Starting phenix.real_space_refine on Thu Aug 6 00:42:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wym_66369/08_2026/9wym_66369.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wym_66369/08_2026/9wym_66369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wym_66369/08_2026/9wym_66369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wym_66369/08_2026/9wym_66369.map" model { file = "/net/cci-nas-00/data/ceres_data/9wym_66369/08_2026/9wym_66369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wym_66369/08_2026/9wym_66369.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 S 44 5.16 5 C 7724 2.51 5 N 1918 2.21 5 O 2487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12181 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5663 Classifications: {'peptide': 717} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 681} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 716, 5651 Classifications: {'peptide': 716} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 716, 5651 Classifications: {'peptide': 716} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 680} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5806 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 172 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'HQN': 2, 'LMT': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 165 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2, 'HQN': 2, 'LMT': 1, 'UQ5': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UQ5:plan-2': 1, 'UQ5:plan-5': 1, 'UQ5:plan-6': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 247 Classifications: {'water': 247} Link IDs: {None: 246} Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 259 Classifications: {'water': 259} Link IDs: {None: 258} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS B 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 224 " occ=0.50 residue: pdb=" N ATRP B 718 " occ=0.33 ... (26 atoms not shown) pdb=" CH2BTRP B 718 " occ=0.67 Time building chain proxies: 3.87, per 1000 atoms: 0.32 Number of scatterers: 12181 At special positions: 0 Unit cell: (108.78, 102.86, 106.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 44 16.00 O 2487 8.00 N 1918 7.00 C 7724 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 746.1 milliseconds 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 79.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.525A pdb=" N THR A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.553A pdb=" N GLY A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 142 through 161 removed outlier: 3.529A pdb=" N SER A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 355 removed outlier: 3.554A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 4.126A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 440 removed outlier: 3.635A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 3.553A pdb=" N THR A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 removed outlier: 4.199A pdb=" N PHE A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR A 468 " --> pdb=" O GLY A 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 464 through 468' Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 537 removed outlier: 4.936A pdb=" N ILE A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.701A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.561A pdb=" N MET A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 612 removed outlier: 3.563A pdb=" N PHE A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.198A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.567A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 681 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.633A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'B' and resid 15 through 33 removed outlier: 4.152A pdb=" N GLY B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 65 removed outlier: 3.558A pdb=" N GLY B 65 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'B' and resid 142 through 161 removed outlier: 3.529A pdb=" N SER B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 removed outlier: 3.554A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) Proline residue: B 352 - end of helix removed outlier: 4.121A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 440 removed outlier: 3.635A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix removed outlier: 3.566A pdb=" N THR B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 removed outlier: 3.893A pdb=" N PHE B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 464 through 468' Processing helix chain 'B' and resid 473 through 488 Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.140A pdb=" N ALA B 497 " --> pdb=" O PHE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.005A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.701A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.638A pdb=" N MET B 583 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 612 removed outlier: 3.580A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.249A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 3.567A pdb=" N VAL B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 681 Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.518A pdb=" N ILE B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 720 through 744 Processing helix chain 'B' and resid 746 through 750 removed outlier: 3.501A pdb=" N ALA B 750 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.412A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 41 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.416A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 41 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 788 hydrogen bonds defined for protein. 2290 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: 2.18 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 4728 1.39 - 1.57: 7248 1.57 - 1.76: 0 1.76 - 1.94: 86 1.94 - 2.12: 14 Bond restraints: 12076 Sorted by residual: bond pdb=" C ASN B 223 " pdb=" N BHIS B 224 " ideal model delta sigma weight residual 1.326 1.425 -0.100 1.12e-02 7.97e+03 7.91e+01 bond pdb=" CE1 HIS B 629 " pdb=" NE2 HIS B 629 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.09e-02 8.42e+03 1.23e+01 bond pdb=" C2C HEM A 803 " pdb=" C3C HEM A 803 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" CG HIS A 629 " pdb=" CD2 HIS A 629 " ideal model delta sigma weight residual 1.354 1.316 0.038 1.10e-02 8.26e+03 1.19e+01 ... (remaining 12071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 16244 2.74 - 5.48: 268 5.48 - 8.21: 17 8.21 - 10.95: 4 10.95 - 13.69: 1 Bond angle restraints: 16534 Sorted by residual: angle pdb=" CA HIS A 224 " pdb=" C HIS A 224 " pdb=" N PRO A 225 " ideal model delta sigma weight residual 117.95 121.78 -3.83 7.70e-01 1.69e+00 2.47e+01 angle pdb=" CA HIS B 537 " pdb=" CB HIS B 537 " pdb=" CG HIS B 537 " ideal model delta sigma weight residual 113.80 118.53 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" CA VAL A 489 " pdb=" C VAL A 489 " pdb=" O VAL A 489 " ideal model delta sigma weight residual 121.58 117.23 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CG MET A 708 " pdb=" SD MET A 708 " pdb=" CE MET A 708 " ideal model delta sigma weight residual 100.90 91.48 9.42 2.20e+00 2.07e-01 1.83e+01 angle pdb=" OE1 GLN B 79 " pdb=" CD GLN B 79 " pdb=" NE2 GLN B 79 " ideal model delta sigma weight residual 122.60 118.33 4.27 1.00e+00 1.00e+00 1.82e+01 ... (remaining 16529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6095 17.66 - 35.33: 483 35.33 - 52.99: 181 52.99 - 70.65: 31 70.65 - 88.32: 25 Dihedral angle restraints: 6815 sinusoidal: 2731 harmonic: 4084 Sorted by residual: dihedral pdb=" C2B HEM B 806 " pdb=" C3B HEM B 806 " pdb=" CAB HEM B 806 " pdb=" CBB HEM B 806 " ideal model delta sinusoidal sigma weight residual 0.00 56.41 -56.41 2 1.00e+01 1.00e-02 3.33e+01 dihedral pdb=" C2C HEM A 801 " pdb=" C3C HEM A 801 " pdb=" CAC HEM A 801 " pdb=" CBC HEM A 801 " ideal model delta sinusoidal sigma weight residual -0.00 -51.72 51.72 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2C HEM B 806 " pdb=" C3C HEM B 806 " pdb=" CAC HEM B 806 " pdb=" CBC HEM B 806 " ideal model delta sinusoidal sigma weight residual -0.00 -33.18 33.18 2 1.00e+01 1.00e-02 1.44e+01 ... (remaining 6812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 934 0.045 - 0.090: 553 0.090 - 0.136: 182 0.136 - 0.181: 55 0.181 - 0.226: 23 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA GLU B 494 " pdb=" N GLU B 494 " pdb=" C GLU B 494 " pdb=" CB GLU B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA SER B 325 " pdb=" N SER B 325 " pdb=" C SER B 325 " pdb=" CB SER B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA PRO A 627 " pdb=" N PRO A 627 " pdb=" C PRO A 627 " pdb=" CB PRO A 627 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1744 not shown) Planarity restraints: 2042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ5 B 801 " -0.026 2.00e-02 2.50e+03 5.16e-02 8.00e+01 pdb=" C1M UQ5 B 801 " -0.000 2.00e-02 2.50e+03 pdb=" C2 UQ5 B 801 " -0.036 2.00e-02 2.50e+03 pdb=" C3 UQ5 B 801 " 0.073 2.00e-02 2.50e+03 pdb=" C4 UQ5 B 801 " 0.082 2.00e-02 2.50e+03 pdb=" C5 UQ5 B 801 " 0.027 2.00e-02 2.50e+03 pdb=" C6 UQ5 B 801 " -0.001 2.00e-02 2.50e+03 pdb=" C7 UQ5 B 801 " 0.034 2.00e-02 2.50e+03 pdb=" O2 UQ5 B 801 " -0.056 2.00e-02 2.50e+03 pdb=" O3 UQ5 B 801 " 0.041 2.00e-02 2.50e+03 pdb=" O4 UQ5 B 801 " -0.098 2.00e-02 2.50e+03 pdb=" O5 UQ5 B 801 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " 0.034 2.00e-02 2.50e+03 3.27e-02 2.14e+01 pdb=" CG TYR A 78 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " -0.032 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR B 78 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " 0.025 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.033 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " -0.065 2.00e-02 2.50e+03 ... (remaining 2039 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 29 2.31 - 2.96: 5769 2.96 - 3.60: 19364 3.60 - 4.25: 31087 4.25 - 4.90: 51387 Nonbonded interactions: 107636 Sorted by model distance: nonbonded pdb="FE FE B 807 " pdb=" O HOH B 916 " model vdw 1.662 2.260 nonbonded pdb="FE FE A 804 " pdb=" O HOH A 916 " model vdw 1.665 2.260 nonbonded pdb=" NE2 HIS A 629 " pdb="FE HEM A 803 " model vdw 2.079 3.080 nonbonded pdb=" NH2 ARG A 131 " pdb=" O HOH A 901 " model vdw 2.204 3.120 nonbonded pdb=" OE1 GLN A 62 " pdb=" OH TYR A 406 " model vdw 2.219 3.040 ... (remaining 107631 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 14 through 223 or resid 225 through 441 or resid 463 throu \ gh 717 or resid 719 through 750)) selection = (chain 'B' and (resid 14 through 223 or resid 225 through 717 or resid 719 throu \ gh 750)) } 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=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.060 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:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 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 : 0.011 0.321 12080 Z= 0.577 Angle : 0.954 13.691 16534 Z= 0.582 Chirality : 0.065 0.226 1747 Planarity : 0.008 0.052 2042 Dihedral : 15.934 88.318 4217 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.72 % Favored : 96.00 % Rotamer: Outliers : 1.87 % Allowed : 13.87 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.25 (0.23), residues: 1431 helix: 2.23 (0.17), residues: 1012 sheet: None (None), residues: 0 loop : -0.36 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG B 328 TYR 0.066 0.009 TYR A 78 PHE 0.048 0.007 PHE A 680 TRP 0.042 0.007 TRP B 669 HIS 0.016 0.005 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00977 / 0.58 (12076) covalent geometry : angle 0.95422 / 0.58 (16534) hydrogen bonds : bond 0.13295 / 8.79 ( 788) hydrogen bonds : angle 4.91008 / 3.62 ( 2290) Misc. bond : bond 0.24981 / 11.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8887 (pt0) cc_final: 0.8438 (tp30) REVERT: A 494 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: A 584 GLU cc_start: 0.9119 (pp20) cc_final: 0.8869 (pp20) REVERT: A 610 MET cc_start: 0.9228 (mtp) cc_final: 0.8764 (ptt) REVERT: B 121 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8481 (tp30) REVERT: B 488 TRP cc_start: 0.8270 (m-90) cc_final: 0.7152 (t60) REVERT: B 494 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: B 584 GLU cc_start: 0.9115 (pp20) cc_final: 0.8849 (pp20) REVERT: B 610 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8612 (ttp) outliers start: 21 outliers final: 7 residues processed: 106 average time/residue: 0.6728 time to fit residues: 77.3751 Evaluate side-chains 95 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 393 MET Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 728 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 621 GLN B 62 GLN B 621 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.064912 restraints weight = 42667.875| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.30 r_work: 0.2569 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.278 12080 Z= 0.133 Angle : 0.580 9.947 16534 Z= 0.281 Chirality : 0.039 0.144 1747 Planarity : 0.004 0.038 2042 Dihedral : 8.805 88.558 1805 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.60 % Favored : 97.12 % Rotamer: Outliers : 1.51 % Allowed : 14.84 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.30 (0.23), residues: 1431 helix: 2.28 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.38 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.011 0.001 TYR A 638 PHE 0.016 0.001 PHE B 492 TRP 0.018 0.001 TRP A 338 HIS 0.009 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (12076) covalent geometry : angle 0.58041 / 0.28 (16534) hydrogen bonds : bond 0.04634 / 3.15 ( 788) hydrogen bonds : angle 4.34112 / 3.20 ( 2290) Misc. bond : bond 0.19413 / 9.71 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7909 (tp30) REVERT: A 309 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: A 494 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: A 584 GLU cc_start: 0.8790 (pp20) cc_final: 0.8492 (pp20) REVERT: A 610 MET cc_start: 0.8821 (mtp) cc_final: 0.8232 (ptm) REVERT: B 488 TRP cc_start: 0.7718 (m-90) cc_final: 0.6623 (t60) REVERT: B 494 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: B 584 GLU cc_start: 0.8807 (pp20) cc_final: 0.8481 (pp20) REVERT: B 610 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8280 (ttp) outliers start: 17 outliers final: 6 residues processed: 106 average time/residue: 0.6711 time to fit residues: 77.1792 Evaluate side-chains 103 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 40 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.063038 restraints weight = 45718.774| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.37 r_work: 0.2533 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2544 r_free = 0.2544 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.334 12080 Z= 0.157 Angle : 0.591 11.439 16534 Z= 0.283 Chirality : 0.040 0.147 1747 Planarity : 0.004 0.039 2042 Dihedral : 8.299 86.752 1790 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 1.96 % Allowed : 14.49 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.25 (0.23), residues: 1431 helix: 2.24 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : -0.37 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.013 0.001 TYR B 324 PHE 0.016 0.001 PHE A 635 TRP 0.018 0.001 TRP A 338 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (12076) covalent geometry : angle 0.59102 / 0.28 (16534) hydrogen bonds : bond 0.04938 / 3.38 ( 788) hydrogen bonds : angle 4.34827 / 3.21 ( 2290) Misc. bond : bond 0.23769 / 11.90 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: A 309 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: A 494 GLU cc_start: 0.7937 (tt0) cc_final: 0.7329 (tm-30) REVERT: A 584 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8510 (pp20) REVERT: A 610 MET cc_start: 0.8839 (mtp) cc_final: 0.8255 (ptm) REVERT: B 430 MET cc_start: 0.8506 (mmm) cc_final: 0.8216 (mmm) REVERT: B 488 TRP cc_start: 0.7710 (m-90) cc_final: 0.6613 (t60) REVERT: B 494 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: B 584 GLU cc_start: 0.8812 (pp20) cc_final: 0.8490 (pp20) REVERT: B 610 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8316 (ttp) outliers start: 22 outliers final: 10 residues processed: 114 average time/residue: 0.6418 time to fit residues: 79.6438 Evaluate side-chains 113 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 125 optimal weight: 0.0570 chunk 5 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.064990 restraints weight = 40654.710| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.23 r_work: 0.2575 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.276 12080 Z= 0.126 Angle : 0.561 10.743 16534 Z= 0.269 Chirality : 0.038 0.143 1747 Planarity : 0.004 0.043 2042 Dihedral : 7.936 86.809 1787 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.37 % Favored : 96.35 % Rotamer: Outliers : 1.78 % Allowed : 14.31 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.30 (0.23), residues: 1431 helix: 2.28 (0.17), residues: 1015 sheet: None (None), residues: 0 loop : -0.41 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.010 0.001 TYR B 324 PHE 0.012 0.001 PHE A 635 TRP 0.019 0.001 TRP B 483 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (12076) covalent geometry : angle 0.56117 / 0.27 (16534) hydrogen bonds : bond 0.04373 / 2.99 ( 788) hydrogen bonds : angle 4.24148 / 3.14 ( 2290) Misc. bond : bond 0.19455 / 9.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8968 (ttp-110) cc_final: 0.8762 (ttp-110) REVERT: A 494 GLU cc_start: 0.7894 (tt0) cc_final: 0.7326 (tm-30) REVERT: A 584 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8494 (pp20) REVERT: A 610 MET cc_start: 0.8814 (mtp) cc_final: 0.8281 (ptm) REVERT: B 430 MET cc_start: 0.8476 (mmm) cc_final: 0.8126 (mmm) REVERT: B 488 TRP cc_start: 0.7729 (m-90) cc_final: 0.6561 (t60) REVERT: B 494 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: B 584 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8456 (pp20) REVERT: B 610 MET cc_start: 0.8724 (mtp) cc_final: 0.8325 (ttp) outliers start: 20 outliers final: 8 residues processed: 116 average time/residue: 0.6570 time to fit residues: 82.7102 Evaluate side-chains 113 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 10 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.066885 restraints weight = 38281.372| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.18 r_work: 0.2618 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 12080 Z= 0.111 Angle : 0.540 9.208 16534 Z= 0.259 Chirality : 0.038 0.176 1747 Planarity : 0.004 0.046 2042 Dihedral : 7.648 87.807 1784 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.23 % Favored : 96.49 % Rotamer: Outliers : 2.04 % Allowed : 14.67 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.42 (0.23), residues: 1431 helix: 2.38 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.38 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 267 TYR 0.009 0.001 TYR B 638 PHE 0.011 0.001 PHE A 635 TRP 0.020 0.001 TRP B 483 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12076) covalent geometry : angle 0.53990 / 0.26 (16534) hydrogen bonds : bond 0.03912 / 2.67 ( 788) hydrogen bonds : angle 4.13191 / 3.07 ( 2290) Misc. bond : bond 0.16823 / 8.44 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: A 494 GLU cc_start: 0.7852 (tt0) cc_final: 0.7284 (tm-30) REVERT: A 584 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8507 (pp20) REVERT: A 610 MET cc_start: 0.8799 (mtp) cc_final: 0.8322 (ttp) REVERT: B 31 ARG cc_start: 0.8993 (ttp-110) cc_final: 0.8661 (ttp-110) REVERT: B 430 MET cc_start: 0.8450 (mmm) cc_final: 0.8110 (mmm) REVERT: B 488 TRP cc_start: 0.7741 (m-90) cc_final: 0.6545 (t60) REVERT: B 494 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: B 584 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8473 (pp20) REVERT: B 610 MET cc_start: 0.8543 (mtp) cc_final: 0.8270 (ttp) outliers start: 23 outliers final: 7 residues processed: 122 average time/residue: 0.6133 time to fit residues: 82.0520 Evaluate side-chains 113 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 0.0470 chunk 67 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.095916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.064371 restraints weight = 46773.799| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.43 r_work: 0.2566 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.293 12080 Z= 0.129 Angle : 0.567 11.038 16534 Z= 0.267 Chirality : 0.039 0.243 1747 Planarity : 0.004 0.049 2042 Dihedral : 7.589 87.200 1784 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.09 % Favored : 96.63 % Rotamer: Outliers : 2.04 % Allowed : 14.67 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.42 (0.23), residues: 1431 helix: 2.41 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -0.43 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 267 TYR 0.011 0.001 TYR B 324 PHE 0.014 0.001 PHE A 635 TRP 0.023 0.001 TRP B 483 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (12076) covalent geometry : angle 0.56655 / 0.27 (16534) hydrogen bonds : bond 0.04386 / 3.00 ( 788) hydrogen bonds : angle 4.17336 / 3.10 ( 2290) Misc. bond : bond 0.20669 / 10.35 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 309 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: A 494 GLU cc_start: 0.7864 (tt0) cc_final: 0.7279 (tm-30) REVERT: A 559 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: A 584 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8497 (pp20) REVERT: A 610 MET cc_start: 0.8754 (mtp) cc_final: 0.8310 (ttp) REVERT: B 430 MET cc_start: 0.8476 (mmm) cc_final: 0.8131 (mmm) REVERT: B 488 TRP cc_start: 0.7707 (m-90) cc_final: 0.6548 (t60) REVERT: B 494 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7713 (tp30) REVERT: B 584 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8484 (pp20) REVERT: B 610 MET cc_start: 0.8544 (mtp) cc_final: 0.8299 (ttp) outliers start: 23 outliers final: 10 residues processed: 115 average time/residue: 0.6178 time to fit residues: 77.7993 Evaluate side-chains 115 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 42 optimal weight: 0.0040 chunk 22 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 57 optimal weight: 0.2980 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.066891 restraints weight = 34681.015| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.06 r_work: 0.2627 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.237 12080 Z= 0.113 Angle : 0.551 9.591 16534 Z= 0.261 Chirality : 0.038 0.278 1747 Planarity : 0.004 0.052 2042 Dihedral : 7.418 87.660 1784 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.23 % Favored : 96.49 % Rotamer: Outliers : 1.87 % Allowed : 15.20 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.50 (0.23), residues: 1431 helix: 2.50 (0.17), residues: 1001 sheet: None (None), residues: 0 loop : -0.42 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 267 TYR 0.009 0.001 TYR B 406 PHE 0.011 0.001 PHE A 635 TRP 0.023 0.001 TRP B 483 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (12076) covalent geometry : angle 0.55080 / 0.26 (16534) hydrogen bonds : bond 0.03931 / 2.68 ( 788) hydrogen bonds : angle 4.11462 / 3.07 ( 2290) Misc. bond : bond 0.16719 / 8.38 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8665 (ttp-110) REVERT: A 494 GLU cc_start: 0.7827 (tt0) cc_final: 0.7236 (tm-30) REVERT: A 559 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: A 584 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8523 (pp20) REVERT: A 610 MET cc_start: 0.8774 (mtp) cc_final: 0.8345 (ttp) REVERT: B 430 MET cc_start: 0.8441 (mmm) cc_final: 0.8103 (mmm) REVERT: B 488 TRP cc_start: 0.7729 (m-90) cc_final: 0.6514 (t60) REVERT: B 494 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7654 (tp30) REVERT: B 584 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8474 (pp20) REVERT: B 610 MET cc_start: 0.8470 (mtp) cc_final: 0.8263 (ttp) outliers start: 21 outliers final: 11 residues processed: 119 average time/residue: 0.5707 time to fit residues: 74.4075 Evaluate side-chains 118 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.064237 restraints weight = 44985.985| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.38 r_work: 0.2565 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.301 12080 Z= 0.136 Angle : 0.583 11.269 16534 Z= 0.273 Chirality : 0.040 0.281 1747 Planarity : 0.004 0.054 2042 Dihedral : 7.461 87.179 1784 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.95 % Favored : 96.77 % Rotamer: Outliers : 1.78 % Allowed : 15.38 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.45 (0.23), residues: 1431 helix: 2.45 (0.17), residues: 999 sheet: None (None), residues: 0 loop : -0.38 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 267 TYR 0.012 0.001 TYR B 324 PHE 0.016 0.001 PHE A 527 TRP 0.027 0.001 TRP B 582 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (12076) covalent geometry : angle 0.58339 / 0.27 (16534) hydrogen bonds : bond 0.04459 / 3.05 ( 788) hydrogen bonds : angle 4.18371 / 3.12 ( 2290) Misc. bond : bond 0.21282 / 10.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 559 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: A 584 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8503 (pp20) REVERT: A 610 MET cc_start: 0.8732 (mtp) cc_final: 0.8307 (ttp) REVERT: B 430 MET cc_start: 0.8464 (mmm) cc_final: 0.8176 (mmm) REVERT: B 488 TRP cc_start: 0.7734 (m-90) cc_final: 0.6518 (t60) REVERT: B 494 GLU cc_start: 0.8325 (tp30) cc_final: 0.7595 (tp30) REVERT: B 584 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8464 (pp20) REVERT: B 610 MET cc_start: 0.8478 (mtp) cc_final: 0.8221 (ttp) outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.5987 time to fit residues: 77.3387 Evaluate side-chains 116 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 105 optimal weight: 0.1980 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.096421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.065492 restraints weight = 38670.657| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.17 r_work: 0.2595 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.277 12080 Z= 0.127 Angle : 0.581 10.779 16534 Z= 0.273 Chirality : 0.039 0.311 1747 Planarity : 0.004 0.059 2042 Dihedral : 7.319 87.053 1781 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.16 % Favored : 96.56 % Rotamer: Outliers : 1.51 % Allowed : 15.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.47 (0.23), residues: 1431 helix: 2.45 (0.17), residues: 1001 sheet: None (None), residues: 0 loop : -0.34 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 267 TYR 0.011 0.001 TYR B 324 PHE 0.013 0.001 PHE A 635 TRP 0.027 0.001 TRP B 483 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.12 (12076) covalent geometry : angle 0.58106 / 0.27 (16534) hydrogen bonds : bond 0.04279 / 2.93 ( 788) hydrogen bonds : angle 4.16934 / 3.12 ( 2290) Misc. bond : bond 0.19503 / 9.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.385 Fit side-chains REVERT: A 488 TRP cc_start: 0.7647 (t60) cc_final: 0.7293 (m-90) REVERT: A 559 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: A 584 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8495 (pp20) REVERT: A 610 MET cc_start: 0.8714 (mtp) cc_final: 0.8265 (ttp) REVERT: B 430 MET cc_start: 0.8457 (mmm) cc_final: 0.8114 (mmm) REVERT: B 488 TRP cc_start: 0.7726 (m-90) cc_final: 0.6520 (t60) REVERT: B 494 GLU cc_start: 0.8351 (tp30) cc_final: 0.7628 (tp30) REVERT: B 584 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8448 (pp20) REVERT: B 610 MET cc_start: 0.8457 (mtp) cc_final: 0.8230 (ttp) outliers start: 17 outliers final: 10 residues processed: 114 average time/residue: 0.5951 time to fit residues: 74.3605 Evaluate side-chains 113 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 104 optimal weight: 0.0470 chunk 132 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 600 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.064115 restraints weight = 44284.930| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.34 r_work: 0.2561 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.308 12080 Z= 0.139 Angle : 0.596 11.676 16534 Z= 0.279 Chirality : 0.040 0.312 1747 Planarity : 0.004 0.060 2042 Dihedral : 7.378 86.856 1781 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.95 % Favored : 96.77 % Rotamer: Outliers : 1.33 % Allowed : 15.91 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.37 (0.23), residues: 1431 helix: 2.36 (0.17), residues: 1006 sheet: None (None), residues: 0 loop : -0.40 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 267 TYR 0.012 0.001 TYR B 324 PHE 0.015 0.001 PHE A 635 TRP 0.031 0.001 TRP B 483 HIS 0.008 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12076) covalent geometry : angle 0.59649 / 0.28 (16534) hydrogen bonds : bond 0.04565 / 3.13 ( 788) hydrogen bonds : angle 4.21519 / 3.15 ( 2290) Misc. bond : bond 0.21714 / 10.88 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2862 Ramachandran restraints generated. 1431 Oldfield, 0 Emsley, 1431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.406 Fit side-chains REVERT: A 31 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8614 (mtm110) REVERT: A 488 TRP cc_start: 0.7695 (t60) cc_final: 0.7275 (m-90) REVERT: A 559 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: A 584 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8505 (pp20) REVERT: A 610 MET cc_start: 0.8595 (mtp) cc_final: 0.8231 (ttp) REVERT: B 488 TRP cc_start: 0.7745 (m-90) cc_final: 0.6522 (t60) REVERT: B 494 GLU cc_start: 0.8361 (tp30) cc_final: 0.7601 (tp30) REVERT: B 584 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8463 (pp20) outliers start: 15 outliers final: 10 residues processed: 114 average time/residue: 0.5832 time to fit residues: 72.7118 Evaluate side-chains 115 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 584 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.094606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.063324 restraints weight = 35987.348| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.09 r_work: 0.2560 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.325 12080 Z= 0.152 Angle : 0.610 12.457 16534 Z= 0.285 Chirality : 0.041 0.307 1747 Planarity : 0.004 0.059 2042 Dihedral : 7.477 86.225 1781 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.02 % Favored : 96.70 % Rotamer: Outliers : 1.51 % Allowed : 15.64 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 2.30 (0.23), residues: 1431 helix: 2.29 (0.17), residues: 1010 sheet: None (None), residues: 0 loop : -0.38 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 267 TYR 0.014 0.001 TYR B 324 PHE 0.016 0.001 PHE A 635 TRP 0.034 0.002 TRP B 483 HIS 0.007 0.001 HIS B 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (12076) covalent geometry : angle 0.61038 / 0.29 (16534) hydrogen bonds : bond 0.04811 / 3.30 ( 788) hydrogen bonds : angle 4.27304 / 3.19 ( 2290) Misc. bond : bond 0.23097 / 11.58 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5058.20 seconds wall clock time: 86 minutes 41.91 seconds (5201.91 seconds total)