Starting phenix.real_space_refine on Sun Dec 29 07:54:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x07_32919/12_2024/7x07_32919.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x07_32919/12_2024/7x07_32919.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/7x07_32919/12_2024/7x07_32919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x07_32919/12_2024/7x07_32919.map" model { file = "/net/cci-nas-00/data/ceres_data/7x07_32919/12_2024/7x07_32919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x07_32919/12_2024/7x07_32919.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= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6489 2.51 5 N 1782 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10125 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5046 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 5051 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 22, 'TRANS': 610} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7PO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.33, per 1000 atoms: 0.63 Number of scatterers: 10125 At special positions: 0 Unit cell: (74.7, 118.69, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1806 8.00 N 1782 7.00 C 6489 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 4 sheets defined 51.6% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.913A pdb=" N LEU A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.741A pdb=" N LEU A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.574A pdb=" N TYR A 110 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 removed outlier: 4.397A pdb=" N CYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.650A pdb=" N GLY A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TRP A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.872A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 186 removed outlier: 4.055A pdb=" N SER A 184 " --> pdb=" O TYR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 217 through 232 removed outlier: 4.089A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.574A pdb=" N ILE A 246 " --> pdb=" O TRP A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.632A pdb=" N PHE A 265 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.856A pdb=" N TYR A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.706A pdb=" N LEU A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 347 through 353 removed outlier: 4.003A pdb=" N ILE A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 removed outlier: 3.825A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 394 removed outlier: 3.908A pdb=" N ALA A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 removed outlier: 4.320A pdb=" N ILE A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 431 removed outlier: 3.647A pdb=" N LEU A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.169A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.606A pdb=" N ALA A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 591 Processing helix chain 'A' and resid 606 through 608 No H-bonds generated for 'chain 'A' and resid 606 through 608' Processing helix chain 'A' and resid 609 through 621 Processing helix chain 'A' and resid 639 through 650 Processing helix chain 'A' and resid 660 through 667 removed outlier: 3.794A pdb=" N LEU A 663 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 701 removed outlier: 4.476A pdb=" N LYS A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.830A pdb=" N LEU B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.741A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 118 through 123' Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.715A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN B 136 " --> pdb=" O TRP B 132 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 181 through 186 Processing helix chain 'B' and resid 192 through 199 removed outlier: 3.688A pdb=" N SER B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 198 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 267 through 289 Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.922A pdb=" N ILE B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 318 through 323 removed outlier: 4.121A pdb=" N LEU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 318 through 323' Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.946A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 4.319A pdb=" N LEU B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 382 through 391 removed outlier: 4.218A pdb=" N ALA B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.350A pdb=" N ALA B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 424 " --> pdb=" O HIS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 512 through 522 removed outlier: 4.224A pdb=" N LEU B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 Processing helix chain 'B' and resid 564 through 568 Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.799A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 621 removed outlier: 3.658A pdb=" N ARG B 612 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 649 Processing helix chain 'B' and resid 661 through 665 removed outlier: 3.737A pdb=" N LYS B 665 " --> pdb=" O SER B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 706 removed outlier: 3.874A pdb=" N LEU B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 721 removed outlier: 3.548A pdb=" N LEU B 713 " --> pdb=" O MET B 709 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN B 714 " --> pdb=" O GLN B 710 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469 removed outlier: 4.836A pdb=" N LEU A 493 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA A 491 " --> pdb=" O PRO A 480 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 482 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 489 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 467 through 469 removed outlier: 3.844A pdb=" N TYR B 532 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 539 through 543 removed outlier: 6.466A pdb=" N PHE B 540 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP B 629 " --> pdb=" O PHE B 540 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 542 " --> pdb=" O ASP B 629 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 671 330 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1626 1.30 - 1.43: 2748 1.43 - 1.56: 5880 1.56 - 1.69: 0 1.69 - 1.83: 80 Bond restraints: 10334 Sorted by residual: bond pdb=" C PRO B 143 " pdb=" O PRO B 143 " ideal model delta sigma weight residual 1.238 1.170 0.068 1.37e-02 5.33e+03 2.48e+01 bond pdb=" N ARG B 236 " pdb=" CA ARG B 236 " ideal model delta sigma weight residual 1.459 1.519 -0.060 1.23e-02 6.61e+03 2.38e+01 bond pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 1.231 1.278 -0.047 1.02e-02 9.61e+03 2.11e+01 bond pdb=" C ALA B 626 " pdb=" O ALA B 626 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.15e-02 7.56e+03 1.99e+01 bond pdb=" N THR B 506 " pdb=" CA THR B 506 " ideal model delta sigma weight residual 1.455 1.510 -0.055 1.27e-02 6.20e+03 1.86e+01 ... (remaining 10329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.46: 13410 3.46 - 6.92: 549 6.92 - 10.39: 10 10.39 - 13.85: 0 13.85 - 17.31: 1 Bond angle restraints: 13970 Sorted by residual: angle pdb=" N ILE B 637 " pdb=" CA ILE B 637 " pdb=" C ILE B 637 " ideal model delta sigma weight residual 109.34 92.03 17.31 2.08e+00 2.31e-01 6.93e+01 angle pdb=" N ILE A 320 " pdb=" CA ILE A 320 " pdb=" C ILE A 320 " ideal model delta sigma weight residual 112.17 105.61 6.56 9.50e-01 1.11e+00 4.77e+01 angle pdb=" N ILE B 151 " pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 112.90 106.87 6.03 9.60e-01 1.09e+00 3.95e+01 angle pdb=" N ALA B 168 " pdb=" CA ALA B 168 " pdb=" C ALA B 168 " ideal model delta sigma weight residual 112.68 104.44 8.24 1.33e+00 5.65e-01 3.84e+01 angle pdb=" N VAL B 102 " pdb=" CA VAL B 102 " pdb=" C VAL B 102 " ideal model delta sigma weight residual 111.91 106.50 5.41 8.90e-01 1.26e+00 3.70e+01 ... (remaining 13965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 5475 17.58 - 35.15: 605 35.15 - 52.73: 113 52.73 - 70.30: 19 70.30 - 87.88: 14 Dihedral angle restraints: 6226 sinusoidal: 2544 harmonic: 3682 Sorted by residual: dihedral pdb=" CA LEU B 96 " pdb=" C LEU B 96 " pdb=" N HIS B 97 " pdb=" CA HIS B 97 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ALA B 170 " pdb=" C ALA B 170 " pdb=" N TYR B 171 " pdb=" CA TYR B 171 " ideal model delta harmonic sigma weight residual 180.00 153.04 26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER B 636 " pdb=" C SER B 636 " pdb=" N ILE B 637 " pdb=" CA ILE B 637 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 921 0.067 - 0.134: 511 0.134 - 0.201: 119 0.201 - 0.267: 7 0.267 - 0.334: 1 Chirality restraints: 1559 Sorted by residual: chirality pdb=" CA ILE B 637 " pdb=" N ILE B 637 " pdb=" C ILE B 637 " pdb=" CB ILE B 637 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB THR A 225 " pdb=" CA THR A 225 " pdb=" OG1 THR A 225 " pdb=" CG2 THR A 225 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE A 657 " pdb=" N ILE A 657 " pdb=" C ILE A 657 " pdb=" CB ILE A 657 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1556 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 143 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C PRO B 143 " 0.065 2.00e-02 2.50e+03 pdb=" O PRO B 143 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 144 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 641 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLY B 641 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 641 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 642 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 622 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C ARG B 622 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG B 622 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO B 623 " -0.020 2.00e-02 2.50e+03 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 298 2.70 - 3.25: 9979 3.25 - 3.80: 14719 3.80 - 4.35: 20324 4.35 - 4.90: 32170 Nonbonded interactions: 77490 Sorted by model distance: nonbonded pdb=" N ILE B 637 " pdb=" O ILE B 637 " model vdw 2.145 2.496 nonbonded pdb=" C SER B 636 " pdb=" O ILE B 637 " model vdw 2.211 3.270 nonbonded pdb=" NH1 ARG B 275 " pdb=" O ASP B 312 " model vdw 2.319 3.120 nonbonded pdb=" O GLY A 188 " pdb=" NH2 ARG A 191 " model vdw 2.325 3.120 nonbonded pdb=" OE2 GLU B 155 " pdb=" OG SER B 213 " model vdw 2.335 3.040 ... (remaining 77485 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 67 through 721) selection = (chain 'B' and resid 67 through 721) } 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: 2.280 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.060 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.013 0.068 10334 Z= 0.833 Angle : 1.657 17.311 13970 Z= 1.222 Chirality : 0.077 0.334 1559 Planarity : 0.008 0.046 1774 Dihedral : 15.382 87.879 3856 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.11 % Favored : 91.18 % Rotamer: Outliers : 1.97 % Allowed : 5.53 % Favored : 92.50 % 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: -4.75 (0.20), residues: 1258 helix: -3.09 (0.15), residues: 739 sheet: -3.69 (0.77), residues: 40 loop : -2.93 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP B 524 HIS 0.020 0.004 HIS B 621 PHE 0.042 0.005 PHE B 204 TYR 0.036 0.006 TYR B 174 ARG 0.015 0.002 ARG B 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 114 LEU cc_start: 0.9135 (tp) cc_final: 0.8910 (tt) REVERT: B 160 LEU cc_start: 0.8818 (tp) cc_final: 0.8434 (tt) REVERT: B 493 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7664 (mp) REVERT: B 501 MET cc_start: 0.7923 (tpp) cc_final: 0.7208 (mmm) REVERT: B 615 MET cc_start: 0.7873 (mtt) cc_final: 0.7389 (mtt) REVERT: B 663 LEU cc_start: 0.9145 (tp) cc_final: 0.8939 (tt) outliers start: 21 outliers final: 8 residues processed: 161 average time/residue: 0.2413 time to fit residues: 54.6795 Evaluate side-chains 120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.2980 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 433 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10334 Z= 0.217 Angle : 0.705 10.372 13970 Z= 0.376 Chirality : 0.042 0.149 1559 Planarity : 0.004 0.037 1774 Dihedral : 7.808 59.404 1454 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.92 % Favored : 92.93 % Rotamer: Outliers : 1.41 % Allowed : 10.50 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.22), residues: 1258 helix: -2.34 (0.17), residues: 765 sheet: -2.00 (1.23), residues: 22 loop : -2.80 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 664 HIS 0.010 0.001 HIS B 621 PHE 0.017 0.001 PHE B 673 TYR 0.015 0.001 TYR A 559 ARG 0.007 0.001 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5721 (tpt) cc_final: 0.5484 (mmm) REVERT: A 505 ILE cc_start: 0.5855 (OUTLIER) cc_final: 0.5503 (mt) REVERT: A 537 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5446 (tp40) REVERT: A 674 ASP cc_start: 0.5696 (p0) cc_final: 0.5198 (p0) REVERT: B 114 LEU cc_start: 0.9111 (tp) cc_final: 0.8832 (tt) REVERT: B 380 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7204 (tt0) REVERT: B 493 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7578 (mp) REVERT: B 501 MET cc_start: 0.7972 (tpp) cc_final: 0.7379 (mmm) REVERT: B 621 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.7713 (m-70) outliers start: 15 outliers final: 9 residues processed: 136 average time/residue: 0.2210 time to fit residues: 43.4854 Evaluate side-chains 124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 0.0270 chunk 39 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 HIS B 584 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10334 Z= 0.231 Angle : 0.655 11.105 13970 Z= 0.344 Chirality : 0.042 0.204 1559 Planarity : 0.004 0.038 1774 Dihedral : 7.358 59.264 1445 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.31 % Favored : 92.61 % Rotamer: Outliers : 1.78 % Allowed : 13.03 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.22), residues: 1258 helix: -2.11 (0.18), residues: 765 sheet: -2.63 (0.96), residues: 34 loop : -2.61 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 664 HIS 0.012 0.001 HIS B 669 PHE 0.033 0.001 PHE A 681 TYR 0.013 0.001 TYR B 620 ARG 0.010 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8949 (tt) REVERT: A 322 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8706 (tp) REVERT: A 537 GLN cc_start: 0.6000 (mm-40) cc_final: 0.5365 (tp40) REVERT: B 380 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7165 (tt0) REVERT: B 493 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7620 (mp) REVERT: B 501 MET cc_start: 0.8066 (tpp) cc_final: 0.7091 (mmt) REVERT: B 618 MET cc_start: 0.7773 (ttp) cc_final: 0.7509 (ttt) REVERT: B 642 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7989 (pttm) REVERT: B 683 LYS cc_start: 0.8435 (tptm) cc_final: 0.8185 (tptt) outliers start: 19 outliers final: 13 residues processed: 138 average time/residue: 0.2331 time to fit residues: 46.5582 Evaluate side-chains 122 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 54 optimal weight: 0.0060 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10334 Z= 0.202 Angle : 0.622 11.609 13970 Z= 0.325 Chirality : 0.042 0.153 1559 Planarity : 0.004 0.036 1774 Dihedral : 6.964 56.890 1443 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.93 % Rotamer: Outliers : 2.53 % Allowed : 15.09 % Favored : 82.38 % 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: -3.43 (0.23), residues: 1258 helix: -1.97 (0.18), residues: 769 sheet: -2.63 (0.94), residues: 34 loop : -2.54 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP B 664 HIS 0.007 0.001 HIS B 621 PHE 0.023 0.001 PHE A 681 TYR 0.010 0.001 TYR B 527 ARG 0.008 0.000 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 322 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8654 (tp) REVERT: A 548 MET cc_start: 0.6228 (tmm) cc_final: 0.5869 (tmm) REVERT: A 559 TYR cc_start: 0.7935 (t80) cc_final: 0.7632 (t80) REVERT: B 81 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8702 (tp) REVERT: B 114 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8635 (tt) REVERT: B 380 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7089 (tt0) REVERT: B 493 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7558 (mp) REVERT: B 501 MET cc_start: 0.8076 (tpp) cc_final: 0.7232 (mmt) REVERT: B 527 TYR cc_start: 0.7215 (m-80) cc_final: 0.6991 (m-80) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.2160 time to fit residues: 44.3534 Evaluate side-chains 122 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 chunk 50 optimal weight: 0.0570 chunk 103 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 30 optimal weight: 0.0060 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10334 Z= 0.160 Angle : 0.598 11.268 13970 Z= 0.312 Chirality : 0.040 0.139 1559 Planarity : 0.003 0.037 1774 Dihedral : 6.565 56.035 1443 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.15 % Favored : 92.77 % Rotamer: Outliers : 1.97 % Allowed : 16.96 % Favored : 81.07 % 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: -3.32 (0.23), residues: 1258 helix: -1.83 (0.18), residues: 780 sheet: -2.58 (0.93), residues: 34 loop : -2.60 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B 664 HIS 0.009 0.001 HIS B 669 PHE 0.015 0.001 PHE A 252 TYR 0.012 0.001 TYR B 181 ARG 0.005 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8832 (tt) REVERT: A 322 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 548 MET cc_start: 0.6162 (tmm) cc_final: 0.5938 (tmm) REVERT: A 559 TYR cc_start: 0.7958 (t80) cc_final: 0.7702 (t80) REVERT: B 81 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8671 (tp) REVERT: B 114 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8630 (tt) REVERT: B 380 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7016 (tt0) REVERT: B 406 TYR cc_start: 0.7244 (t80) cc_final: 0.7008 (t80) REVERT: B 493 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7455 (mp) REVERT: B 501 MET cc_start: 0.8062 (tpp) cc_final: 0.7335 (mmt) REVERT: B 618 MET cc_start: 0.7824 (ttp) cc_final: 0.7574 (ttt) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.2247 time to fit residues: 43.6303 Evaluate side-chains 118 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10334 Z= 0.210 Angle : 0.618 12.121 13970 Z= 0.319 Chirality : 0.042 0.140 1559 Planarity : 0.004 0.074 1774 Dihedral : 6.557 57.061 1443 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.87 % Favored : 92.05 % Rotamer: Outliers : 2.81 % Allowed : 17.34 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.23), residues: 1258 helix: -1.72 (0.18), residues: 780 sheet: -2.57 (0.93), residues: 34 loop : -2.61 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP B 664 HIS 0.004 0.001 HIS B 420 PHE 0.012 0.001 PHE A 517 TYR 0.009 0.001 TYR B 527 ARG 0.006 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8861 (tt) REVERT: A 322 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8581 (tp) REVERT: A 403 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.6582 (mtt) REVERT: A 548 MET cc_start: 0.6197 (tmm) cc_final: 0.5967 (tmm) REVERT: A 559 TYR cc_start: 0.8037 (t80) cc_final: 0.7816 (t80) REVERT: B 81 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 114 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8603 (tt) REVERT: B 380 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7043 (tt0) REVERT: B 493 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7534 (mp) REVERT: B 501 MET cc_start: 0.8330 (tpp) cc_final: 0.7050 (mmt) REVERT: B 618 MET cc_start: 0.7937 (ttp) cc_final: 0.7670 (ttt) outliers start: 30 outliers final: 18 residues processed: 133 average time/residue: 0.1970 time to fit residues: 39.6938 Evaluate side-chains 127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10334 Z= 0.193 Angle : 0.614 11.642 13970 Z= 0.314 Chirality : 0.042 0.240 1559 Planarity : 0.004 0.063 1774 Dihedral : 6.442 58.475 1443 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.72 % Allowed : 18.28 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.23), residues: 1258 helix: -1.60 (0.18), residues: 780 sheet: -2.55 (0.92), residues: 34 loop : -2.58 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP B 664 HIS 0.009 0.001 HIS B 669 PHE 0.012 0.001 PHE A 517 TYR 0.024 0.001 TYR B 620 ARG 0.005 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8798 (tt) REVERT: A 403 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7309 (ttt) REVERT: A 548 MET cc_start: 0.6162 (tmm) cc_final: 0.5913 (tmm) REVERT: A 559 TYR cc_start: 0.8060 (t80) cc_final: 0.7845 (t80) REVERT: B 81 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8727 (tp) REVERT: B 114 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8604 (tt) REVERT: B 380 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7030 (tt0) REVERT: B 618 MET cc_start: 0.7933 (ttp) cc_final: 0.7677 (ttt) outliers start: 29 outliers final: 21 residues processed: 130 average time/residue: 0.1944 time to fit residues: 38.0944 Evaluate side-chains 129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 106 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10334 Z= 0.191 Angle : 0.623 12.688 13970 Z= 0.318 Chirality : 0.042 0.222 1559 Planarity : 0.004 0.061 1774 Dihedral : 6.193 59.561 1441 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.81 % Allowed : 18.46 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.23), residues: 1258 helix: -1.47 (0.19), residues: 780 sheet: -2.45 (0.92), residues: 34 loop : -2.51 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP B 664 HIS 0.007 0.001 HIS B 669 PHE 0.011 0.001 PHE A 517 TYR 0.017 0.001 TYR B 620 ARG 0.005 0.000 ARG B 660 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8769 (tt) REVERT: A 403 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7238 (ttt) REVERT: A 517 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5857 (t80) REVERT: A 548 MET cc_start: 0.6211 (tmm) cc_final: 0.5926 (tmm) REVERT: B 81 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8742 (tp) REVERT: B 114 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8624 (tt) REVERT: B 291 GLU cc_start: 0.8091 (pm20) cc_final: 0.7794 (pm20) REVERT: B 380 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7031 (tt0) REVERT: B 493 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7569 (mp) REVERT: B 618 MET cc_start: 0.7952 (ttp) cc_final: 0.7703 (ttt) outliers start: 30 outliers final: 20 residues processed: 133 average time/residue: 0.1946 time to fit residues: 39.6734 Evaluate side-chains 130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 621 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 88 optimal weight: 0.0870 chunk 34 optimal weight: 0.0980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10334 Z= 0.169 Angle : 0.618 12.617 13970 Z= 0.313 Chirality : 0.041 0.217 1559 Planarity : 0.004 0.055 1774 Dihedral : 5.989 56.431 1441 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.34 % Allowed : 19.21 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.23), residues: 1258 helix: -1.36 (0.19), residues: 789 sheet: -2.10 (0.93), residues: 34 loop : -2.51 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.001 TRP B 664 HIS 0.009 0.001 HIS B 669 PHE 0.009 0.001 PHE A 517 TYR 0.035 0.001 TYR A 174 ARG 0.005 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.156 Fit side-chains revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8764 (tt) REVERT: A 403 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7169 (ttt) REVERT: A 517 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5945 (t80) REVERT: A 548 MET cc_start: 0.6186 (tmm) cc_final: 0.5929 (tmm) REVERT: B 114 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8653 (tt) REVERT: B 380 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7004 (tt0) REVERT: B 493 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7532 (mp) outliers start: 25 outliers final: 17 residues processed: 129 average time/residue: 0.2024 time to fit residues: 39.5676 Evaluate side-chains 127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.0050 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 61 optimal weight: 20.0000 chunk 79 optimal weight: 0.6980 chunk 106 optimal weight: 0.0570 overall best weight: 0.2712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 GLN ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10334 Z= 0.160 Angle : 0.612 12.141 13970 Z= 0.310 Chirality : 0.040 0.220 1559 Planarity : 0.004 0.054 1774 Dihedral : 5.742 59.781 1439 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.44 % Allowed : 19.40 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.23), residues: 1258 helix: -1.21 (0.19), residues: 789 sheet: -1.90 (0.95), residues: 34 loop : -2.50 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP B 664 HIS 0.009 0.001 HIS B 669 PHE 0.028 0.001 PHE A 295 TYR 0.021 0.001 TYR A 174 ARG 0.005 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 403 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7159 (ttt) REVERT: A 517 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5929 (t80) REVERT: A 548 MET cc_start: 0.6116 (tmm) cc_final: 0.5865 (tmm) REVERT: B 114 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 493 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7454 (mp) REVERT: B 615 MET cc_start: 0.7238 (mtt) cc_final: 0.6846 (mtt) outliers start: 26 outliers final: 17 residues processed: 129 average time/residue: 0.2165 time to fit residues: 41.3669 Evaluate side-chains 123 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 406 TYR Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 604 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.5980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.226802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.177879 restraints weight = 11729.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.175836 restraints weight = 19546.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.174571 restraints weight = 16073.514| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10334 Z= 0.475 Angle : 0.778 12.584 13970 Z= 0.390 Chirality : 0.050 0.211 1559 Planarity : 0.005 0.072 1774 Dihedral : 6.670 58.010 1439 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.72 % Allowed : 18.93 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.23), residues: 1258 helix: -1.55 (0.18), residues: 788 sheet: -2.10 (0.87), residues: 42 loop : -2.60 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP B 664 HIS 0.015 0.002 HIS B 621 PHE 0.046 0.002 PHE A 295 TYR 0.037 0.002 TYR A 174 ARG 0.009 0.001 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.49 seconds wall clock time: 41 minutes 15.29 seconds (2475.29 seconds total)