Starting phenix.real_space_refine on Sun Mar 10 21:31:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/03_2024/7lq6_23482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/03_2024/7lq6_23482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/03_2024/7lq6_23482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/03_2024/7lq6_23482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/03_2024/7lq6_23482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lq6_23482/03_2024/7lq6_23482.pdb" } resolution = 3.28 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= 0.009 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 25 5.16 5 C 3332 2.51 5 N 932 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ASP 387": "OD1" <-> "OD2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ASP 443": "OD1" <-> "OD2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ASP 647": "OD1" <-> "OD2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 714": "OD1" <-> "OD2" Residue "A GLU 761": "OE1" <-> "OE2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 789": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5267 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5267 Classifications: {'peptide': 672} Link IDs: {'PTRANS': 39, 'TRANS': 632} Chain breaks: 5 Time building chain proxies: 3.62, per 1000 atoms: 0.69 Number of scatterers: 5267 At special positions: 0 Unit cell: (65.832, 86.932, 127.444, 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 25 16.00 O 978 8.00 N 932 7.00 C 3332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 993.3 milliseconds 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1250 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 41.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.598A pdb=" N LYS A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.857A pdb=" N VAL A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.513A pdb=" N VAL A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.614A pdb=" N ALA A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 removed outlier: 4.020A pdb=" N LEU A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.599A pdb=" N LEU A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.656A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 3.519A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.583A pdb=" N ALA A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 397 " --> pdb=" O MET A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.083A pdb=" N LEU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 4.003A pdb=" N LYS A 431 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 433 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 466 removed outlier: 3.619A pdb=" N GLU A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Proline residue: A 459 - end of helix removed outlier: 4.003A pdb=" N GLN A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.911A pdb=" N LYS A 513 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 565 through 571 removed outlier: 4.094A pdb=" N LEU A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.796A pdb=" N THR A 577 " --> pdb=" O MET A 573 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 removed outlier: 4.012A pdb=" N GLU A 591 " --> pdb=" O PRO A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 617 through 630 removed outlier: 3.951A pdb=" N GLN A 623 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.619A pdb=" N LEU A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 671 " --> pdb=" O ALA A 667 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 675 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 678 " --> pdb=" O MET A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 688 removed outlier: 3.910A pdb=" N GLY A 687 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 738 through 747 removed outlier: 3.533A pdb=" N ARG A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 removed outlier: 3.974A pdb=" N GLN A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 798 " --> pdb=" O CYS A 794 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 201 through 205 removed outlier: 3.594A pdb=" N THR A 203 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA A 105 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR A 440 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR A 107 " --> pdb=" O THR A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.144A pdb=" N ARG A 134 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL A 147 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 144 " --> pdb=" O ILE A 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 169 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A 174 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 319 removed outlier: 3.543A pdb=" N GLY A 317 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 488 removed outlier: 6.555A pdb=" N VAL A 476 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET A 487 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE A 474 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 507 removed outlier: 3.542A pdb=" N ARG A 506 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AA9, first strand: chain 'A' and resid 633 through 634 Processing sheet with id=AB1, first strand: chain 'A' and resid 763 through 768 removed outlier: 3.597A pdb=" N ARG A 781 " --> pdb=" O VAL A 768 " (cutoff:3.500A) 188 hydrogen bonds defined for protein. 513 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: 1.60 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1677 1.33 - 1.45: 653 1.45 - 1.57: 2988 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5366 Sorted by residual: bond pdb=" N ARG A 337 " pdb=" CA ARG A 337 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.30e-02 5.92e+03 6.94e+00 bond pdb=" N THR A 232 " pdb=" CA THR A 232 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.22e-02 6.72e+03 6.80e+00 bond pdb=" N ASP A 234 " pdb=" CA ASP A 234 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" N GLU A 233 " pdb=" CA GLU A 233 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.08e+00 bond pdb=" N ARG A 235 " pdb=" CA ARG A 235 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 ... (remaining 5361 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.11: 162 106.11 - 113.09: 2876 113.09 - 120.07: 1854 120.07 - 127.05: 2322 127.05 - 134.03: 59 Bond angle restraints: 7273 Sorted by residual: angle pdb=" O LEU A 229 " pdb=" C LEU A 229 " pdb=" N LEU A 230 " ideal model delta sigma weight residual 122.36 131.80 -9.44 1.42e+00 4.96e-01 4.42e+01 angle pdb=" CA LEU A 229 " pdb=" C LEU A 229 " pdb=" N LEU A 230 " ideal model delta sigma weight residual 117.96 109.72 8.24 1.51e+00 4.39e-01 2.98e+01 angle pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" C ARG A 364 " ideal model delta sigma weight residual 112.12 105.10 7.02 1.34e+00 5.57e-01 2.74e+01 angle pdb=" N LYS A 367 " pdb=" CA LYS A 367 " pdb=" C LYS A 367 " ideal model delta sigma weight residual 114.56 107.99 6.57 1.27e+00 6.20e-01 2.67e+01 angle pdb=" N ILE A 359 " pdb=" CA ILE A 359 " pdb=" C ILE A 359 " ideal model delta sigma weight residual 111.62 107.63 3.99 7.90e-01 1.60e+00 2.55e+01 ... (remaining 7268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 2889 17.58 - 35.16: 296 35.16 - 52.74: 65 52.74 - 70.32: 18 70.32 - 87.90: 10 Dihedral angle restraints: 3278 sinusoidal: 1339 harmonic: 1939 Sorted by residual: dihedral pdb=" CA GLN A 383 " pdb=" C GLN A 383 " pdb=" N GLN A 384 " pdb=" CA GLN A 384 " ideal model delta harmonic sigma weight residual -180.00 -160.07 -19.93 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA GLN A 744 " pdb=" C GLN A 744 " pdb=" N ARG A 745 " pdb=" CA ARG A 745 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP A 762 " pdb=" CB ASP A 762 " pdb=" CG ASP A 762 " pdb=" OD1 ASP A 762 " ideal model delta sinusoidal sigma weight residual -30.00 -88.08 58.08 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 3275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 511 0.037 - 0.073: 216 0.073 - 0.110: 65 0.110 - 0.146: 24 0.146 - 0.183: 1 Chirality restraints: 817 Sorted by residual: chirality pdb=" CA ARG A 364 " pdb=" N ARG A 364 " pdb=" C ARG A 364 " pdb=" CB ARG A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CG LEU A 695 " pdb=" CB LEU A 695 " pdb=" CD1 LEU A 695 " pdb=" CD2 LEU A 695 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA LEU A 229 " pdb=" N LEU A 229 " pdb=" C LEU A 229 " pdb=" CB LEU A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 814 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 233 " 0.013 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLU A 233 " -0.047 2.00e-02 2.50e+03 pdb=" O GLU A 233 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP A 234 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 586 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO A 587 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 606 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 607 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.025 5.00e-02 4.00e+02 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 5 2.22 - 2.89: 1967 2.89 - 3.56: 6615 3.56 - 4.23: 12060 4.23 - 4.90: 20694 Nonbonded interactions: 41341 Sorted by model distance: nonbonded pdb=" CG ASN A 361 " pdb=" NH1 ARG A 364 " model vdw 1.549 3.350 nonbonded pdb=" ND2 ASN A 361 " pdb=" NH1 ARG A 364 " model vdw 1.733 3.200 nonbonded pdb=" CG ARG A 235 " pdb=" CB LEU A 268 " model vdw 1.987 3.840 nonbonded pdb=" O ARG A 235 " pdb=" NH1 ARG A 235 " model vdw 2.079 2.520 nonbonded pdb=" OD1 ASN A 361 " pdb=" NH1 ARG A 364 " model vdw 2.090 2.520 ... (remaining 41336 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 11.230 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 19.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 : 0.005 0.039 5366 Z= 0.334 Angle : 0.761 9.443 7273 Z= 0.475 Chirality : 0.045 0.183 817 Planarity : 0.005 0.050 950 Dihedral : 15.770 87.903 2028 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.39 % Rotamer: Outliers : 1.41 % Allowed : 3.53 % Favored : 95.06 % 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: -4.83 (0.25), residues: 660 helix: -4.29 (0.17), residues: 252 sheet: -1.92 (0.48), residues: 100 loop : -2.55 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 709 HIS 0.003 0.001 HIS A 179 PHE 0.016 0.002 PHE A 194 TYR 0.006 0.001 TYR A 734 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 293 MET cc_start: 0.8632 (mmt) cc_final: 0.8417 (mmt) REVERT: A 556 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6956 (mtp-110) outliers start: 8 outliers final: 6 residues processed: 54 average time/residue: 0.2444 time to fit residues: 16.3218 Evaluate side-chains 41 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 494 GLN A 623 GLN A 703 ASN A 729 GLN A 756 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5366 Z= 0.255 Angle : 0.561 5.563 7273 Z= 0.287 Chirality : 0.044 0.128 817 Planarity : 0.005 0.045 950 Dihedral : 6.381 57.518 752 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.47 % Allowed : 7.76 % Favored : 89.77 % 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: -3.04 (0.29), residues: 660 helix: -2.38 (0.28), residues: 256 sheet: -1.26 (0.58), residues: 80 loop : -1.81 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 709 HIS 0.003 0.001 HIS A 236 PHE 0.012 0.001 PHE A 625 TYR 0.019 0.001 TYR A 292 ARG 0.007 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 36 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 48 average time/residue: 0.2280 time to fit residues: 13.9959 Evaluate side-chains 42 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 777 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 54 optimal weight: 0.3980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5366 Z= 0.172 Angle : 0.497 5.198 7273 Z= 0.249 Chirality : 0.041 0.126 817 Planarity : 0.004 0.039 950 Dihedral : 5.440 55.009 747 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.94 % Allowed : 10.05 % Favored : 88.01 % 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: -2.09 (0.31), residues: 660 helix: -1.23 (0.32), residues: 260 sheet: -1.15 (0.51), residues: 94 loop : -1.48 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 709 HIS 0.001 0.000 HIS A 179 PHE 0.007 0.001 PHE A 194 TYR 0.012 0.001 TYR A 292 ARG 0.003 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.630 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 0.2034 time to fit residues: 11.6185 Evaluate side-chains 40 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 32 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 777 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 61 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8309 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5366 Z= 0.173 Angle : 0.485 5.584 7273 Z= 0.242 Chirality : 0.041 0.134 817 Planarity : 0.004 0.044 950 Dihedral : 4.873 52.633 743 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.94 % Allowed : 11.46 % Favored : 86.60 % 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: -1.41 (0.32), residues: 660 helix: -0.57 (0.34), residues: 257 sheet: -0.79 (0.54), residues: 87 loop : -1.20 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A 236 PHE 0.008 0.001 PHE A 194 TYR 0.012 0.001 TYR A 292 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7791 (t70) cc_final: 0.7043 (t0) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.2385 time to fit residues: 12.8109 Evaluate side-chains 39 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5366 Z= 0.188 Angle : 0.481 6.026 7273 Z= 0.240 Chirality : 0.042 0.125 817 Planarity : 0.004 0.040 950 Dihedral : 4.784 54.726 743 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.94 % Allowed : 12.35 % Favored : 85.71 % 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: -1.05 (0.33), residues: 660 helix: -0.29 (0.34), residues: 263 sheet: -0.57 (0.55), residues: 87 loop : -0.99 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.002 0.001 HIS A 236 PHE 0.009 0.001 PHE A 194 TYR 0.010 0.001 TYR A 292 ARG 0.001 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.571 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 42 average time/residue: 0.1955 time to fit residues: 10.8345 Evaluate side-chains 42 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 269 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.0970 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5366 Z= 0.171 Angle : 0.472 6.547 7273 Z= 0.236 Chirality : 0.041 0.126 817 Planarity : 0.004 0.041 950 Dihedral : 4.675 54.295 743 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.12 % Allowed : 12.70 % Favored : 85.19 % 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: -0.69 (0.33), residues: 660 helix: 0.10 (0.35), residues: 258 sheet: -0.43 (0.57), residues: 86 loop : -0.86 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.002 0.001 HIS A 236 PHE 0.008 0.001 PHE A 194 TYR 0.013 0.001 TYR A 292 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.638 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.1950 time to fit residues: 11.4269 Evaluate side-chains 40 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 554 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 41 optimal weight: 0.1980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.8294 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5366 Z= 0.143 Angle : 0.473 9.239 7273 Z= 0.234 Chirality : 0.041 0.233 817 Planarity : 0.004 0.043 950 Dihedral : 4.332 53.358 742 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.59 % Allowed : 13.58 % Favored : 84.83 % 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: -0.49 (0.33), residues: 660 helix: 0.36 (0.35), residues: 261 sheet: -0.31 (0.57), residues: 86 loop : -0.85 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.001 0.001 HIS A 236 PHE 0.006 0.001 PHE A 194 TYR 0.012 0.001 TYR A 292 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.649 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 43 average time/residue: 0.2122 time to fit residues: 12.0204 Evaluate side-chains 38 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 56 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.8316 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5366 Z= 0.186 Angle : 0.491 8.516 7273 Z= 0.243 Chirality : 0.042 0.225 817 Planarity : 0.005 0.060 950 Dihedral : 4.415 56.525 742 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.88 % Allowed : 14.46 % Favored : 84.66 % 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: -0.34 (0.33), residues: 660 helix: 0.57 (0.34), residues: 260 sheet: -0.27 (0.57), residues: 86 loop : -0.83 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.001 0.001 HIS A 236 PHE 0.023 0.001 PHE A 495 TYR 0.011 0.001 TYR A 292 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.603 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.2039 time to fit residues: 10.2784 Evaluate side-chains 37 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 0.0470 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5366 Z= 0.154 Angle : 0.484 8.359 7273 Z= 0.239 Chirality : 0.042 0.223 817 Planarity : 0.004 0.057 950 Dihedral : 4.336 56.513 742 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.06 % Allowed : 14.46 % Favored : 84.48 % 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: -0.06 (0.34), residues: 660 helix: 0.90 (0.35), residues: 257 sheet: -0.18 (0.58), residues: 86 loop : -0.72 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 709 HIS 0.001 0.000 HIS A 236 PHE 0.007 0.001 PHE A 194 TYR 0.005 0.001 TYR A 333 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.592 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.1839 time to fit residues: 9.4286 Evaluate side-chains 38 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8335 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5366 Z= 0.237 Angle : 0.525 8.854 7273 Z= 0.256 Chirality : 0.043 0.221 817 Planarity : 0.005 0.056 950 Dihedral : 4.519 58.550 742 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.06 % Allowed : 14.64 % Favored : 84.30 % 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: -0.07 (0.34), residues: 660 helix: 0.92 (0.35), residues: 260 sheet: -0.25 (0.58), residues: 86 loop : -0.77 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 709 HIS 0.001 0.001 HIS A 236 PHE 0.022 0.001 PHE A 495 TYR 0.011 0.001 TYR A 292 ARG 0.002 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1320 Ramachandran restraints generated. 660 Oldfield, 0 Emsley, 660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.623 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.1731 time to fit residues: 9.0884 Evaluate side-chains 39 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 236 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 777 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.0570 chunk 46 optimal weight: 0.3980 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 chunk 42 optimal weight: 0.0980 overall best weight: 0.2498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.060251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.041617 restraints weight = 17883.061| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.52 r_work: 0.2635 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5366 Z= 0.120 Angle : 0.482 8.831 7273 Z= 0.236 Chirality : 0.041 0.219 817 Planarity : 0.004 0.052 950 Dihedral : 4.337 59.888 742 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.71 % Allowed : 14.99 % Favored : 84.30 % 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: 0.16 (0.34), residues: 660 helix: 1.16 (0.35), residues: 260 sheet: -0.13 (0.58), residues: 86 loop : -0.67 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 709 HIS 0.001 0.000 HIS A 236 PHE 0.006 0.001 PHE A 442 TYR 0.011 0.001 TYR A 334 ARG 0.002 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.20 seconds wall clock time: 29 minutes 3.20 seconds (1743.20 seconds total)