (0.20), residues: 703 sheet: -0.78 (0.39), residues: 181 loop : -1.74 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 616 HIS 0.007 0.001 HIS P 396 PHE 0.009 0.001 PHE P 51 TYR 0.019 0.002 TYR B 125 ARG 0.006 0.000 ARG B 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2950 Ramachandran restraints generated. 1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: B 161 MET cc_start: 0.8748 (tpp) cc_final: 0.8259 (tpp) REVERT: B 365 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 434 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7830 (tp30) REVERT: B 679 ASP cc_start: 0.7768 (t0) cc_final: 0.7469 (t0) REVERT: B 689 MET cc_start: 0.8437 (tpp) cc_final: 0.7934 (ttt) REVERT: P 6 MET cc_start: 0.8772 (tpp) cc_final: 0.8497 (tpp) REVERT: P 399 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.5196 (tpp-160) REVERT: P 476 MET cc_start: 0.7841 (tpt) cc_final: 0.7585 (tpp) REVERT: P 564 MET cc_start: 0.4192 (tmm) cc_final: 0.3397 (tpp) REVERT: P 689 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7752 (ttm) outliers start: 20 outliers final: 15 residues processed: 97 average time/residue: 0.2650 time to fit residues: 37.7429 Evaluate side-chains 97 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 728 MET Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 140 MET Chi-restraints excluded: chain P residue 260 LEU Chi-restraints excluded: chain P residue 399 ARG Chi-restraints excluded: chain P residue 434 GLU Chi-restraints excluded: chain P residue 494 ILE Chi-restraints excluded: chain P residue 603 LEU Chi-restraints excluded: chain P residue 689 MET Chi-restraints excluded: chain P residue 697 ILE Chi-restraints excluded: chain P residue 715 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 chunk 102 optimal weight: 8.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 549 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 = 0.3958 r_free = 0.3958 target = 0.136998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103970 restraints weight = 27377.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101708 restraints weight = 18897.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103299 restraints weight = 15708.191| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12180 Z= 0.173 Angle : 0.597 11.349 16416 Z= 0.304 Chirality : 0.040 0.155 1830 Planarity : 0.003 0.030 2135 Dihedral : 5.624 83.343 1679 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.36 % Allowed : 14.50 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1475 helix: 1.54 (0.20), residues: 703 sheet: -0.85 (0.40), residues: 175 loop : -1.64 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 542 HIS 0.004 0.001 HIS P 396 PHE 0.008 0.001 PHE P 647 TYR 0.012 0.001 TYR P 669 ARG 0.006 0.000 ARG B 440 =============================================================================== Job complete usr+sys time: 2809.90 seconds wall clock time: 51 minutes 53.89 seconds (3113.89 seconds total)