Starting phenix.real_space_refine on Fri Jul 3 05:32:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sta_55214/07_2026/9sta_55214.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sta_55214/07_2026/9sta_55214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sta_55214/07_2026/9sta_55214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sta_55214/07_2026/9sta_55214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sta_55214/07_2026/9sta_55214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sta_55214/07_2026/9sta_55214.map" } resolution = 2.4 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= 0.005 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 7685 2.51 5 N 1911 2.21 5 O 2319 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11967 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5641 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5617 Classifications: {'peptide': 711} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 676} 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: 711, 5617 Classifications: {'peptide': 711} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 676} 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: 5771 Chain: "B" Number of atoms: 5639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 710, 5615 Classifications: {'peptide': 710} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} 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: 710, 5615 Classifications: {'peptide': 710} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 674} 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: 5770 Chain: "A" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 133 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2, 'HQE': 2, 'LMT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 196 Ad-hoc single atom residues: {' FE': 1, ' CA': 1} Unusual residues: {'HEM': 2, 'HQE': 2, 'LMT': 2, 'UQ5': 1} Classifications: {'undetermined': 7} Link IDs: {None: 4} Chain breaks: 2 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: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "B" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 176 Classifications: {'water': 176} Link IDs: {None: 175} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS A 224 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 224 " occ=0.50 residue: pdb=" N ATRP A 718 " occ=0.54 ... (26 atoms not shown) pdb=" CH2BTRP A 718 " occ=0.46 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=0.51 ... (26 atoms not shown) pdb=" CH2BTRP B 718 " occ=0.49 Time building chain proxies: 4.14, per 1000 atoms: 0.35 Number of scatterers: 11967 At special positions: 0 Unit cell: (89.54, 104.34, 105.82, 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 2319 8.00 N 1911 7.00 C 7685 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: 1.06 Conformation dependent library (CDL) restraints added in 642.7 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 78.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.875A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 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 129 removed outlier: 4.033A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 142 through 161 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 Proline residue: A 352 - end of helix removed outlier: 4.083A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 390 Processing helix chain 'A' and resid 394 through 402 removed outlier: 4.516A pdb=" N PHE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TRP A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.666A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 473 through 486 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 537 removed outlier: 5.151A 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: 3.568A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 559 removed outlier: 4.098A pdb=" N GLU A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 556 through 559' Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.733A pdb=" N ILE A 564 " --> pdb=" O VAL A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.739A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 603 Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.569A pdb=" N MET A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.101A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.386A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 682 removed outlier: 3.772A pdb=" N SER A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 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 720 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'B' and resid 19 through 33 removed outlier: 4.005A pdb=" N GLY B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 104 Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.941A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'B' and resid 142 through 160 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 Proline residue: B 352 - end of helix removed outlier: 4.079A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 390 Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.509A pdb=" N PHE B 399 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TRP B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 440 removed outlier: 3.659A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix removed outlier: 3.568A pdb=" N THR B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 488 Processing helix chain 'B' and resid 494 through 508 Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.161A 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: 3.560A 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: 3.881A pdb=" N MET B 583 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 604 through 612 Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.022A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 4.402A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 682 removed outlier: 3.737A pdb=" N SER B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.190A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU A 39 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 141 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.776A 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: 6.210A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLU B 39 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU B 141 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.769A 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 313 778 hydrogen bonds defined for protein. 2258 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: 1.39 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4626 1.38 - 1.55: 7291 1.55 - 1.72: 0 1.72 - 1.90: 84 1.90 - 2.07: 16 Bond restraints: 12017 Sorted by residual: bond pdb=" C BHIS B 224 " pdb=" N PRO B 225 " ideal model delta sigma weight residual 1.332 1.376 -0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" N VAL A 637 " pdb=" CA VAL A 637 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" N LEU A 634 " pdb=" CA LEU A 634 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.16e-02 7.43e+03 1.08e+01 bond pdb=" N TYR A 638 " pdb=" CA TYR A 638 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.28e-02 6.10e+03 9.02e+00 bond pdb=" N GLU A 559 " pdb=" CA GLU A 559 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.31e-02 5.83e+03 8.83e+00 ... (remaining 12012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 16193 2.39 - 4.79: 227 4.79 - 7.18: 25 7.18 - 9.58: 4 9.58 - 11.97: 4 Bond angle restraints: 16453 Sorted by residual: angle pdb=" O BHIS A 224 " pdb=" C BHIS A 224 " pdb=" N PRO A 225 " ideal model delta sigma weight residual 121.71 117.65 4.06 6.40e-01 2.44e+00 4.02e+01 angle pdb=" O BHIS B 224 " pdb=" C BHIS B 224 " pdb=" N PRO B 225 " ideal model delta sigma weight residual 121.65 125.49 -3.84 7.30e-01 1.88e+00 2.77e+01 angle pdb=" C GLY A 636 " pdb=" N VAL A 637 " pdb=" CA VAL A 637 " ideal model delta sigma weight residual 122.66 117.86 4.80 9.70e-01 1.06e+00 2.45e+01 angle pdb=" CA BHIS A 224 " pdb=" C BHIS A 224 " pdb=" N PRO A 225 " ideal model delta sigma weight residual 117.71 122.15 -4.44 9.20e-01 1.18e+00 2.33e+01 angle pdb=" CA BHIS B 224 " pdb=" C BHIS B 224 " pdb=" N PRO B 225 " ideal model delta sigma weight residual 117.95 114.36 3.59 7.70e-01 1.69e+00 2.17e+01 ... (remaining 16448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 6008 17.73 - 35.45: 554 35.45 - 53.18: 160 53.18 - 70.90: 35 70.90 - 88.63: 22 Dihedral angle restraints: 6779 sinusoidal: 2722 harmonic: 4057 Sorted by residual: dihedral pdb=" CA GLU A 490 " pdb=" C GLU A 490 " pdb=" N GLY A 491 " pdb=" CA GLY A 491 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL B 560 " pdb=" C VAL B 560 " pdb=" N VAL B 561 " pdb=" CA VAL B 561 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA GLY B 491 " pdb=" C GLY B 491 " pdb=" N PHE B 492 " pdb=" CA PHE B 492 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1610 0.074 - 0.149: 118 0.149 - 0.223: 2 0.223 - 0.297: 0 0.297 - 0.371: 2 Chirality restraints: 1732 Sorted by residual: chirality pdb=" CB VAL A 637 " pdb=" CA VAL A 637 " pdb=" CG1 VAL A 637 " pdb=" CG2 VAL A 637 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB VAL B 637 " pdb=" CA VAL B 637 " pdb=" CG1 VAL B 637 " pdb=" CG2 VAL B 637 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA VAL A 560 " pdb=" N VAL A 560 " pdb=" C VAL A 560 " pdb=" CB VAL A 560 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 1729 not shown) Planarity restraints: 2035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 632 " -0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ALA B 632 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA B 632 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA B 633 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 357 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C GLY A 357 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY A 357 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG A 358 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 558 " 0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C LEU A 558 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU A 558 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 559 " 0.009 2.00e-02 2.50e+03 ... (remaining 2032 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 52 2.43 - 3.05: 7595 3.05 - 3.66: 18935 3.66 - 4.28: 30106 4.28 - 4.90: 48410 Nonbonded interactions: 105098 Sorted by model distance: nonbonded pdb="FE FE A 804 " pdb=" O HOH A 928 " model vdw 1.809 3.000 nonbonded pdb="FE FE B 803 " pdb=" O HOH B 924 " model vdw 1.853 3.000 nonbonded pdb=" O HOH A 901 " pdb=" O HOH A1057 " model vdw 2.204 3.040 nonbonded pdb=" O HOH B 940 " pdb=" O HOH B 951 " model vdw 2.213 3.040 nonbonded pdb=" O HOH A 941 " pdb=" O HOH A 957 " model vdw 2.214 3.040 ... (remaining 105093 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 18 through 223 or resid 225 through 439 or resid 465 throu \ gh 717 or resid 719 through 750)) selection = (chain 'B' and (resid 18 through 223 or resid 225 through 439 or resid 465 throu \ gh 717 or resid 719 through 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=0.46 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: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 : 0.005 0.287 12021 Z= 0.195 Angle : 0.663 11.973 16453 Z= 0.369 Chirality : 0.040 0.371 1732 Planarity : 0.004 0.036 2035 Dihedral : 16.235 88.626 4199 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.80 % Allowed : 15.82 % Favored : 83.38 % 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: 1.71 (0.23), residues: 1425 helix: 1.82 (0.17), residues: 1010 sheet: -0.51 (0.88), residues: 20 loop : -0.52 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 267 TYR 0.020 0.002 TYR A 468 PHE 0.013 0.001 PHE B 492 TRP 0.021 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.19 (12017) covalent geometry : angle 0.66261 / 0.37 (16453) hydrogen bonds : bond 0.14649 / 9.50 ( 778) hydrogen bonds : angle 5.60278 / 4.03 ( 2258) Misc. bond : bond 0.19990 / 9.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 112 average time/residue: 0.5542 time to fit residues: 67.4733 Evaluate side-chains 90 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 637 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 184 ASN B 62 GLN B 184 ASN B 217 HIS B 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.064668 restraints weight = 59786.058| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.82 r_work: 0.2612 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 12021 Z= 0.139 Angle : 0.617 12.527 16453 Z= 0.290 Chirality : 0.040 0.242 1732 Planarity : 0.004 0.040 2035 Dihedral : 7.600 88.258 1772 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.88 % Allowed : 15.46 % Favored : 82.66 % 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: 2.29 (0.23), residues: 1425 helix: 2.25 (0.17), residues: 1013 sheet: -0.94 (1.14), residues: 10 loop : -0.32 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 267 TYR 0.018 0.001 TYR B 30 PHE 0.016 0.001 PHE B 466 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (12017) covalent geometry : angle 0.61679 / 0.29 (16453) hydrogen bonds : bond 0.04893 / 3.33 ( 778) hydrogen bonds : angle 4.20596 / 3.02 ( 2258) Misc. bond : bond 0.11342 / 5.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 494 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 583 MET cc_start: 0.8955 (mpp) cc_final: 0.8481 (mpp) REVERT: A 734 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8578 (tpp) REVERT: B 494 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7844 (tm-30) outliers start: 21 outliers final: 6 residues processed: 105 average time/residue: 0.5837 time to fit residues: 66.8164 Evaluate side-chains 92 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 78 optimal weight: 0.3980 chunk 133 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.061113 restraints weight = 60598.027| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.77 r_work: 0.2594 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.268 12021 Z= 0.186 Angle : 0.645 14.140 16453 Z= 0.298 Chirality : 0.041 0.266 1732 Planarity : 0.004 0.037 2035 Dihedral : 7.611 85.192 1772 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.43 % Allowed : 15.82 % Favored : 82.75 % 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: 2.27 (0.23), residues: 1425 helix: 2.30 (0.17), residues: 1010 sheet: -0.91 (1.18), residues: 10 loop : -0.49 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 267 TYR 0.016 0.001 TYR B 638 PHE 0.010 0.001 PHE A 635 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.18 (12017) covalent geometry : angle 0.64461 / 0.30 (16453) hydrogen bonds : bond 0.05599 / 3.80 ( 778) hydrogen bonds : angle 4.21009 / 3.03 ( 2258) Misc. bond : bond 0.19684 / 9.70 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.7199 (m-80) cc_final: 0.6968 (m-80) REVERT: A 494 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7687 (tm-30) REVERT: A 583 MET cc_start: 0.8995 (mpp) cc_final: 0.8482 (mpp) REVERT: B 487 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7704 (tt) REVERT: B 494 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 528 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5922 (ttt) outliers start: 16 outliers final: 2 residues processed: 96 average time/residue: 0.5834 time to fit residues: 61.0502 Evaluate side-chains 89 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3334 r_free = 0.3334 target = 0.091995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.064627 restraints weight = 74283.830| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.10 r_work: 0.2669 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 12021 Z= 0.119 Angle : 0.573 12.201 16453 Z= 0.268 Chirality : 0.038 0.197 1732 Planarity : 0.004 0.039 2035 Dihedral : 7.257 83.650 1771 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.43 % Allowed : 15.91 % Favored : 82.66 % 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: 2.44 (0.23), residues: 1425 helix: 2.45 (0.17), residues: 1010 sheet: -0.99 (1.28), residues: 10 loop : -0.49 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.018 0.001 TYR B 638 PHE 0.009 0.001 PHE B 527 TRP 0.019 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (12017) covalent geometry : angle 0.57349 / 0.27 (16453) hydrogen bonds : bond 0.04342 / 2.98 ( 778) hydrogen bonds : angle 3.97429 / 2.86 ( 2258) Misc. bond : bond 0.08813 / 4.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.7039 (m-80) cc_final: 0.6778 (m-80) REVERT: A 487 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 494 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 583 MET cc_start: 0.8997 (mpp) cc_final: 0.8464 (mpp) REVERT: B 487 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7605 (tt) REVERT: B 494 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 528 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5783 (ttt) outliers start: 16 outliers final: 3 residues processed: 97 average time/residue: 0.5613 time to fit residues: 59.6044 Evaluate side-chains 91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.087944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.060366 restraints weight = 59760.635| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.83 r_work: 0.2618 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 12021 Z= 0.177 Angle : 0.615 13.805 16453 Z= 0.283 Chirality : 0.040 0.160 1732 Planarity : 0.004 0.037 2035 Dihedral : 7.362 82.733 1771 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.16 % Allowed : 16.00 % 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: 2.41 (0.23), residues: 1425 helix: 2.47 (0.17), residues: 1006 sheet: -1.16 (1.31), residues: 10 loop : -0.60 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.017 0.001 TYR B 638 PHE 0.012 0.001 PHE B 635 TRP 0.018 0.001 TRP B 251 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (12017) covalent geometry : angle 0.61477 / 0.28 (16453) hydrogen bonds : bond 0.05140 / 3.50 ( 778) hydrogen bonds : angle 4.06341 / 2.92 ( 2258) Misc. bond : bond 0.17474 / 8.55 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.7055 (m-80) cc_final: 0.6757 (m-80) REVERT: A 494 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7713 (tm-30) REVERT: A 528 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.6168 (ttt) REVERT: A 583 MET cc_start: 0.9021 (tpp) cc_final: 0.8443 (mpp) REVERT: B 19 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5577 (p90) REVERT: B 487 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7518 (tt) REVERT: B 494 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 528 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.5760 (ttt) outliers start: 13 outliers final: 2 residues processed: 94 average time/residue: 0.5505 time to fit residues: 56.5939 Evaluate side-chains 91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 5 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.062435 restraints weight = 64512.137| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.94 r_work: 0.2642 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.157 12021 Z= 0.131 Angle : 0.578 12.076 16453 Z= 0.268 Chirality : 0.038 0.146 1732 Planarity : 0.004 0.036 2035 Dihedral : 7.169 81.920 1770 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.43 % Allowed : 15.73 % 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: 2.47 (0.23), residues: 1425 helix: 2.52 (0.17), residues: 1006 sheet: -1.20 (1.35), residues: 10 loop : -0.61 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 267 TYR 0.019 0.001 TYR B 638 PHE 0.010 0.001 PHE B 527 TRP 0.020 0.001 TRP B 251 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (12017) covalent geometry : angle 0.57779 / 0.27 (16453) hydrogen bonds : bond 0.04577 / 3.13 ( 778) hydrogen bonds : angle 3.96786 / 2.86 ( 2258) Misc. bond : bond 0.12257 / 5.92 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5958 (p90) REVERT: A 121 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: A 251 TRP cc_start: 0.7353 (t60) cc_final: 0.6770 (t60) REVERT: A 467 PHE cc_start: 0.7027 (m-80) cc_final: 0.6714 (m-80) REVERT: A 487 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7898 (mp) REVERT: A 494 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7750 (tm-30) REVERT: A 528 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5909 (ttt) REVERT: A 583 MET cc_start: 0.9023 (tpp) cc_final: 0.8449 (mpp) REVERT: B 19 PHE cc_start: 0.6263 (OUTLIER) cc_final: 0.5574 (p90) REVERT: B 251 TRP cc_start: 0.7334 (t60) cc_final: 0.6778 (t60) REVERT: B 487 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7508 (tt) REVERT: B 494 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 528 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5697 (ttt) outliers start: 16 outliers final: 3 residues processed: 94 average time/residue: 0.5579 time to fit residues: 57.3401 Evaluate side-chains 91 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 135 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.0570 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 151 GLN B 130 ASN B 568 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.062817 restraints weight = 78861.000| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 4.17 r_work: 0.2637 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 12021 Z= 0.135 Angle : 0.580 12.618 16453 Z= 0.267 Chirality : 0.038 0.146 1732 Planarity : 0.003 0.035 2035 Dihedral : 7.130 81.635 1770 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.16 % Allowed : 16.00 % 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: 2.49 (0.23), residues: 1425 helix: 2.55 (0.17), residues: 1007 sheet: -1.24 (1.37), residues: 10 loop : -0.64 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 267 TYR 0.019 0.001 TYR B 638 PHE 0.011 0.001 PHE A 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (12017) covalent geometry : angle 0.58041 / 0.27 (16453) hydrogen bonds : bond 0.04603 / 3.14 ( 778) hydrogen bonds : angle 3.95093 / 2.85 ( 2258) Misc. bond : bond 0.13332 / 6.46 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5891 (p90) REVERT: A 251 TRP cc_start: 0.7312 (t60) cc_final: 0.6738 (t60) REVERT: A 467 PHE cc_start: 0.7026 (m-80) cc_final: 0.6721 (m-80) REVERT: A 487 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 494 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 528 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5978 (ttt) REVERT: A 583 MET cc_start: 0.9016 (tpp) cc_final: 0.8496 (mpp) REVERT: B 19 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5587 (p90) REVERT: B 251 TRP cc_start: 0.7357 (t60) cc_final: 0.6778 (t60) REVERT: B 487 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 494 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8001 (tm-30) REVERT: B 528 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5727 (ttt) outliers start: 13 outliers final: 1 residues processed: 93 average time/residue: 0.5777 time to fit residues: 58.5441 Evaluate side-chains 89 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 585 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.087213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.059658 restraints weight = 69665.519| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 4.04 r_work: 0.2466 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 12021 Z= 0.150 Angle : 0.598 13.002 16453 Z= 0.276 Chirality : 0.039 0.147 1732 Planarity : 0.003 0.036 2035 Dihedral : 7.161 81.135 1770 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.80 % Allowed : 16.35 % 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: 2.47 (0.23), residues: 1425 helix: 2.54 (0.17), residues: 1007 sheet: -1.28 (1.39), residues: 10 loop : -0.67 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 267 TYR 0.018 0.001 TYR B 638 PHE 0.011 0.001 PHE A 635 TRP 0.017 0.001 TRP B 251 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (12017) covalent geometry : angle 0.59819 / 0.28 (16453) hydrogen bonds : bond 0.04840 / 3.30 ( 778) hydrogen bonds : angle 3.98142 / 2.87 ( 2258) Misc. bond : bond 0.15735 / 7.66 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5940 (p90) REVERT: A 251 TRP cc_start: 0.7263 (t60) cc_final: 0.6679 (t60) REVERT: A 467 PHE cc_start: 0.7039 (m-80) cc_final: 0.6719 (m-80) REVERT: A 487 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7708 (mp) REVERT: A 494 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 528 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5830 (ttt) REVERT: A 583 MET cc_start: 0.8939 (tpp) cc_final: 0.8360 (mpp) REVERT: B 19 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5537 (p90) REVERT: B 251 TRP cc_start: 0.7269 (t60) cc_final: 0.6684 (t60) REVERT: B 487 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7296 (tt) REVERT: B 494 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 528 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5645 (ttt) outliers start: 9 outliers final: 1 residues processed: 90 average time/residue: 0.5896 time to fit residues: 58.0418 Evaluate side-chains 89 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 49 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.089100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.061455 restraints weight = 70222.563| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 4.09 r_work: 0.2510 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 12021 Z= 0.117 Angle : 0.563 11.008 16453 Z= 0.262 Chirality : 0.038 0.145 1732 Planarity : 0.004 0.039 2035 Dihedral : 6.961 80.583 1770 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.63 % Allowed : 16.62 % Favored : 82.75 % 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: 2.53 (0.24), residues: 1425 helix: 2.56 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : -0.63 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 267 TYR 0.019 0.001 TYR B 638 PHE 0.012 0.001 PHE B 492 TRP 0.020 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (12017) covalent geometry : angle 0.56327 / 0.26 (16453) hydrogen bonds : bond 0.04159 / 2.85 ( 778) hydrogen bonds : angle 3.87414 / 2.79 ( 2258) Misc. bond : bond 0.09088 / 4.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5966 (p90) REVERT: A 251 TRP cc_start: 0.7298 (t60) cc_final: 0.6707 (t60) REVERT: A 467 PHE cc_start: 0.7000 (m-80) cc_final: 0.6651 (m-80) REVERT: A 487 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7712 (mp) REVERT: A 494 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7626 (tm-30) REVERT: A 528 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5856 (ttt) REVERT: A 583 MET cc_start: 0.8917 (tpp) cc_final: 0.8314 (mpp) REVERT: B 19 PHE cc_start: 0.6229 (OUTLIER) cc_final: 0.5553 (p90) REVERT: B 251 TRP cc_start: 0.7283 (t60) cc_final: 0.6699 (t60) REVERT: B 494 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 528 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5657 (ttt) outliers start: 7 outliers final: 1 residues processed: 93 average time/residue: 0.5135 time to fit residues: 52.6948 Evaluate side-chains 88 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 528 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3273 r_free = 0.3273 target = 0.088923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.061301 restraints weight = 69596.435| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 4.10 r_work: 0.2496 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2492 r_free = 0.2492 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 12021 Z= 0.125 Angle : 0.576 12.340 16453 Z= 0.264 Chirality : 0.038 0.148 1732 Planarity : 0.003 0.039 2035 Dihedral : 6.982 80.976 1770 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.63 % Allowed : 16.26 % Favored : 83.11 % 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: 2.56 (0.24), residues: 1425 helix: 2.58 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : -0.63 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.019 0.001 TYR A 638 PHE 0.010 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.12 (12017) covalent geometry : angle 0.57610 / 0.26 (16453) hydrogen bonds : bond 0.04361 / 2.98 ( 778) hydrogen bonds : angle 3.87640 / 2.79 ( 2258) Misc. bond : bond 0.11907 / 5.74 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5920 (p90) REVERT: A 251 TRP cc_start: 0.7335 (t60) cc_final: 0.6716 (t60) REVERT: A 487 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7697 (mp) REVERT: A 494 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7615 (tm-30) REVERT: A 528 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5878 (ttt) REVERT: A 583 MET cc_start: 0.8915 (tpp) cc_final: 0.8311 (mpp) REVERT: B 19 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5601 (p90) REVERT: B 251 TRP cc_start: 0.7322 (t60) cc_final: 0.6704 (t60) REVERT: B 494 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7980 (tm-30) outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.5658 time to fit residues: 53.9463 Evaluate side-chains 88 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain B residue 19 PHE Chi-restraints excluded: chain B residue 309 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.088808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.061296 restraints weight = 63107.572| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.95 r_work: 0.2512 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 12021 Z= 0.123 Angle : 0.573 11.556 16453 Z= 0.265 Chirality : 0.038 0.147 1732 Planarity : 0.004 0.067 2035 Dihedral : 6.936 80.481 1770 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.71 % Allowed : 16.44 % 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: 2.57 (0.24), residues: 1425 helix: 2.59 (0.17), residues: 1013 sheet: None (None), residues: 0 loop : -0.62 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 267 TYR 0.022 0.001 TYR A 638 PHE 0.010 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (12017) covalent geometry : angle 0.57305 / 0.27 (16453) hydrogen bonds : bond 0.04259 / 2.91 ( 778) hydrogen bonds : angle 3.86046 / 2.78 ( 2258) Misc. bond : bond 0.10648 / 5.10 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.82 seconds wall clock time: 71 minutes 49.52 seconds (4309.52 seconds total)