Starting phenix.real_space_refine on Wed Sep 25 11:18:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl9_32578/09_2024/7wl9_32578.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl9_32578/09_2024/7wl9_32578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl9_32578/09_2024/7wl9_32578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl9_32578/09_2024/7wl9_32578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl9_32578/09_2024/7wl9_32578.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wl9_32578/09_2024/7wl9_32578.cif" } resolution = 3.78 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 42 5.16 5 Cl 1 4.86 5 C 6653 2.51 5 N 1687 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10194 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5099 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 26, 'TRANS': 638} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5094 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 26, 'TRANS': 635} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.50, per 1000 atoms: 0.64 Number of scatterers: 10194 At special positions: 0 Unit cell: (84.056, 127.68, 123.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 42 16.00 O 1811 8.00 N 1687 7.00 C 6653 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 - 3.00 Amino acid : True - 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 7 sheets defined 65.6% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.826A pdb=" N GLN A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 29 through 34' Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.970A pdb=" N TRP A 74 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 79 through 106 removed outlier: 5.060A pdb=" N LEU A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 Processing helix chain 'A' and resid 112 through 128 removed outlier: 4.174A pdb=" N GLY A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 141 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.591A pdb=" N HIS A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 206 removed outlier: 3.760A pdb=" N ALA A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.568A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 214 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 241 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 268 through 292 Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.633A pdb=" N ALA A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 374 Processing helix chain 'A' and resid 380 through 397 removed outlier: 3.547A pdb=" N PHE A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 417 removed outlier: 3.603A pdb=" N GLN A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.537A pdb=" N VAL A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 446 through 457 removed outlier: 3.875A pdb=" N LEU A 450 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 467 through 474 removed outlier: 3.646A pdb=" N LYS A 473 " --> pdb=" O PRO A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 492 removed outlier: 3.665A pdb=" N ALA A 479 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 490 " --> pdb=" O CYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 removed outlier: 3.623A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 499 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 571 Processing helix chain 'A' and resid 573 through 595 removed outlier: 3.615A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 587 " --> pdb=" O LYS A 583 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 4.061A pdb=" N SER A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 706 removed outlier: 3.761A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 736 removed outlier: 3.741A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 726 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.537A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.565A pdb=" N LEU B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 removed outlier: 3.874A pdb=" N ALA B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 82 removed outlier: 4.128A pdb=" N GLU B 82 " --> pdb=" O ARG B 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 82' Processing helix chain 'B' and resid 83 through 109 removed outlier: 3.571A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 Proline residue: B 123 - end of helix removed outlier: 3.829A pdb=" N VAL B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 155 removed outlier: 3.656A pdb=" N MET B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 206 removed outlier: 3.538A pdb=" N ALA B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.668A pdb=" N VAL B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 240 removed outlier: 3.615A pdb=" N THR B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 268 through 292 removed outlier: 3.537A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 370 removed outlier: 3.603A pdb=" N MET B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B 352 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 396 removed outlier: 3.537A pdb=" N GLU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 416 removed outlier: 3.578A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 437 removed outlier: 3.617A pdb=" N LEU B 425 " --> pdb=" O GLN B 421 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 458 Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 466 through 475 removed outlier: 4.057A pdb=" N ARG B 470 " --> pdb=" O CYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 492 removed outlier: 3.569A pdb=" N ALA B 479 " --> pdb=" O ASN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 removed outlier: 3.779A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 499 " --> pdb=" O ASP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 575 through 595 Processing helix chain 'B' and resid 669 through 685 Processing helix chain 'B' and resid 697 through 706 removed outlier: 4.023A pdb=" N GLU B 701 " --> pdb=" O ASP B 697 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 removed outlier: 3.557A pdb=" N ARG B 717 " --> pdb=" O ARG B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 733 removed outlier: 3.568A pdb=" N ALA B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.900A pdb=" N VAL A 163 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 175 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA5, first strand: chain 'A' and resid 545 through 548 removed outlier: 6.604A pdb=" N LEU A 658 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 530 through 532 removed outlier: 3.595A pdb=" N ASN B 519 " --> pdb=" O ARG B 549 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 549 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE B 547 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N SER B 523 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 12.714A pdb=" N VAL B 545 " --> pdb=" O SER B 523 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B 546 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 658 " --> pdb=" O TYR B 691 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1671 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: 3.12 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3211 1.35 - 1.46: 2296 1.46 - 1.58: 4824 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 10395 Sorted by residual: bond pdb=" C VAL A 339 " pdb=" N LEU A 340 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.60e-02 3.91e+03 2.51e+00 bond pdb=" CA VAL A 163 " pdb=" CB VAL A 163 " ideal model delta sigma weight residual 1.541 1.527 0.015 1.24e-02 6.50e+03 1.37e+00 bond pdb=" N VAL A 26 " pdb=" CA VAL A 26 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.04e+00 bond pdb=" N LYS A 329 " pdb=" CA LYS A 329 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 1.01e+00 bond pdb=" CB PRO B 164 " pdb=" CG PRO B 164 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.81e-01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 13755 1.31 - 2.62: 308 2.62 - 3.93: 49 3.93 - 5.23: 13 5.23 - 6.54: 3 Bond angle restraints: 14128 Sorted by residual: angle pdb=" N VAL B 367 " pdb=" CA VAL B 367 " pdb=" C VAL B 367 " ideal model delta sigma weight residual 112.98 109.21 3.77 1.25e+00 6.40e-01 9.08e+00 angle pdb=" C LEU A 442 " pdb=" N GLU A 443 " pdb=" CA GLU A 443 " ideal model delta sigma weight residual 120.26 123.53 -3.27 1.34e+00 5.57e-01 5.94e+00 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 112.35 109.08 3.27 1.41e+00 5.03e-01 5.36e+00 angle pdb=" C ASP A 669 " pdb=" N VAL A 670 " pdb=" CA VAL A 670 " ideal model delta sigma weight residual 121.97 126.04 -4.07 1.80e+00 3.09e-01 5.11e+00 angle pdb=" C ARG A 79 " pdb=" N VAL A 80 " pdb=" CA VAL A 80 " ideal model delta sigma weight residual 121.97 125.86 -3.89 1.80e+00 3.09e-01 4.68e+00 ... (remaining 14123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 5955 17.51 - 35.01: 184 35.01 - 52.52: 34 52.52 - 70.02: 4 70.02 - 87.53: 3 Dihedral angle restraints: 6180 sinusoidal: 2353 harmonic: 3827 Sorted by residual: dihedral pdb=" CA LEU B 695 " pdb=" C LEU B 695 " pdb=" N GLN B 696 " pdb=" CA GLN B 696 " ideal model delta harmonic sigma weight residual -180.00 -163.48 -16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CB GLU B 259 " pdb=" CG GLU B 259 " pdb=" CD GLU B 259 " pdb=" OE1 GLU B 259 " ideal model delta sinusoidal sigma weight residual 0.00 85.17 -85.17 1 3.00e+01 1.11e-03 9.77e+00 dihedral pdb=" N ARG A 36 " pdb=" CA ARG A 36 " pdb=" CB ARG A 36 " pdb=" CG ARG A 36 " ideal model delta sinusoidal sigma weight residual -180.00 -125.45 -54.55 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1002 0.026 - 0.051: 432 0.051 - 0.076: 192 0.076 - 0.102: 71 0.102 - 0.127: 19 Chirality restraints: 1716 Sorted by residual: chirality pdb=" CA PRO A 553 " pdb=" N PRO A 553 " pdb=" C PRO A 553 " pdb=" CB PRO A 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL B 653 " pdb=" N VAL B 653 " pdb=" C VAL B 653 " pdb=" CB VAL B 653 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA VAL A 524 " pdb=" N VAL A 524 " pdb=" C VAL A 524 " pdb=" CB VAL A 524 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1713 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 75 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO B 76 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 552 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 553 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 553 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 553 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 653 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 654 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 654 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 654 " -0.019 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 948 2.74 - 3.28: 11086 3.28 - 3.82: 16778 3.82 - 4.36: 19649 4.36 - 4.90: 32856 Nonbonded interactions: 81317 Sorted by model distance: nonbonded pdb=" OG SER A 90 " pdb=" O GLY A 417 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 78 " pdb=" OD2 ASP A 87 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 475 " pdb=" OG1 THR A 477 " model vdw 2.219 3.040 nonbonded pdb=" O ASP A 669 " pdb=" N GLY A 672 " model vdw 2.245 3.120 nonbonded pdb=" O THR A 485 " pdb=" OG SER A 489 " model vdw 2.287 3.040 ... (remaining 81312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 733) selection = (chain 'B' and (resid 18 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 51 or (res \ id 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throu \ gh 590 or (resid 591 and (name N or name CA or name C or name O or name CB )) or \ resid 592 through 595 or resid 651 through 733)) } 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.770 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.002 0.044 10395 Z= 0.122 Angle : 0.494 6.543 14128 Z= 0.300 Chirality : 0.037 0.127 1716 Planarity : 0.003 0.040 1757 Dihedral : 9.093 87.528 3714 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.30 % Rotamer: Outliers : 4.27 % Allowed : 5.34 % Favored : 90.38 % 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: -4.11 (0.18), residues: 1319 helix: -2.12 (0.15), residues: 822 sheet: -2.88 (0.81), residues: 27 loop : -3.67 (0.23), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 83 HIS 0.001 0.000 HIS A 656 PHE 0.008 0.001 PHE A 115 TYR 0.007 0.001 TYR A 377 ARG 0.001 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 359 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 TYR cc_start: 0.8021 (t80) cc_final: 0.7431 (t80) REVERT: A 29 GLU cc_start: 0.7174 (tp30) cc_final: 0.5854 (tp30) REVERT: A 66 LYS cc_start: 0.8678 (tppt) cc_final: 0.8466 (tptm) REVERT: A 74 TRP cc_start: 0.8441 (p-90) cc_final: 0.8222 (p-90) REVERT: A 97 VAL cc_start: 0.8607 (t) cc_final: 0.8354 (p) REVERT: A 145 SER cc_start: 0.8419 (m) cc_final: 0.7928 (p) REVERT: A 147 MET cc_start: 0.8102 (mtp) cc_final: 0.7895 (mtp) REVERT: A 192 LEU cc_start: 0.8633 (tp) cc_final: 0.8336 (tp) REVERT: A 195 LEU cc_start: 0.8444 (tp) cc_final: 0.8066 (tp) REVERT: A 199 ILE cc_start: 0.8741 (mt) cc_final: 0.8478 (tp) REVERT: A 200 GLN cc_start: 0.7933 (mt0) cc_final: 0.7569 (tt0) REVERT: A 211 ILE cc_start: 0.8726 (tt) cc_final: 0.8506 (tp) REVERT: A 217 ASP cc_start: 0.7522 (t0) cc_final: 0.7268 (t0) REVERT: A 236 LEU cc_start: 0.8357 (tp) cc_final: 0.8045 (mt) REVERT: A 259 GLU cc_start: 0.7950 (tt0) cc_final: 0.7522 (tt0) REVERT: A 262 GLN cc_start: 0.7793 (mt0) cc_final: 0.7561 (mm-40) REVERT: A 278 THR cc_start: 0.8533 (t) cc_final: 0.8023 (p) REVERT: A 283 MET cc_start: 0.7240 (tpp) cc_final: 0.6887 (tpp) REVERT: A 286 LYS cc_start: 0.9022 (tppt) cc_final: 0.8820 (mmmm) REVERT: A 304 VAL cc_start: 0.8861 (t) cc_final: 0.8651 (m) REVERT: A 355 SER cc_start: 0.8698 (m) cc_final: 0.8418 (p) REVERT: A 361 TYR cc_start: 0.8064 (t80) cc_final: 0.7619 (t80) REVERT: A 369 LYS cc_start: 0.8382 (mmtt) cc_final: 0.8067 (mptt) REVERT: A 371 TYR cc_start: 0.7918 (m-80) cc_final: 0.7550 (m-80) REVERT: A 382 ASN cc_start: 0.8022 (m110) cc_final: 0.7783 (m-40) REVERT: A 443 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 473 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7807 (mptt) REVERT: A 475 ASN cc_start: 0.7120 (t0) cc_final: 0.6780 (t0) REVERT: A 478 ASP cc_start: 0.7344 (m-30) cc_final: 0.6791 (m-30) REVERT: A 484 PHE cc_start: 0.8726 (t80) cc_final: 0.8170 (t80) REVERT: A 488 MET cc_start: 0.7723 (tpp) cc_final: 0.7456 (tpp) REVERT: A 547 ILE cc_start: 0.9107 (mt) cc_final: 0.8771 (mp) REVERT: A 563 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8187 (mmtm) REVERT: A 580 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8357 (mmmm) REVERT: A 677 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7675 (ttp-170) REVERT: A 701 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7428 (mm-30) REVERT: B 37 GLU cc_start: 0.7540 (pt0) cc_final: 0.7100 (pm20) REVERT: B 48 ASP cc_start: 0.7174 (p0) cc_final: 0.6849 (t0) REVERT: B 89 ILE cc_start: 0.8748 (pt) cc_final: 0.8502 (tp) REVERT: B 128 PHE cc_start: 0.6637 (t80) cc_final: 0.6099 (t80) REVERT: B 146 LEU cc_start: 0.8533 (tp) cc_final: 0.7816 (tp) REVERT: B 186 VAL cc_start: 0.8892 (t) cc_final: 0.8687 (p) REVERT: B 188 LEU cc_start: 0.8714 (tp) cc_final: 0.8278 (pp) REVERT: B 199 ILE cc_start: 0.7789 (mp) cc_final: 0.7523 (pt) REVERT: B 235 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7811 (mt0) REVERT: B 237 LYS cc_start: 0.8640 (pttt) cc_final: 0.8272 (pttm) REVERT: B 262 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7729 (tp-100) REVERT: B 329 LYS cc_start: 0.8018 (ptmm) cc_final: 0.7807 (ptmm) REVERT: B 404 THR cc_start: 0.6264 (OUTLIER) cc_final: 0.6045 (m) REVERT: B 463 MET cc_start: 0.7353 (mmm) cc_final: 0.7079 (mmm) REVERT: B 488 MET cc_start: 0.7006 (tpp) cc_final: 0.6185 (tpp) REVERT: B 492 LEU cc_start: 0.8857 (mt) cc_final: 0.7812 (mt) REVERT: B 495 ASP cc_start: 0.7592 (t0) cc_final: 0.7286 (t0) REVERT: B 549 ARG cc_start: 0.7442 (ttt180) cc_final: 0.7213 (ttm-80) REVERT: B 591 LEU cc_start: 0.8810 (mp) cc_final: 0.8107 (mt) REVERT: B 682 GLU cc_start: 0.7932 (tp30) cc_final: 0.7394 (tp30) outliers start: 48 outliers final: 18 residues processed: 391 average time/residue: 0.2550 time to fit residues: 132.9720 Evaluate side-chains 304 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 285 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 0.0070 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 114 GLN A 135 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 GLN A 656 HIS A 696 GLN A 730 GLN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN B 446 GLN B 457 ASN B 474 GLN B 684 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10395 Z= 0.239 Angle : 0.666 9.047 14128 Z= 0.345 Chirality : 0.043 0.164 1716 Planarity : 0.005 0.058 1757 Dihedral : 6.324 86.734 1450 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.08 % Allowed : 13.89 % Favored : 81.03 % 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: -1.95 (0.22), residues: 1319 helix: -0.33 (0.17), residues: 815 sheet: -2.05 (0.96), residues: 34 loop : -2.94 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.008 0.001 HIS A 728 PHE 0.021 0.001 PHE B 719 TYR 0.019 0.002 TYR B 530 ARG 0.006 0.001 ARG B 587 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 307 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8337 (t80) cc_final: 0.8053 (t80) REVERT: A 66 LYS cc_start: 0.8815 (tppt) cc_final: 0.8554 (tptm) REVERT: A 74 TRP cc_start: 0.8461 (p-90) cc_final: 0.8253 (p-90) REVERT: A 145 SER cc_start: 0.8482 (m) cc_final: 0.7946 (p) REVERT: A 182 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6952 (t0) REVERT: A 195 LEU cc_start: 0.8496 (tp) cc_final: 0.7882 (tp) REVERT: A 199 ILE cc_start: 0.8830 (mt) cc_final: 0.8549 (tp) REVERT: A 217 ASP cc_start: 0.7832 (t0) cc_final: 0.7572 (t0) REVERT: A 259 GLU cc_start: 0.7878 (tt0) cc_final: 0.7489 (tt0) REVERT: A 271 ASP cc_start: 0.7618 (m-30) cc_final: 0.7357 (m-30) REVERT: A 277 LEU cc_start: 0.8267 (tt) cc_final: 0.8066 (pp) REVERT: A 283 MET cc_start: 0.7648 (tpp) cc_final: 0.6902 (tpp) REVERT: A 292 PHE cc_start: 0.7993 (m-10) cc_final: 0.7642 (m-10) REVERT: A 361 TYR cc_start: 0.8109 (t80) cc_final: 0.7606 (t80) REVERT: A 369 LYS cc_start: 0.8435 (mmtt) cc_final: 0.8101 (mptt) REVERT: A 371 TYR cc_start: 0.8108 (m-80) cc_final: 0.7818 (m-80) REVERT: A 382 ASN cc_start: 0.8080 (m110) cc_final: 0.7877 (m110) REVERT: A 429 VAL cc_start: 0.8770 (t) cc_final: 0.8524 (m) REVERT: A 430 ILE cc_start: 0.8767 (mm) cc_final: 0.8551 (mm) REVERT: A 440 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6534 (ptt-90) REVERT: A 443 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 461 MET cc_start: 0.7862 (mtm) cc_final: 0.7630 (ptp) REVERT: A 473 LYS cc_start: 0.8518 (mtpt) cc_final: 0.7975 (mmtm) REVERT: A 488 MET cc_start: 0.7942 (tpp) cc_final: 0.7500 (tpp) REVERT: A 499 LEU cc_start: 0.9059 (tp) cc_final: 0.8453 (tt) REVERT: A 563 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8294 (tppp) REVERT: A 580 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8448 (mmmm) REVERT: A 677 ARG cc_start: 0.7946 (ttp80) cc_final: 0.7627 (ttp-170) REVERT: A 701 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7563 (mm-30) REVERT: A 704 GLU cc_start: 0.7467 (tt0) cc_final: 0.7226 (tt0) REVERT: A 715 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8040 (tppt) REVERT: B 37 GLU cc_start: 0.7558 (pt0) cc_final: 0.7161 (pm20) REVERT: B 38 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.8100 (mmm160) REVERT: B 128 PHE cc_start: 0.6838 (t80) cc_final: 0.6243 (t80) REVERT: B 188 LEU cc_start: 0.8604 (tp) cc_final: 0.8380 (tp) REVERT: B 199 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7870 (pt) REVERT: B 207 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 230 GLN cc_start: 0.7604 (tp40) cc_final: 0.7049 (tm-30) REVERT: B 235 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7701 (mm-40) REVERT: B 262 GLN cc_start: 0.8283 (tp40) cc_final: 0.7836 (tp-100) REVERT: B 283 MET cc_start: 0.7726 (ptp) cc_final: 0.7485 (mpp) REVERT: B 302 ILE cc_start: 0.8491 (tp) cc_final: 0.8048 (tp) REVERT: B 404 THR cc_start: 0.6417 (OUTLIER) cc_final: 0.5840 (t) REVERT: B 463 MET cc_start: 0.7427 (mmm) cc_final: 0.7181 (mmm) REVERT: B 478 ASP cc_start: 0.8082 (p0) cc_final: 0.7764 (p0) REVERT: B 488 MET cc_start: 0.7353 (tpp) cc_final: 0.6530 (tpp) REVERT: B 492 LEU cc_start: 0.8870 (mt) cc_final: 0.8205 (mt) REVERT: B 495 ASP cc_start: 0.7719 (t0) cc_final: 0.7441 (t0) REVERT: B 526 SER cc_start: 0.8729 (m) cc_final: 0.8333 (p) REVERT: B 538 ASN cc_start: 0.7379 (p0) cc_final: 0.6771 (p0) REVERT: B 540 GLU cc_start: 0.7726 (pm20) cc_final: 0.7509 (pm20) REVERT: B 586 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7760 (mmp80) REVERT: B 591 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 682 GLU cc_start: 0.8215 (tp30) cc_final: 0.7602 (tp30) outliers start: 57 outliers final: 33 residues processed: 340 average time/residue: 0.2378 time to fit residues: 109.5076 Evaluate side-chains 301 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 713 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10395 Z= 0.257 Angle : 0.681 12.762 14128 Z= 0.349 Chirality : 0.044 0.186 1716 Planarity : 0.004 0.047 1757 Dihedral : 6.520 86.776 1448 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.34 % Allowed : 16.21 % Favored : 78.45 % 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: -1.23 (0.23), residues: 1319 helix: 0.30 (0.18), residues: 831 sheet: -1.68 (1.00), residues: 34 loop : -2.89 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 472 HIS 0.008 0.001 HIS A 728 PHE 0.013 0.001 PHE A 484 TYR 0.022 0.002 TYR B 530 ARG 0.009 0.001 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 292 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8366 (t80) cc_final: 0.8063 (t80) REVERT: A 66 LYS cc_start: 0.8852 (tppt) cc_final: 0.7691 (tptp) REVERT: A 74 TRP cc_start: 0.8536 (p-90) cc_final: 0.8204 (p-90) REVERT: A 145 SER cc_start: 0.8616 (m) cc_final: 0.8049 (p) REVERT: A 195 LEU cc_start: 0.8595 (tp) cc_final: 0.8116 (tp) REVERT: A 199 ILE cc_start: 0.8872 (mt) cc_final: 0.8572 (tp) REVERT: A 200 GLN cc_start: 0.8020 (mt0) cc_final: 0.7526 (mt0) REVERT: A 217 ASP cc_start: 0.7962 (t0) cc_final: 0.7711 (t0) REVERT: A 259 GLU cc_start: 0.7802 (tt0) cc_final: 0.7496 (tt0) REVERT: A 261 PHE cc_start: 0.7613 (m-10) cc_final: 0.7318 (m-10) REVERT: A 262 GLN cc_start: 0.7542 (tp40) cc_final: 0.7016 (tm-30) REVERT: A 271 ASP cc_start: 0.7585 (m-30) cc_final: 0.7272 (m-30) REVERT: A 277 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8123 (pp) REVERT: A 283 MET cc_start: 0.7654 (tpp) cc_final: 0.6889 (tpp) REVERT: A 292 PHE cc_start: 0.8030 (m-10) cc_final: 0.7684 (m-10) REVERT: A 361 TYR cc_start: 0.8131 (t80) cc_final: 0.7456 (t80) REVERT: A 369 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8083 (mptt) REVERT: A 371 TYR cc_start: 0.8263 (m-80) cc_final: 0.7934 (m-80) REVERT: A 376 ASP cc_start: 0.8145 (t0) cc_final: 0.7872 (t0) REVERT: A 429 VAL cc_start: 0.8861 (t) cc_final: 0.8651 (m) REVERT: A 430 ILE cc_start: 0.8883 (mm) cc_final: 0.8670 (mm) REVERT: A 440 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.6811 (ptt90) REVERT: A 443 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 473 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8003 (mppt) REVERT: A 484 PHE cc_start: 0.8795 (t80) cc_final: 0.8432 (t80) REVERT: A 488 MET cc_start: 0.8027 (tpp) cc_final: 0.7800 (tpp) REVERT: A 499 LEU cc_start: 0.9118 (tp) cc_final: 0.8917 (tt) REVERT: A 513 VAL cc_start: 0.9091 (t) cc_final: 0.8862 (p) REVERT: A 517 SER cc_start: 0.8394 (p) cc_final: 0.8001 (p) REVERT: A 535 HIS cc_start: 0.7131 (m90) cc_final: 0.6757 (m170) REVERT: A 563 LYS cc_start: 0.8867 (mmmt) cc_final: 0.8298 (tppp) REVERT: A 580 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8391 (mmtm) REVERT: A 677 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7638 (ttp-170) REVERT: A 691 TYR cc_start: 0.7858 (m-10) cc_final: 0.7641 (m-10) REVERT: A 701 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7509 (mm-30) REVERT: A 704 GLU cc_start: 0.7478 (tt0) cc_final: 0.7172 (tt0) REVERT: A 715 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8067 (tppt) REVERT: B 39 ARG cc_start: 0.6987 (ttm170) cc_final: 0.6470 (ttm110) REVERT: B 128 PHE cc_start: 0.6981 (t80) cc_final: 0.6394 (t80) REVERT: B 134 ARG cc_start: 0.7050 (mtm180) cc_final: 0.6805 (mtm-85) REVERT: B 185 ARG cc_start: 0.7674 (mtt180) cc_final: 0.7317 (mtt180) REVERT: B 199 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7897 (mt) REVERT: B 203 PHE cc_start: 0.8038 (m-80) cc_final: 0.7621 (m-80) REVERT: B 207 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7520 (tm-30) REVERT: B 235 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7699 (mm-40) REVERT: B 237 LYS cc_start: 0.8739 (pttt) cc_final: 0.8358 (ptpp) REVERT: B 262 GLN cc_start: 0.8334 (tp40) cc_final: 0.7862 (tp-100) REVERT: B 287 GLU cc_start: 0.7616 (pp20) cc_final: 0.7151 (pp20) REVERT: B 305 ILE cc_start: 0.8876 (mt) cc_final: 0.8662 (mm) REVERT: B 375 HIS cc_start: 0.5697 (t-90) cc_final: 0.5456 (t-90) REVERT: B 463 MET cc_start: 0.7465 (mmm) cc_final: 0.7201 (mmm) REVERT: B 478 ASP cc_start: 0.8023 (p0) cc_final: 0.7770 (p0) REVERT: B 488 MET cc_start: 0.7324 (tpp) cc_final: 0.6493 (tpp) REVERT: B 492 LEU cc_start: 0.8793 (mt) cc_final: 0.8133 (mt) REVERT: B 495 ASP cc_start: 0.7716 (t0) cc_final: 0.7479 (t0) REVERT: B 512 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.8147 (mtm-85) REVERT: B 519 ASN cc_start: 0.8098 (p0) cc_final: 0.7684 (p0) REVERT: B 526 SER cc_start: 0.8889 (m) cc_final: 0.8659 (p) REVERT: B 579 ASN cc_start: 0.8795 (p0) cc_final: 0.8540 (p0) REVERT: B 586 ARG cc_start: 0.7983 (mmp80) cc_final: 0.7724 (mmp80) REVERT: B 591 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8653 (mt) REVERT: B 677 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7507 (tpp80) REVERT: B 682 GLU cc_start: 0.8192 (tp30) cc_final: 0.7567 (tp30) REVERT: B 724 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7550 (t70) outliers start: 60 outliers final: 39 residues processed: 322 average time/residue: 0.2455 time to fit residues: 106.5335 Evaluate side-chains 321 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 573 ASP Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.0980 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS A 446 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10395 Z= 0.216 Angle : 0.655 12.826 14128 Z= 0.337 Chirality : 0.043 0.154 1716 Planarity : 0.004 0.046 1757 Dihedral : 6.565 86.984 1445 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.43 % Allowed : 17.90 % Favored : 76.67 % 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: -0.90 (0.23), residues: 1319 helix: 0.57 (0.18), residues: 831 sheet: -1.25 (1.00), residues: 33 loop : -2.80 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.016 0.002 HIS A 375 PHE 0.016 0.001 PHE A 346 TYR 0.024 0.002 TYR B 578 ARG 0.009 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 289 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8837 (tppt) cc_final: 0.7878 (tptp) REVERT: A 125 LEU cc_start: 0.8821 (mt) cc_final: 0.8617 (mp) REVERT: A 145 SER cc_start: 0.8629 (m) cc_final: 0.8087 (p) REVERT: A 195 LEU cc_start: 0.8604 (tp) cc_final: 0.7960 (tt) REVERT: A 199 ILE cc_start: 0.8873 (mt) cc_final: 0.8581 (tp) REVERT: A 200 GLN cc_start: 0.8015 (mt0) cc_final: 0.7515 (mt0) REVERT: A 217 ASP cc_start: 0.7981 (t0) cc_final: 0.7753 (t0) REVERT: A 232 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9123 (tt) REVERT: A 259 GLU cc_start: 0.7897 (tt0) cc_final: 0.7539 (tt0) REVERT: A 261 PHE cc_start: 0.7591 (m-10) cc_final: 0.7278 (m-10) REVERT: A 271 ASP cc_start: 0.7568 (m-30) cc_final: 0.7209 (m-30) REVERT: A 283 MET cc_start: 0.7625 (tpp) cc_final: 0.7281 (tpp) REVERT: A 286 LYS cc_start: 0.9150 (mmmm) cc_final: 0.8697 (mmmm) REVERT: A 292 PHE cc_start: 0.8034 (m-10) cc_final: 0.7699 (m-10) REVERT: A 361 TYR cc_start: 0.8136 (t80) cc_final: 0.7434 (t80) REVERT: A 369 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8086 (mptt) REVERT: A 371 TYR cc_start: 0.8250 (m-80) cc_final: 0.7829 (m-80) REVERT: A 376 ASP cc_start: 0.7881 (t0) cc_final: 0.7600 (t0) REVERT: A 429 VAL cc_start: 0.8855 (t) cc_final: 0.8647 (m) REVERT: A 430 ILE cc_start: 0.8920 (mm) cc_final: 0.8650 (mm) REVERT: A 440 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.6303 (ttp-170) REVERT: A 443 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7183 (tm-30) REVERT: A 473 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7980 (mppt) REVERT: A 488 MET cc_start: 0.7984 (tpp) cc_final: 0.7617 (tpp) REVERT: A 499 LEU cc_start: 0.9112 (tp) cc_final: 0.8889 (tt) REVERT: A 513 VAL cc_start: 0.9073 (t) cc_final: 0.8812 (p) REVERT: A 517 SER cc_start: 0.8403 (p) cc_final: 0.7997 (p) REVERT: A 535 HIS cc_start: 0.7084 (m90) cc_final: 0.6810 (m170) REVERT: A 563 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8251 (tppp) REVERT: A 580 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8525 (mmtm) REVERT: A 677 ARG cc_start: 0.7948 (ttp80) cc_final: 0.7549 (ttp-110) REVERT: A 691 TYR cc_start: 0.7780 (m-80) cc_final: 0.7574 (m-10) REVERT: A 696 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6935 (mm-40) REVERT: A 701 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 704 GLU cc_start: 0.7532 (tt0) cc_final: 0.7256 (tt0) REVERT: A 715 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8076 (tppt) REVERT: B 39 ARG cc_start: 0.7142 (ttm170) cc_final: 0.6471 (ttm110) REVERT: B 128 PHE cc_start: 0.7061 (t80) cc_final: 0.6471 (t80) REVERT: B 134 ARG cc_start: 0.7051 (mtm180) cc_final: 0.6758 (mtm-85) REVERT: B 185 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7335 (mtt180) REVERT: B 198 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8235 (tp) REVERT: B 199 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7935 (mt) REVERT: B 203 PHE cc_start: 0.8093 (m-80) cc_final: 0.7715 (m-80) REVERT: B 207 GLN cc_start: 0.8367 (tm130) cc_final: 0.7529 (tm-30) REVERT: B 235 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7687 (mm-40) REVERT: B 237 LYS cc_start: 0.8783 (pttt) cc_final: 0.8355 (ptpp) REVERT: B 240 LEU cc_start: 0.9065 (mt) cc_final: 0.8838 (tp) REVERT: B 262 GLN cc_start: 0.8277 (tp40) cc_final: 0.7806 (tp-100) REVERT: B 375 HIS cc_start: 0.5799 (t-90) cc_final: 0.5551 (t-90) REVERT: B 463 MET cc_start: 0.7409 (mmm) cc_final: 0.7122 (mmm) REVERT: B 478 ASP cc_start: 0.8055 (p0) cc_final: 0.7761 (p0) REVERT: B 488 MET cc_start: 0.7312 (tpp) cc_final: 0.6411 (tpp) REVERT: B 492 LEU cc_start: 0.8786 (mt) cc_final: 0.8040 (mt) REVERT: B 495 ASP cc_start: 0.7735 (t0) cc_final: 0.7529 (t0) REVERT: B 512 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8087 (mtm-85) REVERT: B 519 ASN cc_start: 0.8230 (p0) cc_final: 0.7851 (p0) REVERT: B 526 SER cc_start: 0.8907 (m) cc_final: 0.8680 (p) REVERT: B 549 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.7093 (ttt180) REVERT: B 579 ASN cc_start: 0.8787 (p0) cc_final: 0.8471 (p0) REVERT: B 586 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7706 (mmp80) REVERT: B 591 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8649 (mt) REVERT: B 682 GLU cc_start: 0.7847 (tp30) cc_final: 0.7534 (tp30) REVERT: B 724 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7557 (t70) outliers start: 61 outliers final: 42 residues processed: 324 average time/residue: 0.2442 time to fit residues: 106.5048 Evaluate side-chains 329 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 281 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10395 Z= 0.266 Angle : 0.691 11.736 14128 Z= 0.356 Chirality : 0.044 0.271 1716 Planarity : 0.004 0.051 1757 Dihedral : 6.616 86.607 1445 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 5.25 % Allowed : 19.77 % Favored : 74.98 % 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: -0.81 (0.23), residues: 1319 helix: 0.60 (0.18), residues: 837 sheet: -1.16 (0.97), residues: 33 loop : -2.75 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.016 0.002 HIS A 375 PHE 0.017 0.001 PHE A 130 TYR 0.027 0.002 TYR B 578 ARG 0.010 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 295 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8932 (tppt) cc_final: 0.8112 (tptp) REVERT: A 113 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 125 LEU cc_start: 0.8899 (mt) cc_final: 0.8698 (mp) REVERT: A 145 SER cc_start: 0.8635 (m) cc_final: 0.8100 (p) REVERT: A 195 LEU cc_start: 0.8677 (tp) cc_final: 0.7982 (tt) REVERT: A 199 ILE cc_start: 0.8861 (mt) cc_final: 0.8572 (tp) REVERT: A 200 GLN cc_start: 0.8013 (mt0) cc_final: 0.7560 (mt0) REVERT: A 217 ASP cc_start: 0.8049 (t0) cc_final: 0.7820 (t0) REVERT: A 235 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7811 (mm-40) REVERT: A 261 PHE cc_start: 0.7692 (m-10) cc_final: 0.7323 (m-10) REVERT: A 262 GLN cc_start: 0.7559 (tp40) cc_final: 0.7334 (tp-100) REVERT: A 271 ASP cc_start: 0.7649 (m-30) cc_final: 0.7322 (m-30) REVERT: A 283 MET cc_start: 0.7645 (tpp) cc_final: 0.7320 (tpp) REVERT: A 286 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8702 (mmmm) REVERT: A 292 PHE cc_start: 0.8062 (m-10) cc_final: 0.7727 (m-10) REVERT: A 369 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8097 (mptt) REVERT: A 376 ASP cc_start: 0.7845 (t0) cc_final: 0.7579 (t0) REVERT: A 425 LEU cc_start: 0.8805 (mm) cc_final: 0.8411 (mm) REVERT: A 430 ILE cc_start: 0.8967 (mm) cc_final: 0.8652 (mm) REVERT: A 440 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6937 (ptt90) REVERT: A 443 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7378 (tm-30) REVERT: A 473 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8017 (mppt) REVERT: A 488 MET cc_start: 0.7959 (tpp) cc_final: 0.7650 (tpp) REVERT: A 499 LEU cc_start: 0.9130 (tp) cc_final: 0.8762 (tt) REVERT: A 513 VAL cc_start: 0.9103 (t) cc_final: 0.8841 (p) REVERT: A 517 SER cc_start: 0.8472 (p) cc_final: 0.8079 (p) REVERT: A 535 HIS cc_start: 0.7282 (m90) cc_final: 0.6970 (m170) REVERT: A 537 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7755 (ttmm) REVERT: A 563 LYS cc_start: 0.8835 (mmmt) cc_final: 0.8457 (tppp) REVERT: A 580 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8537 (mmtm) REVERT: A 677 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7654 (ttp-170) REVERT: A 696 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6548 (mm-40) REVERT: A 701 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 704 GLU cc_start: 0.7532 (tt0) cc_final: 0.7270 (tt0) REVERT: A 715 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8045 (tppt) REVERT: B 39 ARG cc_start: 0.7238 (ttm170) cc_final: 0.6490 (ttm110) REVERT: B 134 ARG cc_start: 0.7043 (mtm180) cc_final: 0.6737 (mtm-85) REVERT: B 185 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7388 (mtt180) REVERT: B 198 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 199 ILE cc_start: 0.8297 (mp) cc_final: 0.7967 (mt) REVERT: B 203 PHE cc_start: 0.8117 (m-80) cc_final: 0.7766 (m-80) REVERT: B 207 GLN cc_start: 0.8455 (tm130) cc_final: 0.7634 (tm-30) REVERT: B 235 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7847 (mm-40) REVERT: B 237 LYS cc_start: 0.8845 (pttt) cc_final: 0.8423 (ptpp) REVERT: B 262 GLN cc_start: 0.8344 (tp40) cc_final: 0.7854 (tp-100) REVERT: B 283 MET cc_start: 0.7930 (ptp) cc_final: 0.7603 (mpp) REVERT: B 375 HIS cc_start: 0.5887 (t-90) cc_final: 0.5624 (t-90) REVERT: B 463 MET cc_start: 0.7533 (mmm) cc_final: 0.7076 (mmm) REVERT: B 478 ASP cc_start: 0.8048 (p0) cc_final: 0.7712 (p0) REVERT: B 488 MET cc_start: 0.7340 (tpp) cc_final: 0.6367 (tpp) REVERT: B 492 LEU cc_start: 0.8808 (mt) cc_final: 0.7864 (mt) REVERT: B 512 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8076 (mtm-85) REVERT: B 519 ASN cc_start: 0.8350 (p0) cc_final: 0.7915 (p0) REVERT: B 526 SER cc_start: 0.8985 (m) cc_final: 0.8775 (p) REVERT: B 549 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.6877 (ttt180) REVERT: B 579 ASN cc_start: 0.8802 (p0) cc_final: 0.8468 (p0) REVERT: B 591 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8693 (mt) REVERT: B 682 GLU cc_start: 0.7957 (tp30) cc_final: 0.7609 (tp30) REVERT: B 724 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7687 (t70) outliers start: 59 outliers final: 40 residues processed: 329 average time/residue: 0.2515 time to fit residues: 110.9965 Evaluate side-chains 333 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 288 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 375 HIS Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 31 optimal weight: 0.0370 chunk 127 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 123 optimal weight: 2.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS A 289 ASN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10395 Z= 0.198 Angle : 0.685 12.094 14128 Z= 0.344 Chirality : 0.043 0.278 1716 Planarity : 0.004 0.046 1757 Dihedral : 6.524 87.060 1441 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.72 % Allowed : 21.46 % Favored : 73.82 % 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: -0.64 (0.24), residues: 1319 helix: 0.66 (0.18), residues: 827 sheet: 0.29 (1.22), residues: 22 loop : -2.49 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.013 0.002 HIS A 135 PHE 0.017 0.001 PHE A 346 TYR 0.029 0.002 TYR B 578 ARG 0.010 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 292 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8380 (t80) cc_final: 0.7458 (t80) REVERT: A 113 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 145 SER cc_start: 0.8603 (m) cc_final: 0.8072 (p) REVERT: A 195 LEU cc_start: 0.8623 (tp) cc_final: 0.7919 (tt) REVERT: A 199 ILE cc_start: 0.8844 (mt) cc_final: 0.8407 (tp) REVERT: A 200 GLN cc_start: 0.8018 (mt0) cc_final: 0.7552 (mt0) REVERT: A 202 VAL cc_start: 0.9165 (t) cc_final: 0.8929 (p) REVERT: A 217 ASP cc_start: 0.8007 (t0) cc_final: 0.7783 (t0) REVERT: A 259 GLU cc_start: 0.8130 (tt0) cc_final: 0.7564 (tm-30) REVERT: A 260 ILE cc_start: 0.8593 (tt) cc_final: 0.8179 (tt) REVERT: A 261 PHE cc_start: 0.7530 (m-10) cc_final: 0.7244 (m-10) REVERT: A 271 ASP cc_start: 0.7600 (m-30) cc_final: 0.7271 (m-30) REVERT: A 278 THR cc_start: 0.8748 (p) cc_final: 0.8531 (p) REVERT: A 283 MET cc_start: 0.7584 (tpp) cc_final: 0.7283 (tpp) REVERT: A 286 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8687 (mmmm) REVERT: A 292 PHE cc_start: 0.8055 (m-10) cc_final: 0.7723 (m-10) REVERT: A 361 TYR cc_start: 0.8132 (t80) cc_final: 0.7518 (t80) REVERT: A 369 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8087 (mptt) REVERT: A 376 ASP cc_start: 0.7774 (t0) cc_final: 0.7473 (t0) REVERT: A 425 LEU cc_start: 0.8774 (mm) cc_final: 0.8560 (mm) REVERT: A 430 ILE cc_start: 0.8930 (mm) cc_final: 0.8631 (mm) REVERT: A 440 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.6338 (ttp-170) REVERT: A 443 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 473 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7950 (mppt) REVERT: A 488 MET cc_start: 0.7935 (tpp) cc_final: 0.7731 (tpp) REVERT: A 499 LEU cc_start: 0.9091 (tp) cc_final: 0.8704 (tt) REVERT: A 513 VAL cc_start: 0.9044 (t) cc_final: 0.8785 (p) REVERT: A 517 SER cc_start: 0.8420 (p) cc_final: 0.8033 (p) REVERT: A 535 HIS cc_start: 0.7150 (m90) cc_final: 0.6898 (m170) REVERT: A 563 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8434 (tppp) REVERT: A 580 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8403 (mmmm) REVERT: A 677 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7600 (ttp-170) REVERT: A 701 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7423 (mm-30) REVERT: A 704 GLU cc_start: 0.7491 (tt0) cc_final: 0.7231 (tt0) REVERT: A 715 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8035 (tppt) REVERT: A 732 GLN cc_start: 0.7975 (pp30) cc_final: 0.7628 (pp30) REVERT: B 39 ARG cc_start: 0.7210 (ttm170) cc_final: 0.6396 (ttm110) REVERT: B 134 ARG cc_start: 0.7007 (mtm180) cc_final: 0.6756 (mtm180) REVERT: B 185 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7484 (mtt180) REVERT: B 198 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8346 (tp) REVERT: B 199 ILE cc_start: 0.8255 (mp) cc_final: 0.7929 (mt) REVERT: B 203 PHE cc_start: 0.8087 (m-80) cc_final: 0.7687 (m-80) REVERT: B 207 GLN cc_start: 0.8457 (tm130) cc_final: 0.8046 (tm-30) REVERT: B 235 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7772 (mm-40) REVERT: B 237 LYS cc_start: 0.8811 (pttt) cc_final: 0.8351 (ptpp) REVERT: B 240 LEU cc_start: 0.9002 (tp) cc_final: 0.8706 (tp) REVERT: B 262 GLN cc_start: 0.8238 (tp40) cc_final: 0.7825 (tp-100) REVERT: B 283 MET cc_start: 0.7870 (ptp) cc_final: 0.7556 (mpp) REVERT: B 375 HIS cc_start: 0.5810 (t-90) cc_final: 0.5547 (t-90) REVERT: B 466 CYS cc_start: 0.7889 (t) cc_final: 0.7482 (t) REVERT: B 470 ARG cc_start: 0.7070 (ptt-90) cc_final: 0.6701 (ptt-90) REVERT: B 478 ASP cc_start: 0.8016 (p0) cc_final: 0.7710 (p0) REVERT: B 488 MET cc_start: 0.7293 (tpp) cc_final: 0.6323 (tpp) REVERT: B 492 LEU cc_start: 0.8674 (mt) cc_final: 0.7732 (mt) REVERT: B 512 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8033 (mtm-85) REVERT: B 519 ASN cc_start: 0.8331 (p0) cc_final: 0.7898 (p0) REVERT: B 526 SER cc_start: 0.8960 (m) cc_final: 0.8734 (p) REVERT: B 549 ARG cc_start: 0.7581 (ttm-80) cc_final: 0.7043 (ttt-90) REVERT: B 579 ASN cc_start: 0.8782 (p0) cc_final: 0.8455 (p0) REVERT: B 586 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7650 (mmm160) REVERT: B 587 ARG cc_start: 0.8473 (mmm160) cc_final: 0.7920 (mmm160) REVERT: B 591 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 682 GLU cc_start: 0.7888 (tp30) cc_final: 0.7596 (tp30) REVERT: B 724 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7877 (t0) outliers start: 53 outliers final: 39 residues processed: 323 average time/residue: 0.2598 time to fit residues: 111.0130 Evaluate side-chains 331 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 287 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 93 optimal weight: 0.0170 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10395 Z= 0.202 Angle : 0.692 13.000 14128 Z= 0.348 Chirality : 0.043 0.232 1716 Planarity : 0.004 0.046 1757 Dihedral : 6.493 86.898 1441 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 5.25 % Allowed : 21.55 % Favored : 73.20 % 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: -0.57 (0.24), residues: 1319 helix: 0.71 (0.18), residues: 825 sheet: -0.10 (1.23), residues: 23 loop : -2.42 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.019 0.002 HIS A 135 PHE 0.023 0.001 PHE A 719 TYR 0.033 0.002 TYR B 578 ARG 0.010 0.001 ARG A 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 291 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 121 PHE cc_start: 0.8296 (t80) cc_final: 0.8091 (t80) REVERT: A 145 SER cc_start: 0.8579 (m) cc_final: 0.8077 (p) REVERT: A 195 LEU cc_start: 0.8610 (tp) cc_final: 0.7932 (tt) REVERT: A 199 ILE cc_start: 0.8853 (mt) cc_final: 0.8408 (tp) REVERT: A 200 GLN cc_start: 0.8017 (mt0) cc_final: 0.7547 (mt0) REVERT: A 202 VAL cc_start: 0.9178 (t) cc_final: 0.8951 (p) REVERT: A 217 ASP cc_start: 0.7991 (t0) cc_final: 0.7773 (t0) REVERT: A 259 GLU cc_start: 0.7973 (tt0) cc_final: 0.7507 (tm-30) REVERT: A 260 ILE cc_start: 0.8597 (tt) cc_final: 0.8176 (tt) REVERT: A 261 PHE cc_start: 0.7528 (m-10) cc_final: 0.7245 (m-10) REVERT: A 271 ASP cc_start: 0.7581 (m-30) cc_final: 0.7252 (m-30) REVERT: A 283 MET cc_start: 0.7581 (tpp) cc_final: 0.7302 (tpp) REVERT: A 286 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8678 (mmmm) REVERT: A 292 PHE cc_start: 0.8052 (m-10) cc_final: 0.7721 (m-10) REVERT: A 348 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5632 (p0) REVERT: A 361 TYR cc_start: 0.8065 (t80) cc_final: 0.7546 (t80) REVERT: A 369 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8096 (mptt) REVERT: A 376 ASP cc_start: 0.7850 (t0) cc_final: 0.7496 (t0) REVERT: A 430 ILE cc_start: 0.8919 (mm) cc_final: 0.8575 (mm) REVERT: A 432 MET cc_start: 0.7366 (tpt) cc_final: 0.7160 (tpt) REVERT: A 440 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6716 (ptt90) REVERT: A 443 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7305 (tm-30) REVERT: A 457 ASN cc_start: 0.8009 (m-40) cc_final: 0.7795 (m-40) REVERT: A 473 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7955 (mppt) REVERT: A 488 MET cc_start: 0.7904 (tpp) cc_final: 0.7693 (tpp) REVERT: A 499 LEU cc_start: 0.9082 (tp) cc_final: 0.8709 (tt) REVERT: A 517 SER cc_start: 0.8376 (p) cc_final: 0.8009 (p) REVERT: A 535 HIS cc_start: 0.7201 (m90) cc_final: 0.6881 (m170) REVERT: A 563 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8457 (tppp) REVERT: A 580 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8504 (mmtt) REVERT: A 677 ARG cc_start: 0.7938 (ttp80) cc_final: 0.7676 (ttp80) REVERT: A 686 ILE cc_start: 0.8777 (pt) cc_final: 0.8518 (mm) REVERT: A 696 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7331 (mm-40) REVERT: A 701 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 704 GLU cc_start: 0.7413 (tt0) cc_final: 0.7155 (tt0) REVERT: A 715 LYS cc_start: 0.8475 (mmtt) cc_final: 0.7919 (tppt) REVERT: B 39 ARG cc_start: 0.7240 (ttm170) cc_final: 0.6932 (ttm110) REVERT: B 134 ARG cc_start: 0.7021 (mtm180) cc_final: 0.6688 (mtm-85) REVERT: B 185 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7516 (mtt180) REVERT: B 198 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8246 (tp) REVERT: B 199 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7904 (mt) REVERT: B 203 PHE cc_start: 0.8040 (m-80) cc_final: 0.7661 (m-80) REVERT: B 207 GLN cc_start: 0.8504 (tm130) cc_final: 0.8162 (tm-30) REVERT: B 235 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7781 (mm-40) REVERT: B 237 LYS cc_start: 0.8827 (pttt) cc_final: 0.8344 (ptpp) REVERT: B 240 LEU cc_start: 0.8961 (tp) cc_final: 0.8715 (tp) REVERT: B 262 GLN cc_start: 0.8196 (tp40) cc_final: 0.7786 (tp-100) REVERT: B 283 MET cc_start: 0.7854 (ptp) cc_final: 0.7562 (mpp) REVERT: B 375 HIS cc_start: 0.5827 (t-90) cc_final: 0.5568 (t-90) REVERT: B 466 CYS cc_start: 0.7885 (t) cc_final: 0.7509 (t) REVERT: B 470 ARG cc_start: 0.7052 (ptt-90) cc_final: 0.6785 (ptt-90) REVERT: B 478 ASP cc_start: 0.8003 (p0) cc_final: 0.7705 (p0) REVERT: B 488 MET cc_start: 0.7321 (tpp) cc_final: 0.6372 (tpp) REVERT: B 492 LEU cc_start: 0.8666 (mt) cc_final: 0.7707 (mt) REVERT: B 512 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8157 (mtm-85) REVERT: B 519 ASN cc_start: 0.8385 (p0) cc_final: 0.7877 (p0) REVERT: B 526 SER cc_start: 0.8960 (m) cc_final: 0.8723 (p) REVERT: B 533 ILE cc_start: 0.8960 (pt) cc_final: 0.8703 (tp) REVERT: B 549 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7267 (ttt-90) REVERT: B 579 ASN cc_start: 0.8776 (p0) cc_final: 0.8451 (p0) REVERT: B 582 LEU cc_start: 0.8914 (tt) cc_final: 0.8349 (tp) REVERT: B 586 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7564 (mmm160) REVERT: B 591 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 682 GLU cc_start: 0.7950 (tp30) cc_final: 0.7645 (tp30) REVERT: B 714 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.6989 (mtm-85) REVERT: B 724 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7854 (t0) outliers start: 59 outliers final: 44 residues processed: 323 average time/residue: 0.2713 time to fit residues: 118.3475 Evaluate side-chains 337 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 286 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 111 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10395 Z= 0.220 Angle : 0.704 13.505 14128 Z= 0.354 Chirality : 0.044 0.270 1716 Planarity : 0.004 0.054 1757 Dihedral : 6.516 86.745 1441 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.25 % Allowed : 22.26 % Favored : 72.48 % 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: -0.55 (0.24), residues: 1319 helix: 0.69 (0.18), residues: 832 sheet: -0.51 (1.09), residues: 29 loop : -2.37 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.021 0.002 HIS A 135 PHE 0.019 0.001 PHE A 719 TYR 0.039 0.002 TYR B 578 ARG 0.013 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 294 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8823 (tttp) cc_final: 0.8093 (tptp) REVERT: A 113 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8291 (p) REVERT: A 145 SER cc_start: 0.8567 (m) cc_final: 0.8102 (p) REVERT: A 195 LEU cc_start: 0.8634 (tp) cc_final: 0.7972 (tt) REVERT: A 199 ILE cc_start: 0.8855 (mt) cc_final: 0.8429 (tp) REVERT: A 200 GLN cc_start: 0.8012 (mt0) cc_final: 0.7611 (mt0) REVERT: A 217 ASP cc_start: 0.7997 (t0) cc_final: 0.7764 (t0) REVERT: A 259 GLU cc_start: 0.7917 (tt0) cc_final: 0.7537 (tm-30) REVERT: A 260 ILE cc_start: 0.8635 (tt) cc_final: 0.8203 (tt) REVERT: A 261 PHE cc_start: 0.7541 (m-10) cc_final: 0.7266 (m-10) REVERT: A 271 ASP cc_start: 0.7579 (m-30) cc_final: 0.7254 (m-30) REVERT: A 283 MET cc_start: 0.7585 (tpp) cc_final: 0.7305 (tpp) REVERT: A 286 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8684 (mmmm) REVERT: A 292 PHE cc_start: 0.8077 (m-10) cc_final: 0.7731 (m-10) REVERT: A 348 ASP cc_start: 0.5819 (OUTLIER) cc_final: 0.5585 (p0) REVERT: A 361 TYR cc_start: 0.8157 (t80) cc_final: 0.7655 (t80) REVERT: A 369 LYS cc_start: 0.8433 (mmtt) cc_final: 0.8108 (mptt) REVERT: A 375 HIS cc_start: 0.6767 (m170) cc_final: 0.6566 (m170) REVERT: A 376 ASP cc_start: 0.7916 (t0) cc_final: 0.7601 (t0) REVERT: A 430 ILE cc_start: 0.8949 (mm) cc_final: 0.8584 (mm) REVERT: A 432 MET cc_start: 0.7378 (tpt) cc_final: 0.7164 (tpt) REVERT: A 440 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6948 (ptt90) REVERT: A 443 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 457 ASN cc_start: 0.8008 (m-40) cc_final: 0.7793 (m-40) REVERT: A 473 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7962 (mppt) REVERT: A 499 LEU cc_start: 0.9100 (tp) cc_final: 0.8730 (tt) REVERT: A 513 VAL cc_start: 0.9105 (t) cc_final: 0.8892 (p) REVERT: A 517 SER cc_start: 0.8438 (p) cc_final: 0.8101 (p) REVERT: A 535 HIS cc_start: 0.7212 (m90) cc_final: 0.6945 (m170) REVERT: A 563 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8465 (tppp) REVERT: A 580 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8509 (mmtt) REVERT: A 674 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7716 (mtm180) REVERT: A 677 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7619 (ttp-170) REVERT: A 686 ILE cc_start: 0.8692 (pt) cc_final: 0.8471 (mm) REVERT: A 701 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7439 (mm-30) REVERT: A 704 GLU cc_start: 0.7423 (tt0) cc_final: 0.7180 (tt0) REVERT: A 715 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7889 (tppt) REVERT: A 732 GLN cc_start: 0.8008 (pp30) cc_final: 0.7670 (pp30) REVERT: B 39 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6928 (ttm110) REVERT: B 134 ARG cc_start: 0.6996 (mtm180) cc_final: 0.6661 (mtm-85) REVERT: B 198 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8270 (tp) REVERT: B 199 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7914 (mt) REVERT: B 203 PHE cc_start: 0.8039 (m-80) cc_final: 0.7714 (m-80) REVERT: B 207 GLN cc_start: 0.8585 (tm130) cc_final: 0.8184 (tm-30) REVERT: B 235 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7849 (mm-40) REVERT: B 237 LYS cc_start: 0.8856 (pttt) cc_final: 0.8374 (ptpp) REVERT: B 262 GLN cc_start: 0.8211 (tp40) cc_final: 0.7781 (tp-100) REVERT: B 283 MET cc_start: 0.7825 (ptp) cc_final: 0.7549 (mpp) REVERT: B 375 HIS cc_start: 0.5866 (t-90) cc_final: 0.5585 (t-90) REVERT: B 466 CYS cc_start: 0.7834 (t) cc_final: 0.7522 (t) REVERT: B 470 ARG cc_start: 0.7060 (ptt-90) cc_final: 0.6767 (ptt-90) REVERT: B 478 ASP cc_start: 0.8020 (p0) cc_final: 0.7684 (p0) REVERT: B 488 MET cc_start: 0.7341 (tpp) cc_final: 0.6379 (tpp) REVERT: B 492 LEU cc_start: 0.8635 (mt) cc_final: 0.7683 (mt) REVERT: B 512 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: B 519 ASN cc_start: 0.8426 (p0) cc_final: 0.7889 (p0) REVERT: B 526 SER cc_start: 0.9007 (m) cc_final: 0.8776 (p) REVERT: B 579 ASN cc_start: 0.8776 (p0) cc_final: 0.8455 (p0) REVERT: B 586 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7647 (mmm160) REVERT: B 589 GLN cc_start: 0.8883 (tp40) cc_final: 0.8545 (tp40) REVERT: B 591 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 677 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7685 (tpp80) REVERT: B 682 GLU cc_start: 0.7971 (tp30) cc_final: 0.7771 (tp30) REVERT: B 724 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7611 (t70) outliers start: 59 outliers final: 45 residues processed: 327 average time/residue: 0.2526 time to fit residues: 109.8697 Evaluate side-chains 336 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 284 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 77 optimal weight: 0.0270 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10395 Z= 0.234 Angle : 0.727 13.456 14128 Z= 0.367 Chirality : 0.045 0.282 1716 Planarity : 0.005 0.048 1757 Dihedral : 6.564 86.680 1441 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 4.63 % Allowed : 22.62 % Favored : 72.75 % 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: -0.51 (0.24), residues: 1319 helix: 0.70 (0.18), residues: 831 sheet: -0.39 (1.10), residues: 29 loop : -2.30 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.016 0.002 HIS A 728 PHE 0.038 0.001 PHE A 121 TYR 0.035 0.002 TYR B 578 ARG 0.011 0.001 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 293 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8365 (p) REVERT: A 145 SER cc_start: 0.8612 (m) cc_final: 0.8166 (p) REVERT: A 195 LEU cc_start: 0.8656 (tp) cc_final: 0.8017 (tt) REVERT: A 199 ILE cc_start: 0.8802 (mt) cc_final: 0.8500 (tp) REVERT: A 200 GLN cc_start: 0.8047 (mt0) cc_final: 0.7737 (mt0) REVERT: A 217 ASP cc_start: 0.8003 (t0) cc_final: 0.7780 (t0) REVERT: A 236 LEU cc_start: 0.8562 (mp) cc_final: 0.8312 (mm) REVERT: A 259 GLU cc_start: 0.7987 (tt0) cc_final: 0.7547 (tm-30) REVERT: A 260 ILE cc_start: 0.8612 (tt) cc_final: 0.8170 (tt) REVERT: A 261 PHE cc_start: 0.7591 (m-10) cc_final: 0.7327 (m-10) REVERT: A 271 ASP cc_start: 0.7613 (m-30) cc_final: 0.7232 (m-30) REVERT: A 283 MET cc_start: 0.7583 (tpp) cc_final: 0.7332 (tpp) REVERT: A 286 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8680 (mmmm) REVERT: A 292 PHE cc_start: 0.8111 (m-10) cc_final: 0.7745 (m-10) REVERT: A 348 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5649 (p0) REVERT: A 361 TYR cc_start: 0.8112 (t80) cc_final: 0.7415 (t80) REVERT: A 369 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8124 (mptt) REVERT: A 376 ASP cc_start: 0.7981 (t0) cc_final: 0.7710 (t0) REVERT: A 430 ILE cc_start: 0.8951 (mm) cc_final: 0.8590 (mm) REVERT: A 440 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.6453 (ttt180) REVERT: A 443 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 473 LYS cc_start: 0.8442 (mtpt) cc_final: 0.7971 (mppt) REVERT: A 488 MET cc_start: 0.7907 (tpp) cc_final: 0.7633 (tpp) REVERT: A 492 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8942 (pt) REVERT: A 499 LEU cc_start: 0.9110 (tp) cc_final: 0.8744 (tt) REVERT: A 513 VAL cc_start: 0.9109 (t) cc_final: 0.8901 (p) REVERT: A 517 SER cc_start: 0.8453 (p) cc_final: 0.8146 (p) REVERT: A 563 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8374 (tppp) REVERT: A 677 ARG cc_start: 0.7973 (ttp80) cc_final: 0.7634 (ttp-170) REVERT: A 701 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 715 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7839 (tppt) REVERT: A 732 GLN cc_start: 0.8031 (pp30) cc_final: 0.7672 (pp30) REVERT: B 39 ARG cc_start: 0.7277 (ttm170) cc_final: 0.6942 (ttm110) REVERT: B 134 ARG cc_start: 0.7009 (mtm180) cc_final: 0.6753 (mtm-85) REVERT: B 185 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7699 (mmt90) REVERT: B 196 VAL cc_start: 0.7977 (t) cc_final: 0.7623 (m) REVERT: B 198 ILE cc_start: 0.8663 (tp) cc_final: 0.8282 (tp) REVERT: B 199 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7920 (mt) REVERT: B 203 PHE cc_start: 0.8090 (m-80) cc_final: 0.7736 (m-80) REVERT: B 207 GLN cc_start: 0.8711 (tm130) cc_final: 0.8342 (tm-30) REVERT: B 237 LYS cc_start: 0.8885 (pttt) cc_final: 0.8404 (ptpp) REVERT: B 240 LEU cc_start: 0.8839 (tp) cc_final: 0.8616 (tp) REVERT: B 262 GLN cc_start: 0.8256 (tp40) cc_final: 0.7820 (tp-100) REVERT: B 466 CYS cc_start: 0.7864 (t) cc_final: 0.7565 (t) REVERT: B 470 ARG cc_start: 0.7076 (ptt-90) cc_final: 0.6773 (ptt-90) REVERT: B 478 ASP cc_start: 0.8037 (p0) cc_final: 0.7702 (p0) REVERT: B 488 MET cc_start: 0.7327 (tpp) cc_final: 0.6316 (tpp) REVERT: B 492 LEU cc_start: 0.8618 (mt) cc_final: 0.7567 (mt) REVERT: B 512 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8139 (mtm-85) REVERT: B 519 ASN cc_start: 0.8431 (p0) cc_final: 0.7882 (p0) REVERT: B 526 SER cc_start: 0.9052 (m) cc_final: 0.8842 (p) REVERT: B 549 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7316 (ttt180) REVERT: B 579 ASN cc_start: 0.8719 (p0) cc_final: 0.8337 (p0) REVERT: B 586 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7676 (mmm160) REVERT: B 589 GLN cc_start: 0.8886 (tp40) cc_final: 0.8541 (tp40) REVERT: B 590 LYS cc_start: 0.9009 (ptpp) cc_final: 0.8731 (pttt) REVERT: B 684 GLN cc_start: 0.8840 (tp40) cc_final: 0.8607 (tm-30) REVERT: B 714 ARG cc_start: 0.7573 (mtm-85) cc_final: 0.6948 (mtm-85) REVERT: B 724 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7721 (t70) outliers start: 52 outliers final: 38 residues processed: 324 average time/residue: 0.2462 time to fit residues: 106.6134 Evaluate side-chains 332 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 0.0010 chunk 32 optimal weight: 0.6980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10395 Z= 0.215 Angle : 0.745 13.707 14128 Z= 0.373 Chirality : 0.044 0.289 1716 Planarity : 0.004 0.059 1757 Dihedral : 6.570 86.644 1441 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.01 % Allowed : 23.78 % Favored : 72.22 % 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: -0.45 (0.24), residues: 1319 helix: 0.74 (0.18), residues: 828 sheet: -0.29 (1.12), residues: 29 loop : -2.26 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 74 HIS 0.016 0.002 HIS A 728 PHE 0.015 0.001 PHE A 719 TYR 0.030 0.002 TYR B 578 ARG 0.014 0.001 ARG B 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 294 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8342 (p) REVERT: A 145 SER cc_start: 0.8603 (m) cc_final: 0.8138 (p) REVERT: A 195 LEU cc_start: 0.8601 (tp) cc_final: 0.7979 (tt) REVERT: A 199 ILE cc_start: 0.8788 (mt) cc_final: 0.8486 (tp) REVERT: A 200 GLN cc_start: 0.8016 (mt0) cc_final: 0.7652 (mt0) REVERT: A 217 ASP cc_start: 0.8009 (t0) cc_final: 0.7789 (t0) REVERT: A 235 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7706 (mm-40) REVERT: A 236 LEU cc_start: 0.8535 (mp) cc_final: 0.8311 (mm) REVERT: A 259 GLU cc_start: 0.7948 (tt0) cc_final: 0.7587 (tm-30) REVERT: A 260 ILE cc_start: 0.8600 (tt) cc_final: 0.8312 (tt) REVERT: A 261 PHE cc_start: 0.7581 (m-10) cc_final: 0.7311 (m-10) REVERT: A 271 ASP cc_start: 0.7549 (m-30) cc_final: 0.7211 (m-30) REVERT: A 283 MET cc_start: 0.7570 (tpp) cc_final: 0.7329 (tpp) REVERT: A 286 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8674 (mmmm) REVERT: A 292 PHE cc_start: 0.8099 (m-10) cc_final: 0.7732 (m-10) REVERT: A 348 ASP cc_start: 0.5887 (OUTLIER) cc_final: 0.5643 (p0) REVERT: A 361 TYR cc_start: 0.8075 (t80) cc_final: 0.7497 (t80) REVERT: A 369 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8098 (mptt) REVERT: A 376 ASP cc_start: 0.7961 (t0) cc_final: 0.7733 (t0) REVERT: A 430 ILE cc_start: 0.8923 (mm) cc_final: 0.8566 (mm) REVERT: A 440 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.6703 (ptt90) REVERT: A 443 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7338 (tm-30) REVERT: A 473 LYS cc_start: 0.8426 (mtpt) cc_final: 0.7951 (mppt) REVERT: A 499 LEU cc_start: 0.9096 (tp) cc_final: 0.8724 (tt) REVERT: A 513 VAL cc_start: 0.9125 (t) cc_final: 0.8870 (p) REVERT: A 517 SER cc_start: 0.8433 (p) cc_final: 0.8126 (p) REVERT: A 535 HIS cc_start: 0.7272 (m90) cc_final: 0.7045 (m-70) REVERT: A 563 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8485 (tppp) REVERT: A 677 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7630 (ttp-170) REVERT: A 696 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7216 (mm-40) REVERT: A 697 ASP cc_start: 0.7428 (t0) cc_final: 0.7114 (t0) REVERT: A 701 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 715 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7803 (tppt) REVERT: A 732 GLN cc_start: 0.8028 (pp30) cc_final: 0.7655 (pp30) REVERT: B 134 ARG cc_start: 0.7104 (mtm180) cc_final: 0.6848 (mtm-85) REVERT: B 185 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7709 (mmt90) REVERT: B 196 VAL cc_start: 0.7972 (t) cc_final: 0.7635 (m) REVERT: B 198 ILE cc_start: 0.8653 (tp) cc_final: 0.8222 (tp) REVERT: B 199 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7875 (mt) REVERT: B 203 PHE cc_start: 0.8084 (m-80) cc_final: 0.7667 (m-80) REVERT: B 207 GLN cc_start: 0.8747 (tm130) cc_final: 0.8478 (tm-30) REVERT: B 237 LYS cc_start: 0.8871 (pttt) cc_final: 0.8371 (ptpp) REVERT: B 240 LEU cc_start: 0.8780 (tp) cc_final: 0.8552 (tp) REVERT: B 262 GLN cc_start: 0.8222 (tp40) cc_final: 0.7801 (tp-100) REVERT: B 466 CYS cc_start: 0.7818 (t) cc_final: 0.7532 (t) REVERT: B 470 ARG cc_start: 0.7043 (ptt-90) cc_final: 0.6764 (ptt-90) REVERT: B 478 ASP cc_start: 0.8031 (p0) cc_final: 0.7705 (p0) REVERT: B 488 MET cc_start: 0.7322 (tpp) cc_final: 0.6348 (tpp) REVERT: B 492 LEU cc_start: 0.8557 (mt) cc_final: 0.7617 (mt) REVERT: B 512 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: B 526 SER cc_start: 0.9025 (m) cc_final: 0.8800 (p) REVERT: B 579 ASN cc_start: 0.8587 (p0) cc_final: 0.8225 (p0) REVERT: B 586 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7668 (mmm160) REVERT: B 589 GLN cc_start: 0.8832 (tp40) cc_final: 0.8483 (tp40) REVERT: B 591 LEU cc_start: 0.8809 (mt) cc_final: 0.8580 (mt) REVERT: B 677 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7827 (tpp80) REVERT: B 681 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8404 (ttpp) REVERT: B 714 ARG cc_start: 0.7566 (mtm-85) cc_final: 0.6955 (mtm-85) REVERT: B 724 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7923 (t0) outliers start: 45 outliers final: 36 residues processed: 317 average time/residue: 0.2444 time to fit residues: 103.7605 Evaluate side-chains 330 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 724 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.0470 chunk 15 optimal weight: 0.0570 chunk 29 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.113496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095683 restraints weight = 22844.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099027 restraints weight = 12614.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.101358 restraints weight = 7942.284| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10395 Z= 0.208 Angle : 0.742 13.803 14128 Z= 0.369 Chirality : 0.045 0.292 1716 Planarity : 0.005 0.057 1757 Dihedral : 6.540 86.456 1440 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.65 % Allowed : 24.31 % Favored : 72.04 % 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: -0.44 (0.24), residues: 1319 helix: 0.72 (0.18), residues: 835 sheet: -0.18 (1.13), residues: 29 loop : -2.24 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 74 HIS 0.016 0.002 HIS A 728 PHE 0.042 0.001 PHE A 121 TYR 0.028 0.001 TYR B 578 ARG 0.013 0.001 ARG B 440 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2712.98 seconds wall clock time: 48 minutes 49.54 seconds (2929.54 seconds total)