Starting phenix.real_space_refine on Fri Sep 11 19:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ag8_11776/09_2026/7ag8_11776.cif" } resolution = 2.68 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= 0.001 sd= 0.086 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 2 7.16 5 S 38 5.16 5 C 6956 2.51 5 N 1867 2.21 5 O 2059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10922 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 702, 5356 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 45, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 702, 5356 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 45, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 5495 Chain: "B" Number of atoms: 5472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 715, 5464 Classifications: {'peptide': 715} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 668} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 715, 5464 Classifications: {'peptide': 715} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 46, 'TRANS': 668} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 5605 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} 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: 4.53, per 1000 atoms: 0.41 Number of scatterers: 10922 At special positions: 0 Unit cell: (84.66, 97.11, 124.5, 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 2 26.01 S 38 16.00 O 2059 8.00 N 1867 7.00 C 6956 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 922.8 milliseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2536 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 6 sheets defined 53.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.566A pdb=" N VAL A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.709A pdb=" N ALA A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.546A pdb=" N GLY A 96 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 97' Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 125 through 128 removed outlier: 3.542A pdb=" N ARG A 128 " --> pdb=" O GLY A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 128' Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.891A pdb=" N SER A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.539A pdb=" N ALA A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 removed outlier: 3.579A 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 176 removed outlier: 3.691A pdb=" N VAL A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.921A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 270 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.602A pdb=" N LEU A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 292 through 296 removed outlier: 3.539A pdb=" N GLN A 295 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.596A pdb=" N ASP A 311 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 387 through 400 removed outlier: 3.889A pdb=" N ARG A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 416 removed outlier: 3.627A 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 453 through 464 removed outlier: 3.593A pdb=" N ALA A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 481 Processing helix chain 'A' and resid 495 through 498 removed outlier: 4.034A 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 removed outlier: 3.625A pdb=" N GLY A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.751A pdb=" N SER A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 560 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 635 removed outlier: 4.143A 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 693 through 701 removed outlier: 4.286A pdb=" N PHE A 698 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.686A pdb=" N LEU A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 710 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 711 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 733 Processing helix chain 'B' and resid 44 through 50 removed outlier: 3.873A pdb=" N VAL B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 50 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 111 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.663A pdb=" N ALA B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 156 removed outlier: 3.716A pdb=" N LYS B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 176 removed outlier: 3.643A pdb=" N VAL B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.508A pdb=" N GLY B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.513A pdb=" N ALA B 291 " --> pdb=" O PRO B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 296 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.810A pdb=" N ASP B 311 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 337 Processing helix chain 'B' and resid 356 through 359 Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.128A pdb=" N GLU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 417 removed outlier: 3.574A pdb=" N LEU B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 removed outlier: 4.387A pdb=" N GLY B 421 " --> pdb=" O ARG B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 421' Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 440 Processing helix chain 'B' and resid 453 through 464 Processing helix chain 'B' and resid 468 through 481 Processing helix chain 'B' and resid 495 through 498 removed outlier: 3.904A pdb=" N ARG B 498 " --> pdb=" O GLY B 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.574A pdb=" N GLY B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 530 Processing helix chain 'B' and resid 539 through 560 Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 593 through 596 Processing helix chain 'B' and resid 605 through 617 Processing helix chain 'B' and resid 620 through 634 removed outlier: 3.875A 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 656 through 662 Processing helix chain 'B' and resid 693 through 701 removed outlier: 4.542A pdb=" N PHE B 698 " --> pdb=" O VAL B 694 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.529A pdb=" N ALA B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 711 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 733 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA3, first strand: chain 'A' and resid 667 through 670 Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 345 Processing sheet with id=AA5, first strand: chain 'B' and resid 591 through 592 Processing sheet with id=AA6, first strand: chain 'B' and resid 667 through 670 435 hydrogen bonds defined for protein. 1158 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: 1.89 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 3705 1.36 - 1.53: 7218 1.53 - 1.71: 233 1.71 - 1.88: 72 1.88 - 2.05: 8 Bond restraints: 11236 Sorted by residual: bond pdb=" C ALA B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.11e-02 8.12e+03 1.45e+01 bond pdb=" C PRO B 89 " pdb=" O PRO B 89 " ideal model delta sigma weight residual 1.238 1.189 0.049 1.33e-02 5.65e+03 1.35e+01 bond pdb=" CA ALA A 93 " pdb=" CB ALA A 93 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.48e-02 4.57e+03 1.32e+01 bond pdb=" C TYR B 98 " pdb=" O TYR B 98 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.28e-02 6.10e+03 1.19e+01 bond pdb=" N ASN B 133 " pdb=" CA ASN B 133 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.89e+00 ... (remaining 11231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 14940 1.64 - 3.28: 327 3.28 - 4.93: 69 4.93 - 6.57: 16 6.57 - 8.21: 7 Bond angle restraints: 15359 Sorted by residual: angle pdb=" C PRO B 89 " pdb=" CA PRO B 89 " pdb=" CB PRO B 89 " ideal model delta sigma weight residual 112.26 104.55 7.71 1.67e+00 3.59e-01 2.13e+01 angle pdb=" N ASN B 133 " pdb=" CA ASN B 133 " pdb=" CB ASN B 133 " ideal model delta sigma weight residual 110.49 117.88 -7.39 1.69e+00 3.50e-01 1.91e+01 angle pdb=" CA TRP A 91 " pdb=" C TRP A 91 " pdb=" N PRO A 92 " ideal model delta sigma weight residual 117.57 121.35 -3.78 8.70e-01 1.32e+00 1.88e+01 angle pdb=" CA TRP B 91 " pdb=" C TRP B 91 " pdb=" O TRP B 91 " ideal model delta sigma weight residual 121.34 117.37 3.97 9.40e-01 1.13e+00 1.78e+01 angle pdb=" N PRO B 89 " pdb=" CA PRO B 89 " pdb=" C PRO B 89 " ideal model delta sigma weight residual 113.81 119.72 -5.91 1.45e+00 4.76e-01 1.66e+01 ... (remaining 15354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5988 17.75 - 35.51: 425 35.51 - 53.26: 58 53.26 - 71.02: 24 71.02 - 88.77: 10 Dihedral angle restraints: 6505 sinusoidal: 2510 harmonic: 3995 Sorted by residual: dihedral pdb=" CA TYR B 28 " pdb=" C TYR B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PHE A 129 " pdb=" C PHE A 129 " pdb=" N ALA A 130 " pdb=" CA ALA A 130 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLY B 451 " pdb=" C GLY B 451 " pdb=" N GLU B 452 " pdb=" CA GLU B 452 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1243 0.051 - 0.102: 315 0.102 - 0.152: 48 0.152 - 0.203: 2 0.203 - 0.254: 3 Chirality restraints: 1611 Sorted by residual: chirality pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" C PRO A 92 " pdb=" CB PRO A 92 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ASN B 133 " pdb=" N ASN B 133 " pdb=" C ASN B 133 " pdb=" CB ASN B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1608 not shown) Planarity restraints: 2023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 130 " -0.052 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO B 131 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 95 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C TYR A 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR A 95 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 96 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 133 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.31e+00 pdb=" C ASN B 133 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN B 133 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 134 " -0.014 2.00e-02 2.50e+03 ... (remaining 2020 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1830 2.76 - 3.29: 10441 3.29 - 3.83: 18701 3.83 - 4.36: 23160 4.36 - 4.90: 39543 Nonbonded interactions: 93675 Sorted by model distance: nonbonded pdb=" OH TYR B 337 " pdb=" OG1 THR B 394 " model vdw 2.220 3.040 nonbonded pdb=" OH TYR A 337 " pdb=" OG1 THR A 394 " model vdw 2.227 3.040 nonbonded pdb=" NZ LYS B 274 " pdb=" O THR B 275 " model vdw 2.285 3.120 nonbonded pdb=" NH1 ARG A 146 " pdb=" O MET A 296 " model vdw 2.295 3.120 nonbonded pdb=" O MET B 420 " pdb=" NH1 ARG B 425 " model vdw 2.305 3.120 ... (remaining 93670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 355 or (resid 356 and (name N or n \ ame CA or name C or name O or name CB )) or resid 357 through 417 or resid 419 t \ hrough 512 or (resid 513 and (name N or name CA or name C or name O or name CB ) \ ) or resid 514 through 714 or (resid 715 through 716 and (name N or name CA or n \ ame C or name O or name CB )) or resid 717 through 801)) selection = (chain 'B' and (resid 26 through 194 or (resid 195 and (name N or name CA or nam \ e C or name O or name CB )) or resid 196 through 202 or (resid 203 and (name N o \ r name CA or name C or name O or name CB )) or resid 204 through 205 or resid 22 \ 1 through 417 or resid 419 through 515 or (resid 516 and (name N or name CA or n \ ame C or name O or name CB )) or resid 517 through 556 or (resid 557 through 559 \ and (name N or name CA or name C or name O or name CB )) or resid 560 through 5 \ 89 or (resid 590 through 591 and (name N or name CA or name C or name O or name \ CB )) or resid 592 through 801)) } 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: 1.690 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.260 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.008 0.460 11238 Z= 0.234 Angle : 0.647 8.212 15359 Z= 0.376 Chirality : 0.045 0.254 1611 Planarity : 0.005 0.078 2023 Dihedral : 13.126 88.772 3969 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 0.37 % Allowed : 0.27 % Favored : 99.36 % 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: -0.60 (0.21), residues: 1413 helix: 0.56 (0.22), residues: 584 sheet: -0.45 (1.18), residues: 20 loop : -1.14 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 736 TYR 0.015 0.001 TYR B 98 PHE 0.008 0.001 PHE A 167 TRP 0.038 0.001 TRP B 107 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (11236) covalent geometry : angle 0.64707 / 0.38 (15359) hydrogen bonds : bond 0.18702 / 12.88 ( 435) hydrogen bonds : angle 5.54279 / 3.93 ( 1158) Misc. bond : bond 0.45042 / 26.70 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.439 Fit side-chains REVERT: A 82 GLU cc_start: 0.7071 (pp20) cc_final: 0.6859 (pp20) REVERT: A 94 ASP cc_start: 0.7954 (m-30) cc_final: 0.7748 (m-30) REVERT: A 225 MET cc_start: 0.4987 (pmm) cc_final: 0.3309 (ptm) REVERT: A 392 ARG cc_start: 0.6911 (ptp-110) cc_final: 0.6698 (mtm110) REVERT: B 304 TYR cc_start: 0.7422 (t80) cc_final: 0.6796 (t80) REVERT: B 663 ASP cc_start: 0.7672 (t0) cc_final: 0.7409 (t0) REVERT: B 703 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6870 (mp0) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.6277 time to fit residues: 67.9307 Evaluate side-chains 77 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 97 HIS ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096257 restraints weight = 34539.257| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.60 r_work: 0.3199 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.172 11238 Z= 0.116 Angle : 0.569 11.418 15359 Z= 0.280 Chirality : 0.042 0.149 1611 Planarity : 0.004 0.044 2023 Dihedral : 5.642 73.367 1549 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.68 % Rotamer: Outliers : 0.73 % Allowed : 4.67 % Favored : 94.60 % 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 (0.21), residues: 1413 helix: 0.84 (0.21), residues: 584 sheet: -0.37 (0.94), residues: 30 loop : -0.88 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 395 TYR 0.021 0.001 TYR B 155 PHE 0.007 0.001 PHE A 724 TRP 0.011 0.001 TRP A 341 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (11236) covalent geometry : angle 0.56922 / 0.28 (15359) hydrogen bonds : bond 0.04010 / 2.70 ( 435) hydrogen bonds : angle 4.29533 / 3.10 ( 1158) Misc. bond : bond 0.15917 / 9.51 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.438 Fit side-chains REVERT: A 82 GLU cc_start: 0.7547 (pp20) cc_final: 0.7329 (pp20) REVERT: A 225 MET cc_start: 0.5131 (pmm) cc_final: 0.3423 (ptm) REVERT: A 392 ARG cc_start: 0.7210 (ptp-110) cc_final: 0.6976 (mtm110) REVERT: A 506 GLU cc_start: 0.8530 (tp30) cc_final: 0.8269 (tp30) REVERT: A 596 ASN cc_start: 0.8534 (t0) cc_final: 0.8298 (t0) REVERT: A 607 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: B 133 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7365 (p0) REVERT: B 304 TYR cc_start: 0.7672 (t80) cc_final: 0.6988 (t80) REVERT: B 703 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7361 (mp0) outliers start: 5 outliers final: 1 residues processed: 89 average time/residue: 0.5964 time to fit residues: 57.8460 Evaluate side-chains 81 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 94 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 133 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3531 r_free = 0.3531 target = 0.123661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097296 restraints weight = 30769.146| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.43 r_work: 0.3222 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 11238 Z= 0.110 Angle : 0.540 10.622 15359 Z= 0.262 Chirality : 0.042 0.132 1611 Planarity : 0.004 0.041 2023 Dihedral : 5.447 74.219 1549 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.54 % Favored : 96.39 % Rotamer: Outliers : 0.82 % Allowed : 5.49 % Favored : 93.68 % 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: 0.04 (0.22), residues: 1413 helix: 1.04 (0.21), residues: 584 sheet: 0.47 (1.04), residues: 20 loop : -0.74 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.016 0.001 TYR B 155 PHE 0.008 0.001 PHE B 129 TRP 0.012 0.001 TRP A 191 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (11236) covalent geometry : angle 0.53980 / 0.26 (15359) hydrogen bonds : bond 0.03741 / 2.52 ( 435) hydrogen bonds : angle 4.05172 / 2.93 ( 1158) Misc. bond : bond 0.13055 / 7.82 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.412 Fit side-chains REVERT: A 225 MET cc_start: 0.5159 (pmm) cc_final: 0.3572 (ptm) REVERT: A 392 ARG cc_start: 0.7220 (ptp-110) cc_final: 0.6978 (mtm110) REVERT: A 474 SER cc_start: 0.7775 (t) cc_final: 0.7201 (m) REVERT: A 506 GLU cc_start: 0.8559 (tp30) cc_final: 0.8325 (tp30) REVERT: A 596 ASN cc_start: 0.8524 (t0) cc_final: 0.8292 (t0) REVERT: B 107 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.7013 (t60) REVERT: B 304 TYR cc_start: 0.7662 (t80) cc_final: 0.6953 (t80) REVERT: B 703 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7386 (mp0) outliers start: 6 outliers final: 2 residues processed: 83 average time/residue: 0.5931 time to fit residues: 53.6182 Evaluate side-chains 79 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 4.9990 chunk 138 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.63 > 50:) chunk 13 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 0.1980 chunk 108 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN A 97 HIS ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097117 restraints weight = 39366.069| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.88 r_work: 0.3208 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 11238 Z= 0.101 Angle : 0.527 10.417 15359 Z= 0.255 Chirality : 0.041 0.133 1611 Planarity : 0.004 0.043 2023 Dihedral : 5.136 73.155 1547 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 1.01 % Allowed : 5.68 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.22), residues: 1413 helix: 1.21 (0.22), residues: 581 sheet: 0.30 (1.07), residues: 20 loop : -0.64 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.016 0.001 TYR B 155 PHE 0.009 0.001 PHE B 129 TRP 0.011 0.001 TRP A 191 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (11236) covalent geometry : angle 0.52657 / 0.25 (15359) hydrogen bonds : bond 0.03415 / 2.28 ( 435) hydrogen bonds : angle 3.91582 / 2.83 ( 1158) Misc. bond : bond 0.12465 / 7.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.448 Fit side-chains REVERT: A 392 ARG cc_start: 0.7213 (ptp-110) cc_final: 0.6973 (mtm110) REVERT: A 474 SER cc_start: 0.7825 (t) cc_final: 0.7262 (m) REVERT: A 506 GLU cc_start: 0.8554 (tp30) cc_final: 0.8297 (tp30) REVERT: A 596 ASN cc_start: 0.8531 (t0) cc_final: 0.8278 (t0) REVERT: B 107 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.6929 (t60) REVERT: B 304 TYR cc_start: 0.7641 (t80) cc_final: 0.6923 (t80) REVERT: B 703 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7445 (mp0) outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 0.6115 time to fit residues: 57.8823 Evaluate side-chains 81 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 46 optimal weight: 0.0000 chunk 71 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 49 optimal weight: 0.0270 chunk 99 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.098245 restraints weight = 36700.740| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.73 r_work: 0.3230 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.140 11238 Z= 0.098 Angle : 0.523 10.305 15359 Z= 0.252 Chirality : 0.041 0.129 1611 Planarity : 0.004 0.043 2023 Dihedral : 5.043 72.739 1547 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 1.10 % Allowed : 6.78 % Favored : 92.12 % 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: 0.36 (0.22), residues: 1413 helix: 1.28 (0.22), residues: 584 sheet: 0.53 (1.07), residues: 20 loop : -0.53 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 693 TYR 0.016 0.001 TYR B 155 PHE 0.010 0.001 PHE B 129 TRP 0.011 0.001 TRP A 107 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (11236) covalent geometry : angle 0.52257 / 0.25 (15359) hydrogen bonds : bond 0.03271 / 2.18 ( 435) hydrogen bonds : angle 3.82531 / 2.77 ( 1158) Misc. bond : bond 0.12589 / 7.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.424 Fit side-chains REVERT: A 225 MET cc_start: 0.4559 (pmm) cc_final: 0.2788 (ptm) REVERT: A 392 ARG cc_start: 0.7216 (ptp-110) cc_final: 0.6980 (mtm110) REVERT: A 474 SER cc_start: 0.7828 (t) cc_final: 0.7275 (m) REVERT: A 596 ASN cc_start: 0.8535 (t0) cc_final: 0.8278 (t0) REVERT: B 107 TRP cc_start: 0.7324 (OUTLIER) cc_final: 0.6929 (t60) REVERT: B 304 TYR cc_start: 0.7650 (t80) cc_final: 0.7013 (t80) REVERT: B 516 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6665 (ptmm) REVERT: B 703 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7452 (mp0) outliers start: 9 outliers final: 4 residues processed: 83 average time/residue: 0.6260 time to fit residues: 56.3686 Evaluate side-chains 80 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3526 r_free = 0.3526 target = 0.122833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096600 restraints weight = 34300.256| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.64 r_work: 0.3215 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 11238 Z= 0.120 Angle : 0.534 10.349 15359 Z= 0.257 Chirality : 0.042 0.129 1611 Planarity : 0.004 0.043 2023 Dihedral : 5.119 72.473 1547 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 1.10 % Allowed : 7.23 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.22), residues: 1413 helix: 1.25 (0.22), residues: 584 sheet: 0.48 (1.09), residues: 20 loop : -0.54 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.017 0.001 TYR B 155 PHE 0.012 0.001 PHE B 129 TRP 0.015 0.001 TRP A 107 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (11236) covalent geometry : angle 0.53382 / 0.26 (15359) hydrogen bonds : bond 0.03513 / 2.33 ( 435) hydrogen bonds : angle 3.82487 / 2.76 ( 1158) Misc. bond : bond 0.11628 / 6.97 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.425 Fit side-chains REVERT: A 225 MET cc_start: 0.4572 (pmm) cc_final: 0.2651 (ptm) REVERT: A 392 ARG cc_start: 0.7220 (ptp-110) cc_final: 0.6996 (mtm110) REVERT: A 474 SER cc_start: 0.7823 (t) cc_final: 0.7237 (m) REVERT: A 596 ASN cc_start: 0.8585 (t0) cc_final: 0.8348 (t0) REVERT: B 107 TRP cc_start: 0.7470 (OUTLIER) cc_final: 0.7012 (t60) REVERT: B 304 TYR cc_start: 0.7660 (t80) cc_final: 0.7015 (t80) REVERT: B 516 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6696 (ptmm) REVERT: B 573 ASP cc_start: 0.7700 (m-30) cc_final: 0.7430 (m-30) outliers start: 9 outliers final: 4 residues processed: 81 average time/residue: 0.6118 time to fit residues: 53.8952 Evaluate side-chains 81 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3517 r_free = 0.3517 target = 0.122135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096100 restraints weight = 32266.319| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.53 r_work: 0.3208 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 11238 Z= 0.133 Angle : 0.546 10.491 15359 Z= 0.264 Chirality : 0.042 0.138 1611 Planarity : 0.004 0.043 2023 Dihedral : 5.177 72.207 1547 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 1.01 % Allowed : 7.51 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.28 (0.22), residues: 1413 helix: 1.18 (0.22), residues: 584 sheet: 0.50 (1.08), residues: 20 loop : -0.54 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.018 0.001 TYR B 155 PHE 0.014 0.001 PHE B 129 TRP 0.017 0.001 TRP A 107 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (11236) covalent geometry : angle 0.54611 / 0.26 (15359) hydrogen bonds : bond 0.03621 / 2.39 ( 435) hydrogen bonds : angle 3.84905 / 2.77 ( 1158) Misc. bond : bond 0.10741 / 6.45 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.467 Fit side-chains REVERT: A 225 MET cc_start: 0.4568 (pmm) cc_final: 0.2707 (ptm) REVERT: A 392 ARG cc_start: 0.7215 (ptp-110) cc_final: 0.6997 (mtm110) REVERT: A 596 ASN cc_start: 0.8601 (t0) cc_final: 0.8369 (t0) REVERT: B 107 TRP cc_start: 0.7523 (OUTLIER) cc_final: 0.7004 (t60) REVERT: B 304 TYR cc_start: 0.7648 (t80) cc_final: 0.6977 (t80) REVERT: B 516 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6746 (ptmm) REVERT: B 703 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7478 (mp0) outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 0.6230 time to fit residues: 53.5222 Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.120556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096573 restraints weight = 17517.046| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.59 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 11238 Z= 0.154 Angle : 0.562 10.417 15359 Z= 0.273 Chirality : 0.043 0.136 1611 Planarity : 0.004 0.044 2023 Dihedral : 5.300 72.140 1547 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.10 % Allowed : 7.42 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.22), residues: 1413 helix: 1.09 (0.22), residues: 584 sheet: 0.63 (1.07), residues: 20 loop : -0.58 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 114 TYR 0.019 0.001 TYR B 155 PHE 0.015 0.001 PHE B 129 TRP 0.021 0.001 TRP A 107 HIS 0.005 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.15 (11236) covalent geometry : angle 0.56217 / 0.27 (15359) hydrogen bonds : bond 0.03855 / 2.55 ( 435) hydrogen bonds : angle 3.90834 / 2.81 ( 1158) Misc. bond : bond 0.09520 / 5.74 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.435 Fit side-chains REVERT: A 392 ARG cc_start: 0.7335 (ptp-110) cc_final: 0.7118 (mtm110) REVERT: A 596 ASN cc_start: 0.8679 (t0) cc_final: 0.8453 (t0) REVERT: B 107 TRP cc_start: 0.7733 (OUTLIER) cc_final: 0.7099 (t60) REVERT: B 304 TYR cc_start: 0.7611 (t80) cc_final: 0.6912 (t80) REVERT: B 703 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7564 (mp0) outliers start: 9 outliers final: 5 residues processed: 81 average time/residue: 0.6074 time to fit residues: 53.5698 Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 32 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3591 r_free = 0.3591 target = 0.126143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.101403 restraints weight = 21878.063| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.50 r_work: 0.3422 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 11238 Z= 0.114 Angle : 0.543 10.215 15359 Z= 0.262 Chirality : 0.042 0.135 1611 Planarity : 0.004 0.043 2023 Dihedral : 5.146 71.626 1547 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.01 % Allowed : 7.69 % Favored : 91.30 % 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: 0.32 (0.22), residues: 1413 helix: 1.16 (0.22), residues: 584 sheet: 0.93 (1.03), residues: 20 loop : -0.50 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.017 0.001 TYR B 155 PHE 0.011 0.001 PHE B 129 TRP 0.018 0.001 TRP A 107 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 (11236) covalent geometry : angle 0.54282 / 0.26 (15359) hydrogen bonds : bond 0.03452 / 2.29 ( 435) hydrogen bonds : angle 3.86018 / 2.78 ( 1158) Misc. bond : bond 0.10643 / 6.41 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.447 Fit side-chains REVERT: A 255 MET cc_start: 0.7872 (mtt) cc_final: 0.7351 (ptp) REVERT: A 392 ARG cc_start: 0.7357 (ptp-110) cc_final: 0.7148 (mtm110) REVERT: A 596 ASN cc_start: 0.8729 (t0) cc_final: 0.8505 (t0) REVERT: B 107 TRP cc_start: 0.7687 (OUTLIER) cc_final: 0.7123 (t60) REVERT: B 304 TYR cc_start: 0.7707 (t80) cc_final: 0.7115 (t80) REVERT: B 573 ASP cc_start: 0.7874 (m-30) cc_final: 0.7554 (m-30) REVERT: B 703 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7597 (mp0) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.6047 time to fit residues: 52.0997 Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 83 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.123598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097190 restraints weight = 26626.003| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.87 r_work: 0.3422 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 11238 Z= 0.109 Angle : 0.536 10.015 15359 Z= 0.259 Chirality : 0.041 0.128 1611 Planarity : 0.004 0.044 2023 Dihedral : 5.090 71.532 1547 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.10 % Allowed : 7.51 % Favored : 91.39 % 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: 0.39 (0.22), residues: 1413 helix: 1.23 (0.22), residues: 584 sheet: 0.99 (1.05), residues: 20 loop : -0.46 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 114 TYR 0.016 0.001 TYR B 155 PHE 0.011 0.001 PHE B 129 TRP 0.020 0.001 TRP A 107 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (11236) covalent geometry : angle 0.53576 / 0.26 (15359) hydrogen bonds : bond 0.03347 / 2.22 ( 435) hydrogen bonds : angle 3.81783 / 2.76 ( 1158) Misc. bond : bond 0.11294 / 6.78 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.420 Fit side-chains REVERT: A 225 MET cc_start: 0.4757 (pmm) cc_final: 0.2791 (ptm) REVERT: A 474 SER cc_start: 0.7901 (t) cc_final: 0.7339 (m) REVERT: A 596 ASN cc_start: 0.8678 (t0) cc_final: 0.8437 (t0) REVERT: B 107 TRP cc_start: 0.7506 (OUTLIER) cc_final: 0.7008 (t60) REVERT: B 304 TYR cc_start: 0.7729 (t80) cc_final: 0.7138 (t80) REVERT: B 516 LYS cc_start: 0.7380 (mmtm) cc_final: 0.6861 (ptmm) REVERT: B 573 ASP cc_start: 0.7735 (m-30) cc_final: 0.7435 (m-30) REVERT: B 675 ASP cc_start: 0.7457 (m-30) cc_final: 0.7077 (t0) REVERT: B 703 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7433 (mp0) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 0.6056 time to fit residues: 52.7372 Evaluate side-chains 82 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain B residue 107 TRP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 738 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 89 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 0.0270 chunk 6 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 GLN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** 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 = 0.3563 r_free = 0.3563 target = 0.123953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098451 restraints weight = 21911.063| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.58 r_work: 0.3426 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 11238 Z= 0.108 Angle : 0.540 9.985 15359 Z= 0.261 Chirality : 0.041 0.129 1611 Planarity : 0.004 0.044 2023 Dihedral : 5.058 71.454 1547 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.10 % Rotamer: Outliers : 1.28 % Allowed : 7.33 % Favored : 91.39 % 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 (0.22), residues: 1413 helix: 1.27 (0.22), residues: 584 sheet: 1.15 (1.02), residues: 20 loop : -0.44 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 392 TYR 0.016 0.001 TYR B 155 PHE 0.009 0.001 PHE B 129 TRP 0.020 0.001 TRP A 107 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11236) covalent geometry : angle 0.54005 / 0.26 (15359) hydrogen bonds : bond 0.03293 / 2.18 ( 435) hydrogen bonds : angle 3.79251 / 2.74 ( 1158) Misc. bond : bond 0.11615 / 6.97 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.64 seconds wall clock time: 64 minutes 50.85 seconds (3890.85 seconds total)