Starting phenix.real_space_refine on Fri Mar 14 03:19:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a7c_11677/03_2025/7a7c_11677.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a7c_11677/03_2025/7a7c_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2025/7a7c_11677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2025/7a7c_11677.map" model { file = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2025/7a7c_11677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a7c_11677/03_2025/7a7c_11677.cif" } resolution = 3.16 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= 0.012 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 5} 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: {'GLU:plan': 2, 'ASP:plan': 3} 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: 6.28, per 1000 atoms: 0.67 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.03 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: 2.57 Time building geometry restraints manager: 2.99 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: 3.700 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.920 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- 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 : 0.003 0.050 9628 Z= 0.206 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 : 6.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (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 TRP 0.012 0.001 TRP A 689 HIS 0.005 0.001 HIS A 49 PHE 0.013 0.001 PHE B 129 TYR 0.011 0.001 TYR B 98 ARG 0.004 0.000 ARG B 146 *********************** 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 : 0.958 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2173 time to fit residues: 22.6549 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 : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.097049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080342 restraints weight = 17098.374| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.28 r_work: 0.2972 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9628 Z= 0.382 Angle : 0.581 8.636 13122 Z= 0.289 Chirality : 0.043 0.124 1412 Planarity : 0.005 0.067 1722 Dihedral : 5.024 59.896 1324 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.32 % Allowed : 7.11 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1210 helix: 0.41 (0.22), residues: 568 sheet: -1.36 (1.11), residues: 21 loop : -1.43 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 135 HIS 0.004 0.001 HIS A 49 PHE 0.011 0.001 PHE B 724 TYR 0.016 0.002 TYR B 98 ARG 0.003 0.000 ARG A 496 *********************** 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 53 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 1.076 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.2082 time to fit residues: 16.4714 Evaluate side-chains 46 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.100920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.084155 restraints weight = 16886.310| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.32 r_work: 0.3040 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9628 Z= 0.166 Angle : 0.491 6.880 13122 Z= 0.241 Chirality : 0.039 0.170 1412 Planarity : 0.004 0.057 1722 Dihedral : 4.703 66.510 1324 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.21 % Allowed : 8.81 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1210 helix: 0.80 (0.22), residues: 564 sheet: -0.59 (1.16), residues: 21 loop : -1.37 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 135 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE B 129 TYR 0.010 0.001 TYR B 597 ARG 0.003 0.000 ARG B 373 *********************** 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 63 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 1.065 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 63 average time/residue: 0.1916 time to fit residues: 18.4707 Evaluate side-chains 54 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 109 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.101603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.084877 restraints weight = 16920.634| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.32 r_work: 0.3043 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9628 Z= 0.174 Angle : 0.494 7.462 13122 Z= 0.241 Chirality : 0.038 0.122 1412 Planarity : 0.004 0.051 1722 Dihedral : 4.567 65.828 1324 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.53 % Allowed : 9.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1210 helix: 0.89 (0.22), residues: 573 sheet: -0.35 (1.22), residues: 21 loop : -1.33 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.003 0.001 HIS A 49 PHE 0.007 0.001 PHE B 129 TYR 0.011 0.001 TYR B 98 ARG 0.002 0.000 ARG A 119 *********************** 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 62 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.071 Fit side-chains REVERT: B 141 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8895 (mp) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.1996 time to fit residues: 18.6232 Evaluate side-chains 55 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.101354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083789 restraints weight = 16758.178| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.54 r_work: 0.3012 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9628 Z= 0.177 Angle : 0.490 7.119 13122 Z= 0.239 Chirality : 0.038 0.120 1412 Planarity : 0.004 0.048 1722 Dihedral : 4.509 66.190 1324 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.53 % Allowed : 10.62 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1210 helix: 0.92 (0.22), residues: 573 sheet: -0.37 (1.04), residues: 31 loop : -1.34 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 PHE 0.006 0.001 PHE A 167 TYR 0.008 0.001 TYR B 597 ARG 0.001 0.000 ARG B 373 *********************** 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 59 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 1.094 Fit side-chains REVERT: B 141 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8768 (mp) outliers start: 5 outliers final: 3 residues processed: 59 average time/residue: 0.2029 time to fit residues: 18.1639 Evaluate side-chains 56 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 656 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 0.0470 chunk 10 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.102984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.085442 restraints weight = 16751.038| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.53 r_work: 0.3042 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9628 Z= 0.144 Angle : 0.478 7.039 13122 Z= 0.232 Chirality : 0.038 0.119 1412 Planarity : 0.004 0.045 1722 Dihedral : 4.356 67.543 1324 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.64 % Allowed : 11.04 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1210 helix: 1.10 (0.22), residues: 573 sheet: -0.31 (1.02), residues: 33 loop : -1.29 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 PHE 0.005 0.001 PHE B 129 TYR 0.020 0.001 TYR B 98 ARG 0.001 0.000 ARG B 373 *********************** 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 65 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 1.163 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.2505 time to fit residues: 25.7641 Evaluate side-chains 54 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 3 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 99 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 0.0770 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8298 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.102097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.084536 restraints weight = 16781.642| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.53 r_work: 0.3022 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9628 Z= 0.175 Angle : 0.488 7.637 13122 Z= 0.237 Chirality : 0.038 0.119 1412 Planarity : 0.004 0.044 1722 Dihedral : 4.371 66.644 1324 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.64 % Allowed : 11.68 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.24), residues: 1210 helix: 1.15 (0.22), residues: 579 sheet: -0.27 (1.01), residues: 33 loop : -1.29 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 PHE 0.006 0.001 PHE A 167 TYR 0.023 0.001 TYR B 98 ARG 0.001 0.000 ARG B 373 *********************** 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 61 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 1.037 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.2024 time to fit residues: 18.3717 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 : 1.972 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 0.0040 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 35 optimal weight: 0.0000 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 71 optimal weight: 0.3980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3469 r_free = 0.3469 target = 0.104348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086992 restraints weight = 16886.046| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.48 r_work: 0.3067 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9628 Z= 0.136 Angle : 0.475 7.869 13122 Z= 0.228 Chirality : 0.037 0.119 1412 Planarity : 0.003 0.042 1722 Dihedral : 4.232 68.267 1324 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.74 % Allowed : 11.78 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1210 helix: 1.34 (0.22), residues: 570 sheet: -0.14 (1.03), residues: 33 loop : -1.19 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 PHE 0.005 0.001 PHE B 129 TYR 0.014 0.001 TYR B 98 ARG 0.001 0.000 ARG B 736 *********************** 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 65 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 1.050 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 63 average time/residue: 0.1782 time to fit residues: 17.7373 Evaluate side-chains 56 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 84 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.102076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084263 restraints weight = 16823.739| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.58 r_work: 0.3019 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9628 Z= 0.192 Angle : 0.500 8.015 13122 Z= 0.241 Chirality : 0.039 0.120 1412 Planarity : 0.004 0.043 1722 Dihedral : 4.321 66.664 1324 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.85 % Allowed : 12.21 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1210 helix: 1.30 (0.22), residues: 576 sheet: 0.23 (1.05), residues: 32 loop : -1.25 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 397 HIS 0.004 0.000 HIS A 49 PHE 0.007 0.001 PHE A 167 TYR 0.038 0.001 TYR B 98 ARG 0.001 0.000 ARG A 128 *********************** 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: 8 poor density : 56 time to evaluate : 1.107 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.2273 time to fit residues: 21.2966 Evaluate side-chains 59 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ILE 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 36 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 59 optimal weight: 0.0980 chunk 108 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 72 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: ** 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 = 0.3457 r_free = 0.3457 target = 0.103559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085864 restraints weight = 16909.865| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.57 r_work: 0.3047 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9628 Z= 0.154 Angle : 0.489 8.290 13122 Z= 0.235 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.043 1722 Dihedral : 4.260 67.789 1324 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.74 % Allowed : 11.89 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1210 helix: 1.42 (0.22), residues: 570 sheet: 0.28 (1.06), residues: 32 loop : -1.16 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 PHE 0.005 0.001 PHE A 167 TYR 0.017 0.001 TYR B 98 ARG 0.001 0.000 ARG A 187 ********************** 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 66 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 1.262 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.2777 time to fit residues: 26.8687 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 : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 565 VAL 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 19 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 0.0170 chunk 32 optimal weight: 0.3980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.101140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.083900 restraints weight = 16747.794| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.49 r_work: 0.3032 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9628 Z= 0.183 Angle : 0.498 8.226 13122 Z= 0.240 Chirality : 0.038 0.120 1412 Planarity : 0.003 0.044 1722 Dihedral : 4.312 66.895 1324 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.74 % Allowed : 11.89 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.24), residues: 1210 helix: 1.33 (0.22), residues: 577 sheet: 0.24 (1.05), residues: 32 loop : -1.22 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 397 HIS 0.003 0.000 HIS A 49 PHE 0.007 0.001 PHE A 167 TYR 0.018 0.001 TYR B 98 ARG 0.002 0.000 ARG B 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4324.86 seconds wall clock time: 79 minutes 13.63 seconds (4753.63 seconds total)