Starting phenix.real_space_refine on Wed Mar 4 00:24:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a7c_11677/03_2026/7a7c_11677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a7c_11677/03_2026/7a7c_11677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2026/7a7c_11677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2026/7a7c_11677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2026/7a7c_11677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2026/7a7c_11677.map" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 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 Fe 1 7.16 5 S 32 5.16 5 C 5973 2.51 5 N 1622 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9387 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4277 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 30, 'TRANS': 529} Chain breaks: 4 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 5067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5067 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 43, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.21 Number of scatterers: 9387 At special positions: 0 Unit cell: (84.76, 96.496, 126.488, 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) Fe 1 26.01 S 32 16.00 O 1759 8.00 N 1622 7.00 C 5973 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 333.0 milliseconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 3 sheets defined 56.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.511A pdb=" N VAL A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.574A pdb=" N GLU A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 98 through 110 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 148 through 156 removed outlier: 4.254A pdb=" N LYS A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 177 removed outlier: 3.574A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.917A pdb=" N ALA A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 removed outlier: 3.659A pdb=" N HIS A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 387 through 399 removed outlier: 3.520A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 removed outlier: 3.754A pdb=" N LEU A 404 " --> pdb=" O HIS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 452 through 462 Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.581A pdb=" N ALA A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 removed outlier: 3.626A pdb=" N ARG A 498 " --> pdb=" O GLY A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.815A pdb=" N VAL A 517 " --> pdb=" O ASP A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 558 removed outlier: 3.719A pdb=" N VAL A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 588 No H-bonds generated for 'chain 'A' and resid 586 through 588' Processing helix chain 'A' and resid 605 through 617 Processing helix chain 'A' and resid 620 through 634 removed outlier: 3.920A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 692 through 701 removed outlier: 3.527A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.767A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.573A pdb=" N ALA B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 56' Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.810A pdb=" N GLU B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.648A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 131 through 139 Proline residue: B 136 - end of helix removed outlier: 3.673A pdb=" N ALA B 139 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.960A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.855A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.968A pdb=" N LYS B 158 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 177 removed outlier: 3.510A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 removed outlier: 4.024A pdb=" N VAL B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 287 through 291 Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 357 through 360 Processing helix chain 'B' and resid 378 through 387 removed outlier: 3.551A pdb=" N LEU B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 384 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.648A pdb=" N ARG B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 4.020A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.818A pdb=" N SER B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 492 through 496 removed outlier: 3.786A pdb=" N GLY B 495 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG B 496 " --> pdb=" O ASN B 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 492 through 496' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.685A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 531 Processing helix chain 'B' and resid 539 through 560 removed outlier: 3.795A pdb=" N VAL B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.506A pdb=" N ALA B 585 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 635 removed outlier: 3.905A pdb=" N VAL B 633 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 692 through 701 removed outlier: 4.264A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.815A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 removed outlier: 3.522A pdb=" N PHE B 720 " --> pdb=" O ALA B 716 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 667 through 670 removed outlier: 3.538A pdb=" N THR A 667 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 688 " --> pdb=" O GLY A 680 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AA3, first strand: chain 'B' and resid 667 through 670 403 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 3928 1.39 - 1.56: 5636 1.56 - 1.72: 0 1.72 - 1.89: 60 1.89 - 2.05: 4 Bond restraints: 9628 Sorted by residual: bond pdb=" CA TRP B 39 " pdb=" C TRP B 39 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.26e-01 bond pdb=" CA TRP B 351 " pdb=" C TRP B 351 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.34e-02 5.57e+03 7.06e-01 bond pdb=" CA ILE A 462 " pdb=" C ILE A 462 " ideal model delta sigma weight residual 1.530 1.521 0.009 1.12e-02 7.97e+03 6.65e-01 bond pdb=" CA PRO B 239 " pdb=" C PRO B 239 " ideal model delta sigma weight residual 1.527 1.518 0.009 1.07e-02 8.73e+03 6.49e-01 bond pdb=" CA ASP A 240 " pdb=" C ASP A 240 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 6.00e-01 ... (remaining 9623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 12779 1.43 - 2.87: 278 2.87 - 4.30: 49 4.30 - 5.74: 15 5.74 - 7.17: 1 Bond angle restraints: 13122 Sorted by residual: angle pdb=" N PRO B 642 " pdb=" CA PRO B 642 " pdb=" C PRO B 642 " ideal model delta sigma weight residual 114.68 111.41 3.27 1.04e+00 9.25e-01 9.86e+00 angle pdb=" N ILE A 462 " pdb=" CA ILE A 462 " pdb=" C ILE A 462 " ideal model delta sigma weight residual 111.91 109.66 2.25 8.90e-01 1.26e+00 6.37e+00 angle pdb=" CA TYR B 597 " pdb=" C TYR B 597 " pdb=" N LEU B 598 " ideal model delta sigma weight residual 114.81 118.16 -3.35 1.42e+00 4.96e-01 5.56e+00 angle pdb=" N TYR B 597 " pdb=" CA TYR B 597 " pdb=" C TYR B 597 " ideal model delta sigma weight residual 111.17 113.92 -2.75 1.41e+00 5.03e-01 3.80e+00 angle pdb=" CA PRO B 642 " pdb=" C PRO B 642 " pdb=" O PRO B 642 " ideal model delta sigma weight residual 118.92 121.13 -2.21 1.14e+00 7.69e-01 3.77e+00 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5129 17.94 - 35.88: 413 35.88 - 53.82: 65 53.82 - 71.76: 11 71.76 - 89.70: 9 Dihedral angle restraints: 5627 sinusoidal: 2163 harmonic: 3464 Sorted by residual: dihedral pdb=" CA ARG B 595 " pdb=" C ARG B 595 " pdb=" N ASN B 596 " pdb=" CA ASN B 596 " ideal model delta harmonic sigma weight residual 180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA ALA B 130 " pdb=" C ALA B 130 " pdb=" N PRO B 131 " pdb=" CA PRO B 131 " ideal model delta harmonic sigma weight residual 180.00 158.41 21.59 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 339 " pdb=" C TYR B 339 " pdb=" N GLU B 340 " pdb=" CA GLU B 340 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.052: 404 0.052 - 0.077: 173 0.077 - 0.103: 64 0.103 - 0.129: 14 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA PRO B 367 " pdb=" N PRO B 367 " pdb=" C PRO B 367 " pdb=" CB PRO B 367 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 666 " pdb=" N ILE B 666 " pdb=" C ILE B 666 " pdb=" CB ILE B 666 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE B 364 " pdb=" N ILE B 364 " pdb=" C ILE B 364 " pdb=" CB ILE B 364 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 1409 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 279 " -0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO B 280 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 509 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 510 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 604 " -0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO A 605 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " -0.021 5.00e-02 4.00e+02 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 850 2.74 - 3.28: 9526 3.28 - 3.82: 15195 3.82 - 4.36: 18436 4.36 - 4.90: 32007 Nonbonded interactions: 76014 Sorted by model distance: nonbonded pdb=" O TRP B 91 " pdb=" OH TYR B 98 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR B 113 " pdb=" OD2 ASP B 487 " model vdw 2.236 3.040 nonbonded pdb=" O VAL A 267 " pdb=" OG1 THR A 271 " model vdw 2.256 3.040 nonbonded pdb=" O GLY A 599 " pdb=" ND2 ASN A 602 " model vdw 2.265 3.120 nonbonded pdb=" O TYR B 390 " pdb=" OG1 THR B 394 " model vdw 2.272 3.040 ... (remaining 76009 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.006 0.503 9629 Z= 0.136 Angle : 0.538 7.175 13122 Z= 0.295 Chirality : 0.039 0.129 1412 Planarity : 0.004 0.081 1722 Dihedral : 13.508 89.701 3413 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.24), residues: 1210 helix: 0.27 (0.22), residues: 568 sheet: -1.66 (1.18), residues: 21 loop : -1.50 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.011 0.001 TYR B 98 PHE 0.013 0.001 PHE B 129 TRP 0.012 0.001 TRP A 689 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9628) covalent geometry : angle 0.53775 (13122) hydrogen bonds : bond 0.18263 ( 403) hydrogen bonds : angle 6.06690 ( 1089) Misc. bond : bond 0.50317 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.363 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0864 time to fit residues: 8.9588 Evaluate side-chains 52 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.0060 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 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 = 0.3409 r_free = 0.3409 target = 0.100016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083219 restraints weight = 17129.472| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.31 r_work: 0.3024 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9629 Z= 0.140 Angle : 0.519 7.761 13122 Z= 0.257 Chirality : 0.039 0.121 1412 Planarity : 0.005 0.065 1722 Dihedral : 4.780 64.766 1324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.21 % Allowed : 5.41 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.24), residues: 1210 helix: 0.62 (0.22), residues: 570 sheet: -1.17 (1.13), residues: 21 loop : -1.42 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 253 TYR 0.013 0.001 TYR B 98 PHE 0.009 0.001 PHE B 129 TRP 0.008 0.001 TRP B 135 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9628) covalent geometry : angle 0.51932 (13122) hydrogen bonds : bond 0.03661 ( 403) hydrogen bonds : angle 4.25292 ( 1089) Misc. bond : bond 0.08532 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.382 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.0889 time to fit residues: 7.6395 Evaluate side-chains 50 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 717 GLN ** B 561 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 = 0.3427 r_free = 0.3427 target = 0.101254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.084590 restraints weight = 17090.220| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.30 r_work: 0.3038 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9629 Z= 0.116 Angle : 0.495 7.312 13122 Z= 0.243 Chirality : 0.039 0.169 1412 Planarity : 0.004 0.056 1722 Dihedral : 4.658 65.893 1324 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.21 % Allowed : 7.32 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1210 helix: 0.81 (0.22), residues: 567 sheet: -0.60 (1.18), residues: 21 loop : -1.34 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 373 TYR 0.010 0.001 TYR B 597 PHE 0.008 0.001 PHE B 129 TRP 0.008 0.001 TRP B 135 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9628) covalent geometry : angle 0.49546 (13122) hydrogen bonds : bond 0.03293 ( 403) hydrogen bonds : angle 3.96567 ( 1089) Misc. bond : bond 0.05257 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.314 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.0816 time to fit residues: 7.1062 Evaluate side-chains 53 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 71 optimal weight: 0.0980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 561 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085461 restraints weight = 16955.896| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.58 r_work: 0.3044 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9629 Z= 0.089 Angle : 0.479 7.559 13122 Z= 0.233 Chirality : 0.038 0.134 1412 Planarity : 0.004 0.051 1722 Dihedral : 4.434 67.770 1324 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.42 % Allowed : 9.13 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1210 helix: 1.03 (0.22), residues: 567 sheet: -0.18 (1.22), residues: 21 loop : -1.30 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 736 TYR 0.008 0.001 TYR B 597 PHE 0.007 0.001 PHE B 129 TRP 0.009 0.001 TRP B 135 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9628) covalent geometry : angle 0.47899 (13122) hydrogen bonds : bond 0.02797 ( 403) hydrogen bonds : angle 3.72391 ( 1089) Misc. bond : bond 0.05389 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.609 Fit side-chains REVERT: B 141 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8772 (mp) outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.0832 time to fit residues: 8.3891 Evaluate side-chains 57 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083666 restraints weight = 16923.236| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.55 r_work: 0.3010 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9629 Z= 0.123 Angle : 0.496 7.247 13122 Z= 0.242 Chirality : 0.039 0.120 1412 Planarity : 0.004 0.049 1722 Dihedral : 4.468 66.221 1324 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.85 % Allowed : 9.66 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1210 helix: 1.00 (0.22), residues: 573 sheet: 0.02 (1.23), residues: 21 loop : -1.30 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.019 0.001 TYR B 98 PHE 0.007 0.001 PHE A 167 TRP 0.011 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9628) covalent geometry : angle 0.49616 (13122) hydrogen bonds : bond 0.03047 ( 403) hydrogen bonds : angle 3.73910 ( 1089) Misc. bond : bond 0.03898 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.263 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.0886 time to fit residues: 7.8702 Evaluate side-chains 52 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.102684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084985 restraints weight = 16940.803| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.57 r_work: 0.3033 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 9629 Z= 0.098 Angle : 0.481 7.771 13122 Z= 0.234 Chirality : 0.038 0.120 1412 Planarity : 0.004 0.046 1722 Dihedral : 4.370 67.314 1324 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.64 % Allowed : 10.40 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.24), residues: 1210 helix: 1.13 (0.22), residues: 579 sheet: -0.23 (1.03), residues: 33 loop : -1.31 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 373 TYR 0.012 0.001 TYR B 98 PHE 0.006 0.001 PHE A 167 TRP 0.010 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9628) covalent geometry : angle 0.48071 (13122) hydrogen bonds : bond 0.02821 ( 403) hydrogen bonds : angle 3.64746 ( 1089) Misc. bond : bond 0.06702 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.294 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 61 average time/residue: 0.0716 time to fit residues: 6.9264 Evaluate side-chains 55 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 117 optimal weight: 8.9990 chunk 8 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 79 optimal weight: 0.0970 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087430 restraints weight = 16775.363| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.55 r_work: 0.3074 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 9629 Z= 0.084 Angle : 0.477 7.737 13122 Z= 0.229 Chirality : 0.037 0.118 1412 Planarity : 0.003 0.043 1722 Dihedral : 4.219 68.789 1324 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.21 % Allowed : 10.83 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1210 helix: 1.35 (0.22), residues: 570 sheet: -0.10 (1.04), residues: 33 loop : -1.23 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 187 TYR 0.007 0.001 TYR B 98 PHE 0.005 0.001 PHE B 129 TRP 0.011 0.001 TRP B 397 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 9628) covalent geometry : angle 0.47729 (13122) hydrogen bonds : bond 0.02535 ( 403) hydrogen bonds : angle 3.49799 ( 1089) Misc. bond : bond 0.07658 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.303 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.0765 time to fit residues: 7.6715 Evaluate side-chains 57 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 116 optimal weight: 0.0970 chunk 108 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 chunk 115 optimal weight: 0.0970 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 1 optimal weight: 6.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.088236 restraints weight = 16766.315| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.46 r_work: 0.3104 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 9629 Z= 0.084 Angle : 0.482 7.638 13122 Z= 0.230 Chirality : 0.037 0.124 1412 Planarity : 0.003 0.042 1722 Dihedral : 4.144 68.801 1324 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.53 % Allowed : 11.36 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.24), residues: 1210 helix: 1.48 (0.22), residues: 569 sheet: 0.73 (1.32), residues: 21 loop : -1.19 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 119 TYR 0.017 0.001 TYR B 98 PHE 0.005 0.001 PHE B 129 TRP 0.012 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 9628) covalent geometry : angle 0.48235 (13122) hydrogen bonds : bond 0.02482 ( 403) hydrogen bonds : angle 3.42246 ( 1089) Misc. bond : bond 0.07595 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.351 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 0.0903 time to fit residues: 8.5925 Evaluate side-chains 61 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.086888 restraints weight = 16739.205| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.45 r_work: 0.3082 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 9629 Z= 0.097 Angle : 0.493 7.991 13122 Z= 0.236 Chirality : 0.038 0.119 1412 Planarity : 0.003 0.042 1722 Dihedral : 4.168 67.934 1324 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.64 % Allowed : 11.25 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1210 helix: 1.48 (0.22), residues: 571 sheet: 1.18 (1.34), residues: 20 loop : -1.20 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.017 0.001 TYR B 98 PHE 0.006 0.001 PHE A 167 TRP 0.012 0.001 TRP B 397 HIS 0.004 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9628) covalent geometry : angle 0.49330 (13122) hydrogen bonds : bond 0.02653 ( 403) hydrogen bonds : angle 3.43946 ( 1089) Misc. bond : bond 0.06728 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.380 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.0871 time to fit residues: 8.2087 Evaluate side-chains 60 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085969 restraints weight = 16775.412| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.52 r_work: 0.3044 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9629 Z= 0.103 Angle : 0.497 8.284 13122 Z= 0.238 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.042 1722 Dihedral : 4.215 67.601 1324 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.85 % Allowed : 11.04 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1210 helix: 1.45 (0.22), residues: 571 sheet: 0.31 (1.06), residues: 32 loop : -1.20 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.018 0.001 TYR B 98 PHE 0.006 0.001 PHE A 167 TRP 0.014 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9628) covalent geometry : angle 0.49730 (13122) hydrogen bonds : bond 0.02761 ( 403) hydrogen bonds : angle 3.49030 ( 1089) Misc. bond : bond 0.06641 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.275 Fit side-chains REVERT: A 609 MET cc_start: 0.8537 (mmm) cc_final: 0.8276 (mtt) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.0717 time to fit residues: 7.3478 Evaluate side-chains 62 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 732 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 49 HIS ** 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 = 0.3458 r_free = 0.3458 target = 0.103561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.086127 restraints weight = 16631.871| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.52 r_work: 0.3049 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9629 Z= 0.101 Angle : 0.493 8.289 13122 Z= 0.236 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.042 1722 Dihedral : 4.223 67.801 1324 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.74 % Allowed : 11.25 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.24), residues: 1210 helix: 1.47 (0.22), residues: 570 sheet: 0.30 (1.06), residues: 32 loop : -1.21 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.024 0.001 TYR B 98 PHE 0.006 0.001 PHE A 167 TRP 0.014 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 9628) covalent geometry : angle 0.49337 (13122) hydrogen bonds : bond 0.02755 ( 403) hydrogen bonds : angle 3.49272 ( 1089) Misc. bond : bond 0.06828 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1852.97 seconds wall clock time: 32 minutes 30.34 seconds (1950.34 seconds total)