Starting phenix.real_space_refine on Mon Jun 9 03:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wl9_32578/06_2025/7wl9_32578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wl9_32578/06_2025/7wl9_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/cci-nas-00/data/ceres_data/7wl9_32578/06_2025/7wl9_32578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wl9_32578/06_2025/7wl9_32578.map" model { file = "/net/cci-nas-00/data/ceres_data/7wl9_32578/06_2025/7wl9_32578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wl9_32578/06_2025/7wl9_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 6.71, per 1000 atoms: 0.66 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 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: 1.08 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: 3.24 Time building geometry restraints manager: 2.89 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: 2.180 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.330 Find NCS groups from input model: 0.710 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- 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= 0.105 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 Details of bonding type rmsd hydrogen bonds : bond 0.23322 ( 572) hydrogen bonds : angle 6.95843 ( 1671) covalent geometry : bond 0.00183 (10395) covalent geometry : angle 0.49354 (14128) *********************** 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 to be fit. rotamer outliers: 48 poor density : 359 time to evaluate : 1.084 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: 0.2626 time to fit residues: 137.1033 Evaluate side-chains 304 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 285 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.115488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098076 restraints weight = 22707.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101434 restraints weight = 12601.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.103661 restraints weight = 7952.835| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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= 0.174 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 Details of bonding type rmsd hydrogen bonds : bond 0.04720 ( 572) hydrogen bonds : angle 4.24243 ( 1671) covalent geometry : bond 0.00363 (10395) covalent geometry : angle 0.66625 (14128) *********************** 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 to be fit. rotamer outliers: 57 poor density : 307 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8473 (t80) cc_final: 0.8153 (t80) REVERT: A 66 LYS cc_start: 0.8956 (tppt) cc_final: 0.8634 (tptm) REVERT: A 97 VAL cc_start: 0.8634 (t) cc_final: 0.8416 (p) REVERT: A 145 SER cc_start: 0.8429 (m) cc_final: 0.7869 (p) REVERT: A 160 HIS cc_start: 0.7021 (t-90) cc_final: 0.6779 (t-90) REVERT: A 182 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7213 (t0) REVERT: A 195 LEU cc_start: 0.8523 (tp) cc_final: 0.7872 (tp) REVERT: A 199 ILE cc_start: 0.8879 (mt) cc_final: 0.8592 (tp) REVERT: A 217 ASP cc_start: 0.8072 (t0) cc_final: 0.7763 (t0) REVERT: A 236 LEU cc_start: 0.8466 (tp) cc_final: 0.8251 (mp) REVERT: A 259 GLU cc_start: 0.8138 (tt0) cc_final: 0.7705 (tt0) REVERT: A 262 GLN cc_start: 0.8152 (mt0) cc_final: 0.7949 (tp40) REVERT: A 271 ASP cc_start: 0.7847 (m-30) cc_final: 0.7542 (m-30) REVERT: A 277 LEU cc_start: 0.8363 (tt) cc_final: 0.8141 (pp) REVERT: A 283 MET cc_start: 0.7965 (tpp) cc_final: 0.7127 (tpp) REVERT: A 292 PHE cc_start: 0.8120 (m-10) cc_final: 0.7723 (m-10) REVERT: A 361 TYR cc_start: 0.8047 (t80) cc_final: 0.7538 (t80) REVERT: A 369 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8085 (mptt) REVERT: A 371 TYR cc_start: 0.8239 (m-80) cc_final: 0.7944 (m-80) REVERT: A 429 VAL cc_start: 0.8817 (t) cc_final: 0.8558 (m) REVERT: A 430 ILE cc_start: 0.8699 (mm) cc_final: 0.8475 (mm) REVERT: A 440 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.6434 (ptt-90) REVERT: A 443 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 461 MET cc_start: 0.8199 (mtm) cc_final: 0.7812 (ptp) REVERT: A 473 LYS cc_start: 0.8631 (mtpt) cc_final: 0.7983 (mmtm) REVERT: A 488 MET cc_start: 0.8201 (tpp) cc_final: 0.7710 (tpp) REVERT: A 499 LEU cc_start: 0.8991 (tp) cc_final: 0.8412 (tt) REVERT: A 563 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8371 (tppp) REVERT: A 580 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8459 (mmmm) REVERT: A 677 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7812 (ttp-170) REVERT: A 701 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 704 GLU cc_start: 0.7622 (tt0) cc_final: 0.7353 (tt0) REVERT: A 715 LYS cc_start: 0.8378 (mmtt) cc_final: 0.8096 (tppt) REVERT: B 37 GLU cc_start: 0.7707 (pt0) cc_final: 0.7092 (pm20) REVERT: B 38 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8170 (mmm160) REVERT: B 128 PHE cc_start: 0.7038 (t80) cc_final: 0.6360 (t80) REVERT: B 188 LEU cc_start: 0.8685 (tp) cc_final: 0.8466 (tp) REVERT: B 199 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7895 (pt) REVERT: B 207 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 230 GLN cc_start: 0.7722 (tp40) cc_final: 0.7140 (tm-30) REVERT: B 235 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7937 (mm-40) REVERT: B 237 LYS cc_start: 0.8885 (pttt) cc_final: 0.8584 (pttt) REVERT: B 262 GLN cc_start: 0.8509 (tp40) cc_final: 0.8050 (tp-100) REVERT: B 283 MET cc_start: 0.8010 (ptp) cc_final: 0.7591 (mpp) REVERT: B 302 ILE cc_start: 0.8513 (tp) cc_final: 0.8046 (tp) REVERT: B 398 PHE cc_start: 0.7221 (m-80) cc_final: 0.6993 (m-80) REVERT: B 404 THR cc_start: 0.6360 (OUTLIER) cc_final: 0.5741 (t) REVERT: B 463 MET cc_start: 0.7653 (mmm) cc_final: 0.7375 (mmm) REVERT: B 477 THR cc_start: 0.8567 (m) cc_final: 0.8352 (t) REVERT: B 478 ASP cc_start: 0.8161 (p0) cc_final: 0.7771 (p0) REVERT: B 488 MET cc_start: 0.7726 (tpp) cc_final: 0.6785 (tpp) REVERT: B 492 LEU cc_start: 0.8944 (mt) cc_final: 0.8243 (mt) REVERT: B 495 ASP cc_start: 0.7883 (t0) cc_final: 0.7616 (t0) REVERT: B 512 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8221 (mtm-85) REVERT: B 519 ASN cc_start: 0.7832 (p0) cc_final: 0.7616 (p0) REVERT: B 526 SER cc_start: 0.8823 (m) cc_final: 0.8420 (p) REVERT: B 538 ASN cc_start: 0.7543 (p0) cc_final: 0.6901 (p0) REVERT: B 540 GLU cc_start: 0.7761 (pm20) cc_final: 0.7454 (pm20) REVERT: B 549 ARG cc_start: 0.7813 (ttt180) cc_final: 0.7543 (ttm-80) REVERT: B 573 ASP cc_start: 0.8373 (t0) cc_final: 0.8098 (p0) REVERT: B 586 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7856 (mmp80) REVERT: B 587 ARG cc_start: 0.8609 (mmm160) cc_final: 0.8387 (mmm160) REVERT: B 591 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8651 (mt) REVERT: B 682 GLU cc_start: 0.8330 (tp30) cc_final: 0.7690 (tp30) REVERT: B 724 ASP cc_start: 0.8225 (m-30) cc_final: 0.7988 (t0) outliers start: 57 outliers final: 33 residues processed: 340 average time/residue: 0.2415 time to fit residues: 111.6613 Evaluate side-chains 304 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 266 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 93 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 382 ASN ** 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 538 ASN ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095329 restraints weight = 23077.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098833 restraints weight = 12501.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101174 restraints weight = 7752.321| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10395 Z= 0.179 Angle : 0.669 12.746 14128 Z= 0.341 Chirality : 0.043 0.154 1716 Planarity : 0.004 0.046 1757 Dihedral : 6.478 86.774 1448 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 5.25 % Allowed : 15.67 % Favored : 79.07 % 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: -1.21 (0.23), residues: 1319 helix: 0.29 (0.18), residues: 833 sheet: -1.68 (1.00), residues: 34 loop : -2.86 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 472 HIS 0.008 0.001 HIS A 728 PHE 0.013 0.001 PHE A 484 TYR 0.021 0.002 TYR A 530 ARG 0.008 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 572) hydrogen bonds : angle 4.07507 ( 1671) covalent geometry : bond 0.00376 (10395) covalent geometry : angle 0.66887 (14128) *********************** 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 350 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 291 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PHE cc_start: 0.8540 (t80) cc_final: 0.8192 (t80) REVERT: A 66 LYS cc_start: 0.8987 (tppt) cc_final: 0.7800 (tptp) REVERT: A 97 VAL cc_start: 0.8675 (t) cc_final: 0.8447 (p) REVERT: A 145 SER cc_start: 0.8542 (m) cc_final: 0.7952 (p) REVERT: A 160 HIS cc_start: 0.7066 (t-90) cc_final: 0.6810 (t-90) REVERT: A 195 LEU cc_start: 0.8604 (tp) cc_final: 0.8122 (tp) REVERT: A 199 ILE cc_start: 0.8913 (mt) cc_final: 0.8597 (tp) REVERT: A 200 GLN cc_start: 0.8216 (mt0) cc_final: 0.7563 (mt0) REVERT: A 217 ASP cc_start: 0.8174 (t0) cc_final: 0.7865 (t0) REVERT: A 259 GLU cc_start: 0.8130 (tt0) cc_final: 0.7735 (tt0) REVERT: A 261 PHE cc_start: 0.7968 (m-10) cc_final: 0.7598 (m-10) REVERT: A 262 GLN cc_start: 0.8231 (mt0) cc_final: 0.7989 (tp40) REVERT: A 271 ASP cc_start: 0.7881 (m-30) cc_final: 0.7515 (m-30) REVERT: A 277 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8192 (pp) REVERT: A 283 MET cc_start: 0.7980 (tpp) cc_final: 0.7115 (tpp) REVERT: A 292 PHE cc_start: 0.8137 (m-10) cc_final: 0.7753 (m-10) REVERT: A 361 TYR cc_start: 0.8123 (t80) cc_final: 0.7381 (t80) REVERT: A 369 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8058 (mptt) REVERT: A 371 TYR cc_start: 0.8356 (m-80) cc_final: 0.8063 (m-80) REVERT: A 376 ASP cc_start: 0.8428 (t0) cc_final: 0.8125 (t0) REVERT: A 429 VAL cc_start: 0.8895 (t) cc_final: 0.8670 (m) REVERT: A 430 ILE cc_start: 0.8818 (mm) cc_final: 0.8603 (mm) REVERT: A 440 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6650 (ptt90) REVERT: A 443 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 473 LYS cc_start: 0.8629 (mtpt) cc_final: 0.7998 (mppt) REVERT: A 484 PHE cc_start: 0.8949 (t80) cc_final: 0.8492 (t80) REVERT: A 488 MET cc_start: 0.8314 (tpp) cc_final: 0.7966 (tpp) REVERT: A 513 VAL cc_start: 0.9115 (t) cc_final: 0.8859 (p) REVERT: A 517 SER cc_start: 0.8470 (p) cc_final: 0.7992 (p) REVERT: A 535 HIS cc_start: 0.7197 (m90) cc_final: 0.6761 (m170) REVERT: A 563 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8377 (tppp) REVERT: A 580 LYS cc_start: 0.8834 (mmtt) cc_final: 0.8363 (mmtm) REVERT: A 677 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7908 (ttp-110) REVERT: A 691 TYR cc_start: 0.7801 (m-10) cc_final: 0.7492 (m-10) REVERT: A 701 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 704 GLU cc_start: 0.7600 (tt0) cc_final: 0.7280 (tt0) REVERT: A 715 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8123 (tppt) REVERT: B 38 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8247 (mmm160) REVERT: B 39 ARG cc_start: 0.7091 (ttm170) cc_final: 0.6397 (ttm110) REVERT: B 128 PHE cc_start: 0.7166 (t80) cc_final: 0.6489 (t80) REVERT: B 134 ARG cc_start: 0.7134 (mtm180) cc_final: 0.6851 (mtm-85) REVERT: B 185 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7346 (mtt180) REVERT: B 199 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7933 (mt) REVERT: B 203 PHE cc_start: 0.8047 (m-80) cc_final: 0.7590 (m-80) REVERT: B 207 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 235 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8001 (mm-40) REVERT: B 237 LYS cc_start: 0.8940 (pttt) cc_final: 0.8532 (pttt) REVERT: B 262 GLN cc_start: 0.8547 (tp40) cc_final: 0.8071 (tp-100) REVERT: B 287 GLU cc_start: 0.7777 (pp20) cc_final: 0.7348 (pp20) REVERT: B 305 ILE cc_start: 0.8920 (mt) cc_final: 0.8699 (mm) REVERT: B 375 HIS cc_start: 0.5917 (t-90) cc_final: 0.5635 (t-90) REVERT: B 398 PHE cc_start: 0.7289 (m-80) cc_final: 0.7046 (m-80) REVERT: B 463 MET cc_start: 0.7703 (mmm) cc_final: 0.7399 (mmm) REVERT: B 477 THR cc_start: 0.8608 (m) cc_final: 0.8278 (t) REVERT: B 478 ASP cc_start: 0.8229 (p0) cc_final: 0.7822 (p0) REVERT: B 488 MET cc_start: 0.7721 (tpp) cc_final: 0.6776 (tpp) REVERT: B 492 LEU cc_start: 0.8883 (mt) cc_final: 0.8183 (mt) REVERT: B 495 ASP cc_start: 0.7907 (t0) cc_final: 0.7679 (t0) REVERT: B 512 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.7962 (mtm-85) REVERT: B 519 ASN cc_start: 0.8095 (p0) cc_final: 0.7661 (p0) REVERT: B 526 SER cc_start: 0.8994 (m) cc_final: 0.8726 (p) REVERT: B 540 GLU cc_start: 0.7743 (pm20) cc_final: 0.7473 (pm20) REVERT: B 549 ARG cc_start: 0.7758 (ttt180) cc_final: 0.7441 (ttm-80) REVERT: B 579 ASN cc_start: 0.8845 (p0) cc_final: 0.8562 (p0) REVERT: B 586 ARG cc_start: 0.8264 (mmp80) cc_final: 0.7911 (mmp80) REVERT: B 677 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7480 (tpp80) REVERT: B 682 GLU cc_start: 0.8292 (tp30) cc_final: 0.7635 (tp30) REVERT: B 713 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6982 (mt) REVERT: B 724 ASP cc_start: 0.8331 (m-30) cc_final: 0.8079 (t0) outliers start: 59 outliers final: 39 residues processed: 320 average time/residue: 0.2466 time to fit residues: 106.6583 Evaluate side-chains 323 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 A residue 696 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 207 GLN ** B 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095895 restraints weight = 22650.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.099338 restraints weight = 12479.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101703 restraints weight = 7880.877| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10395 Z= 0.142 Angle : 0.645 12.820 14128 Z= 0.329 Chirality : 0.043 0.154 1716 Planarity : 0.004 0.043 1757 Dihedral : 6.544 87.077 1447 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.97 % Allowed : 16.92 % Favored : 77.11 % 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: -0.76 (0.23), residues: 1319 helix: 0.68 (0.18), residues: 816 sheet: -1.11 (1.08), residues: 29 loop : -2.63 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.015 0.002 HIS A 375 PHE 0.019 0.001 PHE A 128 TYR 0.018 0.001 TYR B 530 ARG 0.009 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 572) hydrogen bonds : angle 3.94898 ( 1671) covalent geometry : bond 0.00306 (10395) covalent geometry : angle 0.64517 (14128) *********************** 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 361 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLU cc_start: 0.7810 (tp30) cc_final: 0.7521 (tp30) REVERT: A 62 PHE cc_start: 0.8479 (t80) cc_final: 0.8142 (t80) REVERT: A 66 LYS cc_start: 0.8943 (tppt) cc_final: 0.7908 (tptp) REVERT: A 97 VAL cc_start: 0.8604 (t) cc_final: 0.8402 (p) REVERT: A 125 LEU cc_start: 0.8847 (mt) cc_final: 0.8631 (mp) REVERT: A 145 SER cc_start: 0.8534 (m) cc_final: 0.7975 (p) REVERT: A 160 HIS cc_start: 0.7028 (t-90) cc_final: 0.6801 (t-90) REVERT: A 195 LEU cc_start: 0.8635 (tp) cc_final: 0.7989 (tt) REVERT: A 199 ILE cc_start: 0.8910 (mt) cc_final: 0.8602 (tp) REVERT: A 200 GLN cc_start: 0.8221 (mt0) cc_final: 0.7595 (mt0) REVERT: A 217 ASP cc_start: 0.8158 (t0) cc_final: 0.7895 (t0) REVERT: A 248 ASN cc_start: 0.7591 (t0) cc_final: 0.7384 (t0) REVERT: A 259 GLU cc_start: 0.8141 (tt0) cc_final: 0.7728 (tt0) REVERT: A 261 PHE cc_start: 0.7947 (m-10) cc_final: 0.7608 (m-10) REVERT: A 262 GLN cc_start: 0.8194 (mt0) cc_final: 0.7950 (tp40) REVERT: A 271 ASP cc_start: 0.7816 (m-30) cc_final: 0.7413 (m-30) REVERT: A 277 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8193 (pp) REVERT: A 283 MET cc_start: 0.7950 (tpp) cc_final: 0.7571 (tpp) REVERT: A 286 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8687 (mmmm) REVERT: A 292 PHE cc_start: 0.8156 (m-10) cc_final: 0.7778 (m-10) REVERT: A 361 TYR cc_start: 0.8072 (t80) cc_final: 0.7329 (t80) REVERT: A 369 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8051 (mptt) REVERT: A 371 TYR cc_start: 0.8357 (m-80) cc_final: 0.7964 (m-80) REVERT: A 376 ASP cc_start: 0.8156 (t0) cc_final: 0.7810 (t0) REVERT: A 429 VAL cc_start: 0.8885 (t) cc_final: 0.8655 (m) REVERT: A 430 ILE cc_start: 0.8858 (mm) cc_final: 0.8581 (mm) REVERT: A 440 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6151 (ttp-170) REVERT: A 443 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 473 LYS cc_start: 0.8580 (mtpt) cc_final: 0.7967 (mppt) REVERT: A 484 PHE cc_start: 0.8932 (t80) cc_final: 0.8681 (t80) REVERT: A 488 MET cc_start: 0.8266 (tpp) cc_final: 0.7845 (tpp) REVERT: A 513 VAL cc_start: 0.9068 (t) cc_final: 0.8788 (p) REVERT: A 517 SER cc_start: 0.8445 (p) cc_final: 0.8020 (p) REVERT: A 535 HIS cc_start: 0.7187 (m90) cc_final: 0.6768 (m170) REVERT: A 537 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7686 (mtpp) REVERT: A 563 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8551 (tppp) REVERT: A 580 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8528 (mmtm) REVERT: A 677 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7869 (ttp-110) REVERT: A 691 TYR cc_start: 0.7723 (m-80) cc_final: 0.7468 (m-10) REVERT: A 701 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 704 GLU cc_start: 0.7517 (tt0) cc_final: 0.7186 (tt0) REVERT: A 715 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8095 (tppt) REVERT: B 38 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8196 (mmm160) REVERT: B 39 ARG cc_start: 0.7155 (ttm170) cc_final: 0.6435 (ttm110) REVERT: B 118 TYR cc_start: 0.7104 (m-80) cc_final: 0.6859 (m-80) REVERT: B 128 PHE cc_start: 0.7204 (t80) cc_final: 0.6540 (t80) REVERT: B 134 ARG cc_start: 0.7125 (mtm180) cc_final: 0.6791 (mtm-85) REVERT: B 185 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7400 (mtt180) REVERT: B 198 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8263 (tp) REVERT: B 199 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7947 (mt) REVERT: B 203 PHE cc_start: 0.8123 (m-80) cc_final: 0.7700 (m-80) REVERT: B 207 GLN cc_start: 0.8364 (tm130) cc_final: 0.7505 (tm-30) REVERT: B 230 GLN cc_start: 0.7805 (tp40) cc_final: 0.7212 (tm-30) REVERT: B 235 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7963 (mm-40) REVERT: B 237 LYS cc_start: 0.8918 (pttt) cc_final: 0.8444 (pttp) REVERT: B 262 GLN cc_start: 0.8489 (tp40) cc_final: 0.7998 (tp-100) REVERT: B 287 GLU cc_start: 0.7772 (pp20) cc_final: 0.7279 (pp20) REVERT: B 292 PHE cc_start: 0.8124 (m-10) cc_final: 0.7839 (m-10) REVERT: B 305 ILE cc_start: 0.8871 (mt) cc_final: 0.8658 (mm) REVERT: B 375 HIS cc_start: 0.5981 (t-90) cc_final: 0.5694 (t-90) REVERT: B 398 PHE cc_start: 0.7298 (m-80) cc_final: 0.6998 (m-80) REVERT: B 463 MET cc_start: 0.7623 (mmm) cc_final: 0.7343 (mmm) REVERT: B 470 ARG cc_start: 0.7151 (ptp-170) cc_final: 0.6921 (ptt-90) REVERT: B 477 THR cc_start: 0.8591 (m) cc_final: 0.8366 (t) REVERT: B 478 ASP cc_start: 0.8202 (p0) cc_final: 0.7759 (p0) REVERT: B 488 MET cc_start: 0.7682 (tpp) cc_final: 0.6701 (tpp) REVERT: B 492 LEU cc_start: 0.8869 (mt) cc_final: 0.8129 (mt) REVERT: B 519 ASN cc_start: 0.8151 (p0) cc_final: 0.7699 (p0) REVERT: B 526 SER cc_start: 0.8985 (m) cc_final: 0.8733 (p) REVERT: B 549 ARG cc_start: 0.7755 (ttt180) cc_final: 0.7460 (ttm-80) REVERT: B 579 ASN cc_start: 0.8795 (p0) cc_final: 0.8480 (p0) REVERT: B 586 ARG cc_start: 0.8215 (mmp80) cc_final: 0.7838 (mmp80) REVERT: B 682 GLU cc_start: 0.8270 (tp30) cc_final: 0.7602 (tp30) outliers start: 67 outliers final: 45 residues processed: 330 average time/residue: 0.2467 time to fit residues: 110.7884 Evaluate side-chains 330 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 696 GLN Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 126 THR 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 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 462 PHE 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 678 MET Chi-restraints excluded: chain B residue 681 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 703 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.111936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093934 restraints weight = 22585.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097299 restraints weight = 12514.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.099287 restraints weight = 7904.762| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10395 Z= 0.181 Angle : 0.675 11.691 14128 Z= 0.344 Chirality : 0.044 0.272 1716 Planarity : 0.004 0.048 1757 Dihedral : 6.477 86.529 1443 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 4.90 % Allowed : 19.15 % Favored : 75.96 % 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: -0.80 (0.23), residues: 1319 helix: 0.66 (0.18), residues: 832 sheet: -1.07 (1.05), residues: 29 loop : -2.81 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.010 0.002 HIS A 375 PHE 0.016 0.001 PHE A 130 TYR 0.018 0.002 TYR A 556 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 572) hydrogen bonds : angle 3.97733 ( 1671) covalent geometry : bond 0.00382 (10395) covalent geometry : angle 0.67458 (14128) *********************** 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 351 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 296 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.9046 (tppt) cc_final: 0.8078 (tptp) REVERT: A 113 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 125 LEU cc_start: 0.8885 (mt) cc_final: 0.8676 (mp) REVERT: A 145 SER cc_start: 0.8591 (m) cc_final: 0.8047 (p) REVERT: A 160 HIS cc_start: 0.7037 (t-90) cc_final: 0.6815 (t-90) REVERT: A 195 LEU cc_start: 0.8636 (tp) cc_final: 0.7933 (tt) REVERT: A 199 ILE cc_start: 0.8914 (mt) cc_final: 0.8617 (tp) REVERT: A 200 GLN cc_start: 0.8174 (mt0) cc_final: 0.7586 (mt0) REVERT: A 217 ASP cc_start: 0.8205 (t0) cc_final: 0.7925 (t0) REVERT: A 259 GLU cc_start: 0.8281 (tt0) cc_final: 0.7830 (tt0) REVERT: A 261 PHE cc_start: 0.8004 (m-10) cc_final: 0.7602 (m-10) REVERT: A 262 GLN cc_start: 0.8268 (mt0) cc_final: 0.7974 (tp40) REVERT: A 271 ASP cc_start: 0.7848 (m-30) cc_final: 0.7485 (m-30) REVERT: A 277 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 283 MET cc_start: 0.7973 (tpp) cc_final: 0.7617 (tpp) REVERT: A 286 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8675 (mmmm) REVERT: A 292 PHE cc_start: 0.8201 (m-10) cc_final: 0.7818 (m-10) REVERT: A 361 TYR cc_start: 0.8102 (t80) cc_final: 0.7347 (t80) REVERT: A 369 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8069 (mptt) REVERT: A 376 ASP cc_start: 0.8116 (t0) cc_final: 0.7769 (t0) REVERT: A 421 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7339 (mm110) REVERT: A 425 LEU cc_start: 0.8875 (mm) cc_final: 0.8463 (mm) REVERT: A 429 VAL cc_start: 0.8901 (t) cc_final: 0.8674 (m) REVERT: A 430 ILE cc_start: 0.8894 (mm) cc_final: 0.8576 (mm) REVERT: A 440 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.6758 (ptt90) REVERT: A 443 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 473 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8006 (mppt) REVERT: A 484 PHE cc_start: 0.8957 (t80) cc_final: 0.8740 (t80) REVERT: A 488 MET cc_start: 0.8276 (tpp) cc_final: 0.7865 (tpp) REVERT: A 513 VAL cc_start: 0.9122 (t) cc_final: 0.8814 (p) REVERT: A 517 SER cc_start: 0.8483 (p) cc_final: 0.8126 (p) REVERT: A 535 HIS cc_start: 0.7324 (m90) cc_final: 0.6895 (m170) REVERT: A 537 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7547 (ttpp) REVERT: A 563 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8552 (tppp) REVERT: A 580 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8523 (mmtm) REVERT: A 677 ARG cc_start: 0.8218 (ttp80) cc_final: 0.7790 (ttp-170) REVERT: A 691 TYR cc_start: 0.7818 (m-80) cc_final: 0.7569 (m-10) REVERT: A 701 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 704 GLU cc_start: 0.7566 (tt0) cc_final: 0.7247 (tt0) REVERT: A 715 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8061 (tppt) REVERT: A 732 GLN cc_start: 0.8040 (pp30) cc_final: 0.7691 (pp30) REVERT: B 38 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8198 (mmm160) REVERT: B 39 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6456 (ttm110) REVERT: B 89 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8691 (tp) REVERT: B 128 PHE cc_start: 0.7336 (t80) cc_final: 0.6628 (t80) REVERT: B 134 ARG cc_start: 0.7135 (mtm180) cc_final: 0.6820 (mtm-85) REVERT: B 185 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7439 (mtt180) REVERT: B 198 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8370 (tp) REVERT: B 199 ILE cc_start: 0.8330 (mp) cc_final: 0.7998 (mt) REVERT: B 203 PHE cc_start: 0.8168 (m-80) cc_final: 0.7733 (m-80) REVERT: B 207 GLN cc_start: 0.8448 (tm130) cc_final: 0.7586 (tm-30) REVERT: B 230 GLN cc_start: 0.7718 (tp40) cc_final: 0.7196 (tm-30) REVERT: B 235 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8059 (mm-40) REVERT: B 237 LYS cc_start: 0.8936 (pttt) cc_final: 0.8461 (pttp) REVERT: B 240 LEU cc_start: 0.9133 (tp) cc_final: 0.8791 (tp) REVERT: B 262 GLN cc_start: 0.8547 (tp40) cc_final: 0.8053 (tp-100) REVERT: B 283 MET cc_start: 0.8153 (ptp) cc_final: 0.7683 (mpp) REVERT: B 292 PHE cc_start: 0.8101 (m-10) cc_final: 0.7845 (m-10) REVERT: B 305 ILE cc_start: 0.8914 (mt) cc_final: 0.8704 (mm) REVERT: B 375 HIS cc_start: 0.6081 (t-90) cc_final: 0.5863 (t-90) REVERT: B 398 PHE cc_start: 0.7310 (m-80) cc_final: 0.6986 (m-80) REVERT: B 463 MET cc_start: 0.7675 (mmm) cc_final: 0.7251 (mmm) REVERT: B 470 ARG cc_start: 0.7207 (ptp-170) cc_final: 0.6915 (ptt-90) REVERT: B 472 TRP cc_start: 0.8630 (t-100) cc_final: 0.8248 (t-100) REVERT: B 477 THR cc_start: 0.8741 (m) cc_final: 0.8441 (t) REVERT: B 478 ASP cc_start: 0.8235 (p0) cc_final: 0.7921 (p0) REVERT: B 488 MET cc_start: 0.7684 (tpp) cc_final: 0.6665 (tpp) REVERT: B 492 LEU cc_start: 0.8847 (mt) cc_final: 0.8045 (mt) REVERT: B 512 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8071 (mtm110) REVERT: B 519 ASN cc_start: 0.8257 (p0) cc_final: 0.7777 (p0) REVERT: B 526 SER cc_start: 0.9056 (m) cc_final: 0.8783 (p) REVERT: B 549 ARG cc_start: 0.7839 (ttt180) cc_final: 0.7537 (ttm-80) REVERT: B 579 ASN cc_start: 0.8795 (p0) cc_final: 0.8481 (p0) REVERT: B 586 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7954 (mmm160) REVERT: B 682 GLU cc_start: 0.8261 (tp30) cc_final: 0.7541 (tp30) REVERT: B 724 ASP cc_start: 0.8374 (m-30) cc_final: 0.8114 (t0) outliers start: 55 outliers final: 43 residues processed: 326 average time/residue: 0.2605 time to fit residues: 115.3072 Evaluate side-chains 336 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 277 LEU 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 A residue 696 GLN Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 126 THR 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 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 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 694 LEU Chi-restraints excluded: chain B residue 703 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 79 optimal weight: 0.0570 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.5696 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.112593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094519 restraints weight = 22792.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097934 restraints weight = 12621.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.100145 restraints weight = 7949.592| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10395 Z= 0.155 Angle : 0.676 12.270 14128 Z= 0.342 Chirality : 0.044 0.272 1716 Planarity : 0.004 0.046 1757 Dihedral : 6.496 86.645 1441 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.34 % Allowed : 19.77 % Favored : 74.89 % 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: -0.67 (0.23), residues: 1319 helix: 0.73 (0.18), residues: 825 sheet: -0.93 (1.06), residues: 29 loop : -2.64 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 83 HIS 0.019 0.002 HIS A 135 PHE 0.017 0.001 PHE A 346 TYR 0.018 0.002 TYR A 556 ARG 0.011 0.000 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 572) hydrogen bonds : angle 3.93603 ( 1671) covalent geometry : bond 0.00336 (10395) covalent geometry : angle 0.67613 (14128) *********************** 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 353 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.9012 (tppt) cc_final: 0.8379 (tptm) REVERT: A 113 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8286 (p) REVERT: A 145 SER cc_start: 0.8552 (m) cc_final: 0.7995 (p) REVERT: A 160 HIS cc_start: 0.6935 (t-90) cc_final: 0.6726 (t-90) REVERT: A 195 LEU cc_start: 0.8666 (tp) cc_final: 0.7944 (tt) REVERT: A 199 ILE cc_start: 0.8894 (mt) cc_final: 0.8445 (tp) REVERT: A 200 GLN cc_start: 0.8202 (mt0) cc_final: 0.7612 (mt0) REVERT: A 202 VAL cc_start: 0.9118 (t) cc_final: 0.8876 (p) REVERT: A 217 ASP cc_start: 0.8202 (t0) cc_final: 0.7921 (t0) REVERT: A 259 GLU cc_start: 0.8264 (tt0) cc_final: 0.7957 (tt0) REVERT: A 262 GLN cc_start: 0.8266 (mt0) cc_final: 0.7882 (tp-100) REVERT: A 271 ASP cc_start: 0.7842 (m-30) cc_final: 0.7466 (m-30) REVERT: A 278 THR cc_start: 0.8937 (p) cc_final: 0.8723 (p) REVERT: A 283 MET cc_start: 0.7961 (tpp) cc_final: 0.7640 (tpp) REVERT: A 286 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8666 (mmmm) REVERT: A 292 PHE cc_start: 0.8205 (m-10) cc_final: 0.7819 (m-10) REVERT: A 361 TYR cc_start: 0.8088 (t80) cc_final: 0.7330 (t80) REVERT: A 369 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8062 (mptt) REVERT: A 376 ASP cc_start: 0.8069 (t0) cc_final: 0.7670 (t0) REVERT: A 421 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7339 (mm110) REVERT: A 425 LEU cc_start: 0.8852 (mm) cc_final: 0.8586 (mm) REVERT: A 429 VAL cc_start: 0.8918 (t) cc_final: 0.8687 (m) REVERT: A 430 ILE cc_start: 0.8894 (mm) cc_final: 0.8546 (mm) REVERT: A 440 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6243 (ttp-170) REVERT: A 443 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7319 (tm-30) REVERT: A 473 LYS cc_start: 0.8574 (mtpt) cc_final: 0.7962 (mppt) REVERT: A 484 PHE cc_start: 0.8955 (t80) cc_final: 0.8720 (t80) REVERT: A 488 MET cc_start: 0.8250 (tpp) cc_final: 0.7888 (tpp) REVERT: A 513 VAL cc_start: 0.9069 (t) cc_final: 0.8785 (p) REVERT: A 517 SER cc_start: 0.8526 (p) cc_final: 0.8122 (p) REVERT: A 535 HIS cc_start: 0.7307 (m90) cc_final: 0.6883 (m170) REVERT: A 537 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7812 (ttmm) REVERT: A 563 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8538 (tppp) REVERT: A 580 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8394 (mmmm) REVERT: A 677 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7863 (ttp80) REVERT: A 701 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 704 GLU cc_start: 0.7512 (tt0) cc_final: 0.7194 (tt0) REVERT: A 715 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8032 (tppt) REVERT: B 38 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.8174 (mmm160) REVERT: B 39 ARG cc_start: 0.7230 (ttm170) cc_final: 0.6501 (ttm110) REVERT: B 134 ARG cc_start: 0.7092 (mtm180) cc_final: 0.6761 (mtm-85) REVERT: B 185 ARG cc_start: 0.7989 (mtt180) cc_final: 0.7548 (mtt180) REVERT: B 198 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8388 (tp) REVERT: B 199 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7970 (mt) REVERT: B 203 PHE cc_start: 0.8138 (m-80) cc_final: 0.7702 (m-80) REVERT: B 207 GLN cc_start: 0.8494 (tm130) cc_final: 0.8044 (tm-30) REVERT: B 230 GLN cc_start: 0.7716 (tp40) cc_final: 0.7154 (tm-30) REVERT: B 235 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8095 (mm-40) REVERT: B 237 LYS cc_start: 0.8919 (pttt) cc_final: 0.8427 (pttp) REVERT: B 240 LEU cc_start: 0.9115 (tp) cc_final: 0.8765 (tp) REVERT: B 262 GLN cc_start: 0.8504 (tp40) cc_final: 0.8070 (tp-100) REVERT: B 283 MET cc_start: 0.8128 (ptp) cc_final: 0.7647 (mpp) REVERT: B 292 PHE cc_start: 0.8045 (m-10) cc_final: 0.7803 (m-10) REVERT: B 375 HIS cc_start: 0.6056 (t-90) cc_final: 0.5838 (t-90) REVERT: B 398 PHE cc_start: 0.7319 (m-80) cc_final: 0.6947 (m-80) REVERT: B 470 ARG cc_start: 0.7218 (ptp-170) cc_final: 0.6931 (ptt-90) REVERT: B 472 TRP cc_start: 0.8597 (t-100) cc_final: 0.8231 (t-100) REVERT: B 477 THR cc_start: 0.8731 (m) cc_final: 0.8350 (t) REVERT: B 478 ASP cc_start: 0.8227 (p0) cc_final: 0.7711 (p0) REVERT: B 488 MET cc_start: 0.7690 (tpp) cc_final: 0.6634 (tpp) REVERT: B 492 LEU cc_start: 0.8814 (mt) cc_final: 0.7993 (mt) REVERT: B 512 ARG cc_start: 0.8385 (mtm-85) cc_final: 0.8077 (mtm-85) REVERT: B 519 ASN cc_start: 0.8267 (p0) cc_final: 0.7742 (p0) REVERT: B 526 SER cc_start: 0.9062 (m) cc_final: 0.8801 (p) REVERT: B 549 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7526 (ttm-80) REVERT: B 579 ASN cc_start: 0.8795 (p0) cc_final: 0.8458 (p0) REVERT: B 582 LEU cc_start: 0.8939 (tt) cc_final: 0.8391 (tp) REVERT: B 586 ARG cc_start: 0.8210 (mmp80) cc_final: 0.7956 (mmm160) REVERT: B 682 GLU cc_start: 0.8254 (tp30) cc_final: 0.7536 (tp30) outliers start: 60 outliers final: 46 residues processed: 327 average time/residue: 0.2542 time to fit residues: 113.5166 Evaluate side-chains 342 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 292 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 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 A residue 675 SER Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 126 THR 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 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 462 PHE Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.0470 chunk 81 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.112232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094388 restraints weight = 23002.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.097687 restraints weight = 12707.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.099981 restraints weight = 8093.686| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10395 Z= 0.158 Angle : 0.696 12.652 14128 Z= 0.349 Chirality : 0.043 0.271 1716 Planarity : 0.004 0.047 1757 Dihedral : 6.517 86.548 1441 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 5.34 % Allowed : 20.66 % Favored : 74.00 % 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: -0.59 (0.24), residues: 1319 helix: 0.77 (0.18), residues: 826 sheet: -0.15 (1.25), residues: 23 loop : -2.58 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.012 0.001 HIS A 728 PHE 0.025 0.001 PHE A 719 TYR 0.026 0.001 TYR B 578 ARG 0.012 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 572) hydrogen bonds : angle 3.89635 ( 1671) covalent geometry : bond 0.00343 (10395) covalent geometry : angle 0.69626 (14128) *********************** 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 358 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 298 time to evaluate : 0.940 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 145 SER cc_start: 0.8542 (m) cc_final: 0.7993 (p) REVERT: A 160 HIS cc_start: 0.6960 (t-90) cc_final: 0.6754 (t-90) REVERT: A 195 LEU cc_start: 0.8678 (tp) cc_final: 0.7996 (tt) REVERT: A 199 ILE cc_start: 0.8897 (mt) cc_final: 0.8443 (tp) REVERT: A 200 GLN cc_start: 0.8222 (mt0) cc_final: 0.7634 (mt0) REVERT: A 202 VAL cc_start: 0.9127 (t) cc_final: 0.8914 (p) REVERT: A 217 ASP cc_start: 0.8232 (t0) cc_final: 0.7939 (t0) REVERT: A 259 GLU cc_start: 0.8283 (tt0) cc_final: 0.7501 (tt0) REVERT: A 261 PHE cc_start: 0.7942 (m-10) cc_final: 0.7622 (m-10) REVERT: A 262 GLN cc_start: 0.8275 (mt0) cc_final: 0.7910 (tp-100) REVERT: A 271 ASP cc_start: 0.7829 (m-30) cc_final: 0.7422 (m-30) REVERT: A 283 MET cc_start: 0.7933 (tpp) cc_final: 0.7627 (tpp) REVERT: A 286 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8690 (mmmm) REVERT: A 292 PHE cc_start: 0.8194 (m-10) cc_final: 0.7817 (m-10) REVERT: A 361 TYR cc_start: 0.8098 (t80) cc_final: 0.7325 (t80) REVERT: A 369 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8066 (mptt) REVERT: A 376 ASP cc_start: 0.8110 (t0) cc_final: 0.7720 (t0) REVERT: A 421 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7353 (mm110) REVERT: A 429 VAL cc_start: 0.8910 (t) cc_final: 0.8694 (m) REVERT: A 430 ILE cc_start: 0.8909 (mm) cc_final: 0.8552 (mm) REVERT: A 440 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.6222 (ttp-170) REVERT: A 443 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 473 LYS cc_start: 0.8570 (mtpt) cc_final: 0.7976 (mppt) REVERT: A 484 PHE cc_start: 0.8968 (t80) cc_final: 0.8756 (t80) REVERT: A 488 MET cc_start: 0.8254 (tpp) cc_final: 0.7890 (tpp) REVERT: A 517 SER cc_start: 0.8550 (p) cc_final: 0.8150 (p) REVERT: A 521 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 535 HIS cc_start: 0.7324 (m90) cc_final: 0.6850 (m170) REVERT: A 537 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7824 (ttmm) REVERT: A 563 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8548 (tppp) REVERT: A 580 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8420 (mmmm) REVERT: A 677 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7921 (ttp80) REVERT: A 686 ILE cc_start: 0.8884 (pt) cc_final: 0.8445 (mt) REVERT: A 696 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7051 (tp40) REVERT: A 701 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 704 GLU cc_start: 0.7550 (tt0) cc_final: 0.7302 (tt0) REVERT: A 715 LYS cc_start: 0.8498 (mmtt) cc_final: 0.7930 (tppt) REVERT: A 732 GLN cc_start: 0.8082 (pp30) cc_final: 0.7731 (pp30) REVERT: B 38 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.8179 (mmm160) REVERT: B 39 ARG cc_start: 0.7250 (ttm170) cc_final: 0.6533 (ttm110) REVERT: B 89 ILE cc_start: 0.9104 (mm) cc_final: 0.8831 (tp) REVERT: B 134 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6724 (mtm-85) REVERT: B 185 ARG cc_start: 0.8024 (mtt180) cc_final: 0.7598 (mtt180) REVERT: B 196 VAL cc_start: 0.7953 (t) cc_final: 0.7581 (m) REVERT: B 198 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8312 (tp) REVERT: B 199 ILE cc_start: 0.8262 (mp) cc_final: 0.7947 (mt) REVERT: B 203 PHE cc_start: 0.8112 (m-80) cc_final: 0.7707 (m-80) REVERT: B 207 GLN cc_start: 0.8548 (tm130) cc_final: 0.8088 (tm-30) REVERT: B 229 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: B 230 GLN cc_start: 0.7743 (tp40) cc_final: 0.7201 (tm-30) REVERT: B 235 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8178 (mm-40) REVERT: B 237 LYS cc_start: 0.8933 (pttt) cc_final: 0.8434 (pttp) REVERT: B 262 GLN cc_start: 0.8503 (tp40) cc_final: 0.8001 (tp-100) REVERT: B 283 MET cc_start: 0.8120 (ptp) cc_final: 0.7629 (mpp) REVERT: B 292 PHE cc_start: 0.8079 (m-10) cc_final: 0.7852 (m-10) REVERT: B 305 ILE cc_start: 0.8892 (mt) cc_final: 0.8684 (mm) REVERT: B 375 HIS cc_start: 0.6084 (t-90) cc_final: 0.5756 (t-90) REVERT: B 398 PHE cc_start: 0.7339 (m-80) cc_final: 0.6939 (m-80) REVERT: B 470 ARG cc_start: 0.7233 (ptp-170) cc_final: 0.6966 (ptt-90) REVERT: B 472 TRP cc_start: 0.8599 (t-100) cc_final: 0.8244 (t-100) REVERT: B 477 THR cc_start: 0.8730 (m) cc_final: 0.8358 (t) REVERT: B 478 ASP cc_start: 0.8201 (p0) cc_final: 0.7676 (p0) REVERT: B 488 MET cc_start: 0.7723 (tpp) cc_final: 0.6639 (tpp) REVERT: B 492 LEU cc_start: 0.8789 (mt) cc_final: 0.7792 (mt) REVERT: B 512 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: B 519 ASN cc_start: 0.8287 (p0) cc_final: 0.7735 (p0) REVERT: B 526 SER cc_start: 0.9098 (m) cc_final: 0.8833 (p) REVERT: B 549 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7107 (ttm-80) REVERT: B 579 ASN cc_start: 0.8807 (p0) cc_final: 0.8474 (p0) REVERT: B 677 ARG cc_start: 0.8260 (tpp80) cc_final: 0.7715 (tpp80) REVERT: B 682 GLU cc_start: 0.7968 (tp30) cc_final: 0.7634 (tp30) outliers start: 60 outliers final: 47 residues processed: 330 average time/residue: 0.2534 time to fit residues: 113.9499 Evaluate side-chains 346 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 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 311 THR 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 521 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 A residue 675 SER Chi-restraints excluded: chain A residue 696 GLN Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 126 THR 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 202 VAL Chi-restraints excluded: chain B residue 229 PHE 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 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093835 restraints weight = 22802.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.097122 restraints weight = 12673.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.099396 restraints weight = 8068.881| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10395 Z= 0.167 Angle : 0.709 12.828 14128 Z= 0.358 Chirality : 0.044 0.234 1716 Planarity : 0.004 0.048 1757 Dihedral : 6.557 86.468 1441 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.97 % Allowed : 21.02 % Favored : 73.02 % 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: -0.56 (0.23), residues: 1319 helix: 0.75 (0.18), residues: 823 sheet: -0.61 (1.08), residues: 29 loop : -2.45 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.015 0.001 HIS A 728 PHE 0.033 0.001 PHE A 121 TYR 0.036 0.002 TYR B 578 ARG 0.010 0.001 ARG A 685 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 572) hydrogen bonds : angle 3.91477 ( 1671) covalent geometry : bond 0.00363 (10395) covalent geometry : angle 0.70881 (14128) *********************** 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 366 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 299 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.8334 (t80) cc_final: 0.8086 (t80) REVERT: A 125 LEU cc_start: 0.8913 (mp) cc_final: 0.8709 (mp) REVERT: A 145 SER cc_start: 0.8541 (m) cc_final: 0.8021 (p) REVERT: A 160 HIS cc_start: 0.6986 (t-90) cc_final: 0.6778 (t-90) REVERT: A 195 LEU cc_start: 0.8671 (tp) cc_final: 0.8030 (tt) REVERT: A 199 ILE cc_start: 0.8902 (mt) cc_final: 0.8472 (tp) REVERT: A 200 GLN cc_start: 0.8219 (mt0) cc_final: 0.7689 (mt0) REVERT: A 202 VAL cc_start: 0.9149 (t) cc_final: 0.8935 (p) REVERT: A 217 ASP cc_start: 0.8251 (t0) cc_final: 0.7962 (t0) REVERT: A 236 LEU cc_start: 0.8554 (tp) cc_final: 0.8288 (tt) REVERT: A 259 GLU cc_start: 0.7923 (tt0) cc_final: 0.7690 (tt0) REVERT: A 261 PHE cc_start: 0.7940 (m-10) cc_final: 0.7593 (m-10) REVERT: A 262 GLN cc_start: 0.8294 (mt0) cc_final: 0.7919 (tp-100) REVERT: A 271 ASP cc_start: 0.7851 (m-30) cc_final: 0.7429 (m-30) REVERT: A 283 MET cc_start: 0.7943 (tpp) cc_final: 0.7660 (tpp) REVERT: A 286 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8686 (mmmm) REVERT: A 292 PHE cc_start: 0.8219 (m-10) cc_final: 0.7821 (m-10) REVERT: A 348 ASP cc_start: 0.6326 (OUTLIER) cc_final: 0.6066 (p0) REVERT: A 361 TYR cc_start: 0.8083 (t80) cc_final: 0.7343 (t80) REVERT: A 369 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8061 (mptt) REVERT: A 376 ASP cc_start: 0.8230 (t0) cc_final: 0.7874 (t0) REVERT: A 421 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7309 (mm110) REVERT: A 429 VAL cc_start: 0.8970 (t) cc_final: 0.8765 (m) REVERT: A 430 ILE cc_start: 0.8907 (mm) cc_final: 0.8534 (mm) REVERT: A 440 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6789 (ptt90) REVERT: A 443 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 473 LYS cc_start: 0.8576 (mtpt) cc_final: 0.7984 (mppt) REVERT: A 484 PHE cc_start: 0.8975 (t80) cc_final: 0.8766 (t80) REVERT: A 488 MET cc_start: 0.8263 (tpp) cc_final: 0.7848 (tpp) REVERT: A 513 VAL cc_start: 0.9120 (t) cc_final: 0.8897 (p) REVERT: A 517 SER cc_start: 0.8556 (p) cc_final: 0.8182 (p) REVERT: A 521 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7947 (mm) REVERT: A 535 HIS cc_start: 0.7385 (m90) cc_final: 0.7007 (m90) REVERT: A 537 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7831 (ttmm) REVERT: A 563 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8574 (tppp) REVERT: A 580 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8461 (mmtt) REVERT: A 677 ARG cc_start: 0.8223 (ttp80) cc_final: 0.7812 (ttp-170) REVERT: A 696 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7051 (tp40) REVERT: A 701 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 715 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7911 (tppt) REVERT: A 732 GLN cc_start: 0.8104 (pp30) cc_final: 0.7740 (pp30) REVERT: B 38 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8173 (mmm160) REVERT: B 39 ARG cc_start: 0.7254 (ttm170) cc_final: 0.6843 (ttm110) REVERT: B 89 ILE cc_start: 0.9092 (mm) cc_final: 0.8832 (tp) REVERT: B 134 ARG cc_start: 0.7081 (mtm180) cc_final: 0.6718 (mtm-85) REVERT: B 185 ARG cc_start: 0.8055 (mtt180) cc_final: 0.7648 (mtt180) REVERT: B 196 VAL cc_start: 0.7966 (t) cc_final: 0.7605 (m) REVERT: B 198 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8332 (tp) REVERT: B 199 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7988 (mt) REVERT: B 203 PHE cc_start: 0.8150 (m-80) cc_final: 0.7767 (m-80) REVERT: B 207 GLN cc_start: 0.8672 (tm130) cc_final: 0.8191 (tm-30) REVERT: B 229 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 230 GLN cc_start: 0.7774 (tp40) cc_final: 0.7248 (tm-30) REVERT: B 235 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8215 (mm-40) REVERT: B 237 LYS cc_start: 0.8930 (pttt) cc_final: 0.8441 (pttp) REVERT: B 240 LEU cc_start: 0.9110 (tp) cc_final: 0.8768 (tp) REVERT: B 262 GLN cc_start: 0.8467 (tp40) cc_final: 0.8006 (tp-100) REVERT: B 283 MET cc_start: 0.8101 (ptp) cc_final: 0.7616 (mpp) REVERT: B 292 PHE cc_start: 0.8066 (m-10) cc_final: 0.7848 (m-10) REVERT: B 375 HIS cc_start: 0.6119 (t-90) cc_final: 0.5760 (t-90) REVERT: B 398 PHE cc_start: 0.7368 (m-80) cc_final: 0.6975 (m-80) REVERT: B 470 ARG cc_start: 0.7237 (ptp-170) cc_final: 0.6932 (ttp80) REVERT: B 472 TRP cc_start: 0.8588 (t-100) cc_final: 0.8241 (t-100) REVERT: B 477 THR cc_start: 0.8733 (m) cc_final: 0.8376 (t) REVERT: B 478 ASP cc_start: 0.8212 (p0) cc_final: 0.7834 (p0) REVERT: B 488 MET cc_start: 0.7740 (tpp) cc_final: 0.6625 (tpp) REVERT: B 492 LEU cc_start: 0.8762 (mt) cc_final: 0.7729 (mt) REVERT: B 512 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8070 (mtm-85) REVERT: B 519 ASN cc_start: 0.8331 (p0) cc_final: 0.7773 (p0) REVERT: B 526 SER cc_start: 0.9143 (m) cc_final: 0.8891 (p) REVERT: B 549 ARG cc_start: 0.7854 (ttt180) cc_final: 0.7112 (ttm-80) REVERT: B 579 ASN cc_start: 0.8805 (p0) cc_final: 0.8460 (p0) REVERT: B 586 ARG cc_start: 0.8188 (mmp80) cc_final: 0.7924 (mmm160) REVERT: B 587 ARG cc_start: 0.8653 (mmm160) cc_final: 0.8332 (mmm160) REVERT: B 682 GLU cc_start: 0.8069 (tp30) cc_final: 0.7635 (tp30) outliers start: 67 outliers final: 50 residues processed: 335 average time/residue: 0.2941 time to fit residues: 135.2815 Evaluate side-chains 351 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 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 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 521 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 A residue 675 SER Chi-restraints excluded: chain A residue 696 GLN 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 126 THR 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 202 VAL Chi-restraints excluded: chain B residue 229 PHE 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 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 430 ILE Chi-restraints excluded: chain B residue 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL 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 678 MET Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 703 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 89 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.094108 restraints weight = 22910.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097505 restraints weight = 12641.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099783 restraints weight = 7955.877| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10395 Z= 0.156 Angle : 0.721 13.665 14128 Z= 0.361 Chirality : 0.044 0.256 1716 Planarity : 0.005 0.058 1757 Dihedral : 6.586 86.474 1441 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 5.08 % Allowed : 22.35 % Favored : 72.57 % 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: -0.50 (0.24), residues: 1319 helix: 0.77 (0.18), residues: 823 sheet: -0.43 (1.09), residues: 29 loop : -2.40 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 83 HIS 0.015 0.001 HIS A 728 PHE 0.028 0.001 PHE A 121 TYR 0.044 0.002 TYR B 578 ARG 0.014 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 572) hydrogen bonds : angle 3.93107 ( 1671) covalent geometry : bond 0.00350 (10395) covalent geometry : angle 0.72135 (14128) *********************** 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 352 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7771 (mtt-85) REVERT: A 62 PHE cc_start: 0.8625 (t80) cc_final: 0.8256 (t80) REVERT: A 121 PHE cc_start: 0.8345 (t80) cc_final: 0.8113 (t80) REVERT: A 125 LEU cc_start: 0.8897 (mp) cc_final: 0.8691 (mp) REVERT: A 145 SER cc_start: 0.8549 (m) cc_final: 0.8052 (p) REVERT: A 195 LEU cc_start: 0.8668 (tp) cc_final: 0.8003 (tt) REVERT: A 199 ILE cc_start: 0.8896 (mt) cc_final: 0.8471 (tp) REVERT: A 200 GLN cc_start: 0.8209 (mt0) cc_final: 0.7675 (mt0) REVERT: A 217 ASP cc_start: 0.8233 (t0) cc_final: 0.7948 (t0) REVERT: A 236 LEU cc_start: 0.8555 (tp) cc_final: 0.8282 (tt) REVERT: A 259 GLU cc_start: 0.7882 (tt0) cc_final: 0.7645 (tt0) REVERT: A 261 PHE cc_start: 0.7929 (m-10) cc_final: 0.7567 (m-10) REVERT: A 262 GLN cc_start: 0.8280 (mt0) cc_final: 0.7910 (tp-100) REVERT: A 271 ASP cc_start: 0.7835 (m-30) cc_final: 0.7438 (m-30) REVERT: A 283 MET cc_start: 0.7938 (tpp) cc_final: 0.7641 (tpp) REVERT: A 286 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8691 (mmmm) REVERT: A 292 PHE cc_start: 0.8216 (m-10) cc_final: 0.7816 (m-10) REVERT: A 348 ASP cc_start: 0.6323 (OUTLIER) cc_final: 0.6064 (p0) REVERT: A 361 TYR cc_start: 0.8075 (t80) cc_final: 0.7337 (t80) REVERT: A 369 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8059 (mptt) REVERT: A 376 ASP cc_start: 0.8246 (t0) cc_final: 0.7885 (t0) REVERT: A 429 VAL cc_start: 0.8963 (t) cc_final: 0.8746 (m) REVERT: A 430 ILE cc_start: 0.8914 (mm) cc_final: 0.8521 (mm) REVERT: A 440 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6741 (ptt90) REVERT: A 443 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 473 LYS cc_start: 0.8569 (mtpt) cc_final: 0.7981 (mppt) REVERT: A 484 PHE cc_start: 0.8943 (t80) cc_final: 0.8723 (t80) REVERT: A 488 MET cc_start: 0.8187 (tpp) cc_final: 0.7872 (tpp) REVERT: A 513 VAL cc_start: 0.9116 (t) cc_final: 0.8855 (p) REVERT: A 517 SER cc_start: 0.8568 (p) cc_final: 0.8215 (p) REVERT: A 521 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 535 HIS cc_start: 0.7385 (m90) cc_final: 0.7003 (m90) REVERT: A 537 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7833 (ttmm) REVERT: A 563 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8551 (tppp) REVERT: A 677 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7800 (ttp-170) REVERT: A 701 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 715 LYS cc_start: 0.8417 (mmtt) cc_final: 0.7855 (tppt) REVERT: A 732 GLN cc_start: 0.8077 (pp30) cc_final: 0.7703 (pp30) REVERT: B 38 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8161 (mmm160) REVERT: B 39 ARG cc_start: 0.7259 (ttm170) cc_final: 0.6852 (ttm110) REVERT: B 89 ILE cc_start: 0.9083 (mm) cc_final: 0.8826 (tp) REVERT: B 134 ARG cc_start: 0.7072 (mtm180) cc_final: 0.6698 (mtm-85) REVERT: B 196 VAL cc_start: 0.7969 (t) cc_final: 0.7609 (m) REVERT: B 198 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8287 (tp) REVERT: B 199 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.8013 (mt) REVERT: B 203 PHE cc_start: 0.8179 (m-80) cc_final: 0.7818 (m-80) REVERT: B 207 GLN cc_start: 0.8676 (tm130) cc_final: 0.8226 (tm-30) REVERT: B 229 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 230 GLN cc_start: 0.7762 (tp40) cc_final: 0.7208 (tm-30) REVERT: B 237 LYS cc_start: 0.8918 (pttt) cc_final: 0.8432 (pttp) REVERT: B 240 LEU cc_start: 0.9007 (tp) cc_final: 0.8724 (tp) REVERT: B 262 GLN cc_start: 0.8438 (tp40) cc_final: 0.7990 (tp-100) REVERT: B 292 PHE cc_start: 0.8057 (m-10) cc_final: 0.7844 (m-10) REVERT: B 375 HIS cc_start: 0.6092 (t-90) cc_final: 0.5751 (t-90) REVERT: B 398 PHE cc_start: 0.7354 (m-80) cc_final: 0.6950 (m-80) REVERT: B 472 TRP cc_start: 0.8548 (t-100) cc_final: 0.8215 (t-100) REVERT: B 477 THR cc_start: 0.8727 (m) cc_final: 0.8356 (t) REVERT: B 478 ASP cc_start: 0.8176 (p0) cc_final: 0.7636 (p0) REVERT: B 488 MET cc_start: 0.7750 (tpp) cc_final: 0.6637 (tpp) REVERT: B 492 LEU cc_start: 0.8730 (mt) cc_final: 0.7709 (mt) REVERT: B 512 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8071 (mtm-85) REVERT: B 519 ASN cc_start: 0.8348 (p0) cc_final: 0.7782 (p0) REVERT: B 526 SER cc_start: 0.9127 (m) cc_final: 0.8894 (p) REVERT: B 579 ASN cc_start: 0.8830 (p0) cc_final: 0.8470 (p0) REVERT: B 586 ARG cc_start: 0.8170 (mmp80) cc_final: 0.7816 (mmp80) REVERT: B 590 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8801 (ptpp) REVERT: B 677 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7548 (tpp80) REVERT: B 681 LYS cc_start: 0.8708 (tppt) cc_final: 0.8498 (ttmm) REVERT: B 682 GLU cc_start: 0.8152 (tp30) cc_final: 0.7596 (tp30) outliers start: 57 outliers final: 47 residues processed: 329 average time/residue: 0.2602 time to fit residues: 116.1378 Evaluate side-chains 345 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 182 ASP Chi-restraints excluded: chain A residue 239 VAL 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 521 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 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 126 THR 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 229 PHE 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 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 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 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 115 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3724 r_free = 0.3724 target = 0.112038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.094336 restraints weight = 22879.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.097636 restraints weight = 12639.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.099939 restraints weight = 8043.731| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10395 Z= 0.156 Angle : 0.739 13.904 14128 Z= 0.370 Chirality : 0.044 0.274 1716 Planarity : 0.005 0.053 1757 Dihedral : 6.587 86.615 1441 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.72 % Allowed : 23.24 % 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: -0.52 (0.23), residues: 1319 helix: 0.74 (0.18), residues: 826 sheet: -0.28 (1.10), residues: 29 loop : -2.39 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 83 HIS 0.016 0.001 HIS A 728 PHE 0.027 0.001 PHE A 121 TYR 0.048 0.002 TYR B 578 ARG 0.014 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03873 ( 572) hydrogen bonds : angle 3.94213 ( 1671) covalent geometry : bond 0.00349 (10395) covalent geometry : angle 0.73895 (14128) ********************** 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 351 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 298 time to evaluate : 1.068 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: 0.8618 (t80) cc_final: 0.8273 (t80) REVERT: A 66 LYS cc_start: 0.9057 (tppt) cc_final: 0.8834 (tppt) REVERT: A 103 MET cc_start: 0.7207 (mmm) cc_final: 0.6814 (mmm) REVERT: A 121 PHE cc_start: 0.8359 (t80) cc_final: 0.8066 (t80) REVERT: A 145 SER cc_start: 0.8541 (m) cc_final: 0.8034 (p) REVERT: A 195 LEU cc_start: 0.8635 (tp) cc_final: 0.8006 (tt) REVERT: A 199 ILE cc_start: 0.8849 (mt) cc_final: 0.8543 (tp) REVERT: A 200 GLN cc_start: 0.8249 (mt0) cc_final: 0.7681 (mt0) REVERT: A 217 ASP cc_start: 0.8226 (t0) cc_final: 0.7939 (t0) REVERT: A 236 LEU cc_start: 0.8545 (tp) cc_final: 0.8271 (tt) REVERT: A 259 GLU cc_start: 0.7890 (tt0) cc_final: 0.7631 (tt0) REVERT: A 261 PHE cc_start: 0.7949 (m-10) cc_final: 0.7565 (m-10) REVERT: A 262 GLN cc_start: 0.8295 (mt0) cc_final: 0.7941 (tp-100) REVERT: A 271 ASP cc_start: 0.7842 (m-30) cc_final: 0.7444 (m-30) REVERT: A 283 MET cc_start: 0.7922 (tpp) cc_final: 0.7637 (tpp) REVERT: A 286 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8679 (mmmm) REVERT: A 292 PHE cc_start: 0.8216 (m-10) cc_final: 0.7807 (m-10) REVERT: A 348 ASP cc_start: 0.6338 (OUTLIER) cc_final: 0.6081 (p0) REVERT: A 361 TYR cc_start: 0.8080 (t80) cc_final: 0.7233 (t80) REVERT: A 369 LYS cc_start: 0.8452 (mmtt) cc_final: 0.8066 (mptt) REVERT: A 376 ASP cc_start: 0.8250 (t0) cc_final: 0.8004 (t0) REVERT: A 429 VAL cc_start: 0.8951 (t) cc_final: 0.8738 (m) REVERT: A 430 ILE cc_start: 0.8910 (mm) cc_final: 0.8523 (mm) REVERT: A 432 MET cc_start: 0.7779 (tpt) cc_final: 0.7544 (tpt) REVERT: A 440 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6553 (ptt90) REVERT: A 443 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 473 LYS cc_start: 0.8565 (mtpt) cc_final: 0.7983 (mppt) REVERT: A 484 PHE cc_start: 0.8922 (t80) cc_final: 0.8693 (t80) REVERT: A 488 MET cc_start: 0.8182 (tpp) cc_final: 0.7867 (tpp) REVERT: A 513 VAL cc_start: 0.9101 (t) cc_final: 0.8843 (p) REVERT: A 517 SER cc_start: 0.8577 (p) cc_final: 0.8214 (p) REVERT: A 521 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7883 (mm) REVERT: A 535 HIS cc_start: 0.7385 (m90) cc_final: 0.7028 (m90) REVERT: A 537 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7691 (ttpp) REVERT: A 563 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8576 (tppp) REVERT: A 677 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7793 (ttp-170) REVERT: A 697 ASP cc_start: 0.7425 (t0) cc_final: 0.7170 (t0) REVERT: A 701 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 715 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7832 (tppt) REVERT: B 38 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8161 (mmm160) REVERT: B 39 ARG cc_start: 0.7263 (ttm170) cc_final: 0.6854 (ttm110) REVERT: B 89 ILE cc_start: 0.9088 (mm) cc_final: 0.8834 (mm) REVERT: B 134 ARG cc_start: 0.7054 (mtm180) cc_final: 0.6677 (mtm-85) REVERT: B 185 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7817 (mmt90) REVERT: B 196 VAL cc_start: 0.7969 (t) cc_final: 0.7623 (m) REVERT: B 198 ILE cc_start: 0.8708 (tp) cc_final: 0.8352 (tp) REVERT: B 199 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7979 (mt) REVERT: B 203 PHE cc_start: 0.8239 (m-80) cc_final: 0.7795 (m-80) REVERT: B 207 GLN cc_start: 0.8777 (tm130) cc_final: 0.8355 (tm-30) REVERT: B 229 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: B 230 GLN cc_start: 0.7747 (tp40) cc_final: 0.7137 (tm-30) REVERT: B 237 LYS cc_start: 0.8915 (pttt) cc_final: 0.8426 (pttp) REVERT: B 240 LEU cc_start: 0.8976 (tp) cc_final: 0.8671 (tp) REVERT: B 262 GLN cc_start: 0.8434 (tp40) cc_final: 0.7976 (tp-100) REVERT: B 283 MET cc_start: 0.8104 (ptp) cc_final: 0.7574 (mpp) REVERT: B 292 PHE cc_start: 0.8050 (m-10) cc_final: 0.7842 (m-10) REVERT: B 375 HIS cc_start: 0.6075 (t-90) cc_final: 0.5739 (t-90) REVERT: B 398 PHE cc_start: 0.7310 (m-80) cc_final: 0.6910 (m-80) REVERT: B 472 TRP cc_start: 0.8541 (t-100) cc_final: 0.8213 (t-100) REVERT: B 478 ASP cc_start: 0.8174 (p0) cc_final: 0.7716 (p0) REVERT: B 488 MET cc_start: 0.7751 (tpp) cc_final: 0.6633 (tpp) REVERT: B 492 LEU cc_start: 0.8719 (mt) cc_final: 0.7695 (mt) REVERT: B 512 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8086 (mtm-85) REVERT: B 519 ASN cc_start: 0.8355 (p0) cc_final: 0.7785 (p0) REVERT: B 526 SER cc_start: 0.9128 (m) cc_final: 0.8896 (p) REVERT: B 579 ASN cc_start: 0.8815 (p0) cc_final: 0.8396 (p0) REVERT: B 587 ARG cc_start: 0.8657 (mmm160) cc_final: 0.8447 (mmm160) REVERT: B 590 LYS cc_start: 0.9135 (ptpp) cc_final: 0.8862 (ptpp) REVERT: B 677 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7684 (tpp80) REVERT: B 682 GLU cc_start: 0.8080 (tp30) cc_final: 0.7377 (tp30) REVERT: B 685 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7956 (ttp80) outliers start: 53 outliers final: 44 residues processed: 328 average time/residue: 0.2987 time to fit residues: 132.1560 Evaluate side-chains 345 residues out of total 1133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 1.583 ------------------------------------------------------------------------------- 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 182 ASP Chi-restraints excluded: chain A residue 239 VAL 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 521 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 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 199 ILE Chi-restraints excluded: chain B residue 229 PHE 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 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 473 LYS Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL 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 694 LEU Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain B residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 40 optimal weight: 0.0570 chunk 1 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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** ** 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 = 0.3724 r_free = 0.3724 target = 0.111933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.094184 restraints weight = 22794.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.097560 restraints weight = 12636.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099826 restraints weight = 7953.617| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10395 Z= 0.154 Angle : 0.734 13.800 14128 Z= 0.367 Chirality : 0.045 0.280 1716 Planarity : 0.005 0.052 1757 Dihedral : 6.581 86.426 1441 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.63 % Allowed : 23.24 % Favored : 72.13 % 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: -0.50 (0.23), residues: 1319 helix: 0.73 (0.18), residues: 827 sheet: -0.16 (1.10), residues: 29 loop : -2.34 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 74 HIS 0.016 0.001 HIS A 728 PHE 0.025 0.001 PHE A 121 TYR 0.034 0.002 TYR B 578 ARG 0.012 0.001 ARG B 440 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 572) hydrogen bonds : angle 3.93212 ( 1671) covalent geometry : bond 0.00344 (10395) covalent geometry : angle 0.73395 (14128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3997.16 seconds wall clock time: 71 minutes 35.97 seconds (4295.97 seconds total)