Starting phenix.real_space_refine on Fri Jul 3 07:01:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pq_56721/07_2026/28pq_56721.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pq_56721/07_2026/28pq_56721.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/28pq_56721/07_2026/28pq_56721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pq_56721/07_2026/28pq_56721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28pq_56721/07_2026/28pq_56721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pq_56721/07_2026/28pq_56721.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= 0.010 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 7623 2.51 5 N 1905 2.21 5 O 2770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s 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: 12350 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5618 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 711, 5608 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, 5608 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: 5777 Chain: "B" Number of atoms: 5616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 710, 5606 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, 5606 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: 5776 Chain: "A" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2, 'LMT': 1} Classifications: {'undetermined': 3} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2, 'LMT': 2, 'UQ5': 1} Classifications: {'undetermined': 5} Link IDs: {None: 2} 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: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 384 Classifications: {'water': 384} Link IDs: {None: 383} Chain: "B" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 431 Classifications: {'water': 431} Link IDs: {None: 430} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 224 " occ=0.58 ... (18 atoms not shown) pdb=" NE2BHIS A 224 " occ=0.42 residue: pdb=" N AHIS B 224 " occ=0.59 ... (18 atoms not shown) pdb=" NE2BHIS B 224 " occ=0.41 Time building chain proxies: 5.18, per 1000 atoms: 0.42 Number of scatterers: 12350 At special positions: 0 Unit cell: (107.3, 85.1, 108.04, 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 2770 8.00 N 1905 7.00 C 7623 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: 1.19 Conformation dependent library (CDL) restraints added in 633.9 milliseconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 78.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.796A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 3.920A 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 128 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 317 through 321 removed outlier: 3.660A pdb=" N GLN A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix removed outlier: 3.971A 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 439 removed outlier: 3.663A 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 489 Processing helix chain 'A' and resid 491 through 509 Processing helix chain 'A' and resid 512 through 537 removed outlier: 5.145A 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: 3.634A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 555 " --> pdb=" O VAL A 551 " (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: 4.199A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.854A 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 612 Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.181A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 4.808A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 682 removed outlier: 3.722A 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: 3.793A pdb=" N GLY B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.551A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 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 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 removed outlier: 3.759A pdb=" N THR B 272 " --> pdb=" O PRO B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.681A pdb=" N GLN B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix removed outlier: 3.954A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 removed outlier: 3.555A pdb=" N GLY B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) 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: 3.640A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix removed outlier: 3.644A 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 509 Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.222A 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: 3.638A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 571 through 576 removed outlier: 3.545A pdb=" N ARG B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.995A pdb=" N MET B 583 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 580 through 585' Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 605 through 612 Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.207A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 4.676A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 682 removed outlier: 3.711A 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: 6.153A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (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 'B' and resid 47 through 50 removed outlier: 6.229A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 783 hydrogen bonds defined for protein. 2271 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: 2.24 Time building geometry restraints manager: 1.56 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: 4630 1.38 - 1.55: 7199 1.55 - 1.72: 0 1.72 - 1.90: 84 1.90 - 2.07: 16 Bond restraints: 11929 Sorted by residual: bond pdb=" C VAL B 561 " pdb=" N PRO B 562 " ideal model delta sigma weight residual 1.336 1.377 -0.041 1.20e-02 6.94e+03 1.17e+01 bond pdb=" C VAL A 561 " pdb=" N PRO A 562 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.57e+00 bond pdb=" CB THR A 196 " pdb=" CG2 THR A 196 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.68e-01 bond pdb=" CB THR B 196 " pdb=" CG2 THR B 196 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 9.02e-01 bond pdb=" CA ARG A 720 " pdb=" C ARG A 720 " ideal model delta sigma weight residual 1.522 1.535 -0.014 1.45e-02 4.76e+03 8.91e-01 ... (remaining 11924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 16141 2.36 - 4.73: 157 4.73 - 7.09: 21 7.09 - 9.45: 6 9.45 - 11.82: 4 Bond angle restraints: 16329 Sorted by residual: angle pdb=" N ILE A 392 " pdb=" CA ILE A 392 " pdb=" C ILE A 392 " ideal model delta sigma weight residual 111.81 108.59 3.22 8.60e-01 1.35e+00 1.40e+01 angle pdb=" C LEU A 634 " pdb=" N PHE A 635 " pdb=" CA PHE A 635 " ideal model delta sigma weight residual 120.65 116.83 3.82 1.32e+00 5.74e-01 8.36e+00 angle pdb=" CA TRP B 338 " pdb=" CB TRP B 338 " pdb=" CG TRP B 338 " ideal model delta sigma weight residual 113.60 119.03 -5.43 1.90e+00 2.77e-01 8.18e+00 angle pdb=" CA TRP A 338 " pdb=" CB TRP A 338 " pdb=" CG TRP A 338 " ideal model delta sigma weight residual 113.60 118.92 -5.32 1.90e+00 2.77e-01 7.85e+00 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 120.88 -8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 16324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6003 17.94 - 35.88: 537 35.88 - 53.82: 162 53.82 - 71.76: 36 71.76 - 89.70: 25 Dihedral angle restraints: 6763 sinusoidal: 2714 harmonic: 4049 Sorted by residual: 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 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 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 -157.77 -22.23 0 5.00e+00 4.00e-02 1.98e+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 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1123 0.030 - 0.059: 397 0.059 - 0.089: 140 0.089 - 0.119: 54 0.119 - 0.148: 16 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CB VAL B 561 " pdb=" CA VAL B 561 " pdb=" CG1 VAL B 561 " pdb=" CG2 VAL B 561 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA TRP B 588 " pdb=" N TRP B 588 " pdb=" C TRP B 588 " pdb=" CB TRP B 588 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA THR B 546 " pdb=" N THR B 546 " pdb=" C THR B 546 " pdb=" CB THR B 546 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 1727 not shown) Planarity restraints: 2023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 420 " -0.014 2.00e-02 2.50e+03 1.15e-02 2.31e+00 pdb=" CG PHE A 420 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 420 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 420 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 420 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 420 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 420 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 588 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 589 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 589 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 589 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 147 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" CD GLN B 147 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN B 147 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN B 147 " -0.008 2.00e-02 2.50e+03 ... (remaining 2020 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 222 2.56 - 3.15: 9893 3.15 - 3.73: 21284 3.73 - 4.32: 30376 4.32 - 4.90: 47967 Nonbonded interactions: 109742 Sorted by model distance: nonbonded pdb="FE FE A 804 " pdb=" O HOH A 976 " model vdw 1.978 3.000 nonbonded pdb="FE FE B 805 " pdb=" O HOH B1064 " model vdw 1.980 3.000 nonbonded pdb=" NE2 HIS B 537 " pdb="FE FE B 805 " model vdw 2.200 3.080 nonbonded pdb=" NE2 HIS A 537 " pdb="FE FE A 804 " model vdw 2.205 3.080 nonbonded pdb=" O GLU B 494 " pdb=" OG1 THR B 498 " model vdw 2.222 3.040 ... (remaining 109737 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 750)) selection = (chain 'B' and (resid 18 through 223 or resid 225 through 439 or resid 465 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=0.41 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: 6.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.660 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:9.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11933 Z= 0.135 Angle : 0.605 11.817 16329 Z= 0.294 Chirality : 0.038 0.148 1730 Planarity : 0.004 0.037 2023 Dihedral : 16.368 89.697 4187 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 1.26 % Allowed : 14.98 % Favored : 83.77 % 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: 1.90 (0.23), residues: 1419 helix: 2.08 (0.17), residues: 983 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 267 TYR 0.016 0.002 TYR A 324 PHE 0.026 0.001 PHE A 420 TRP 0.023 0.002 TRP B 251 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (11929) covalent geometry : angle 0.60493 / 0.29 (16329) hydrogen bonds : bond 0.13757 / 9.61 ( 783) hydrogen bonds : angle 5.11965 / 3.73 ( 2271) Misc. bond : bond 0.00958 / 0.47 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.474 Fit side-chains REVERT: B 584 GLU cc_start: 0.7815 (pp20) cc_final: 0.7235 (tm-30) outliers start: 14 outliers final: 0 residues processed: 129 average time/residue: 0.6640 time to fit residues: 92.3862 Evaluate side-chains 94 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN B 58 GLN B 62 GLN B 213 ASN B 568 HIS B 621 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.064122 restraints weight = 43172.436| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 3.30 r_work: 0.2526 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 11933 Z= 0.140 Angle : 0.627 12.434 16329 Z= 0.291 Chirality : 0.040 0.140 1730 Planarity : 0.004 0.057 2023 Dihedral : 7.507 87.474 1766 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 2.87 % Allowed : 16.77 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.18 (0.23), residues: 1419 helix: 2.28 (0.17), residues: 994 sheet: -1.84 (0.74), residues: 20 loop : -0.52 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 513 TYR 0.013 0.001 TYR B 324 PHE 0.014 0.001 PHE A 420 TRP 0.021 0.001 TRP B 338 HIS 0.008 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11929) covalent geometry : angle 0.62685 / 0.29 (16329) hydrogen bonds : bond 0.04892 / 3.33 ( 783) hydrogen bonds : angle 4.16655 / 3.04 ( 2271) Misc. bond : bond 0.06202 / 3.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.401 Fit side-chains REVERT: A 126 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: A 467 PHE cc_start: 0.7337 (m-80) cc_final: 0.7026 (m-80) REVERT: A 508 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8481 (mp) REVERT: A 584 GLU cc_start: 0.8270 (pm20) cc_final: 0.7916 (mm-30) REVERT: B 168 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8013 (tpt-90) REVERT: B 489 VAL cc_start: 0.6873 (OUTLIER) cc_final: 0.6661 (t) REVERT: B 494 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7905 (mm-30) REVERT: B 508 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 514 ARG cc_start: 0.7361 (ttp80) cc_final: 0.7067 (ppp80) REVERT: B 584 GLU cc_start: 0.8702 (pp20) cc_final: 0.8000 (tm-30) outliers start: 32 outliers final: 6 residues processed: 116 average time/residue: 0.5491 time to fit residues: 69.1926 Evaluate side-chains 106 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 510 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 105 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 120 optimal weight: 0.1980 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 568 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.059326 restraints weight = 39449.230| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 3.17 r_work: 0.2436 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.207 11933 Z= 0.234 Angle : 0.676 13.821 16329 Z= 0.318 Chirality : 0.043 0.146 1730 Planarity : 0.004 0.046 2023 Dihedral : 7.810 84.705 1766 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.76 % Favored : 97.03 % Rotamer: Outliers : 2.51 % Allowed : 16.68 % Favored : 80.81 % 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: 2.05 (0.23), residues: 1419 helix: 2.18 (0.17), residues: 998 sheet: -2.09 (0.70), residues: 20 loop : -0.57 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 267 TYR 0.018 0.002 TYR B 324 PHE 0.019 0.002 PHE A 635 TRP 0.020 0.002 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.23 (11929) covalent geometry : angle 0.67617 / 0.32 (16329) hydrogen bonds : bond 0.06343 / 4.29 ( 783) hydrogen bonds : angle 4.27710 / 3.13 ( 2271) Misc. bond : bond 0.16066 / 7.89 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.310 Fit side-chains REVERT: A 467 PHE cc_start: 0.7408 (m-80) cc_final: 0.7004 (m-80) REVERT: A 508 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 494 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 508 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 584 GLU cc_start: 0.8706 (pp20) cc_final: 0.8014 (tm-30) outliers start: 28 outliers final: 10 residues processed: 116 average time/residue: 0.5057 time to fit residues: 64.0405 Evaluate side-chains 108 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 118 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS B 217 HIS B 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.063128 restraints weight = 32112.967| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.94 r_work: 0.2521 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2533 r_free = 0.2533 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 11933 Z= 0.133 Angle : 0.611 12.436 16329 Z= 0.281 Chirality : 0.039 0.138 1730 Planarity : 0.004 0.050 2023 Dihedral : 7.532 86.780 1766 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.97 % Favored : 96.82 % Rotamer: Outliers : 2.06 % Allowed : 17.49 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 2.19 (0.23), residues: 1419 helix: 2.31 (0.17), residues: 1003 sheet: -2.44 (0.69), residues: 20 loop : -0.59 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.018 0.001 TYR B 362 PHE 0.012 0.001 PHE A 635 TRP 0.022 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (11929) covalent geometry : angle 0.61090 / 0.28 (16329) hydrogen bonds : bond 0.04878 / 3.32 ( 783) hydrogen bonds : angle 4.04118 / 2.95 ( 2271) Misc. bond : bond 0.08331 / 4.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.302 Fit side-chains REVERT: A 126 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: A 467 PHE cc_start: 0.7358 (m-80) cc_final: 0.6949 (m-80) REVERT: A 508 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8420 (mp) REVERT: A 584 GLU cc_start: 0.8351 (pm20) cc_final: 0.7961 (mm-30) REVERT: B 123 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8190 (tp) REVERT: B 362 TYR cc_start: 0.8213 (m-80) cc_final: 0.7963 (m-80) REVERT: B 494 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 508 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8346 (mp) REVERT: B 584 GLU cc_start: 0.8665 (pp20) cc_final: 0.7920 (tm-30) outliers start: 23 outliers final: 9 residues processed: 105 average time/residue: 0.5588 time to fit residues: 64.0588 Evaluate side-chains 107 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 109 optimal weight: 3.9990 chunk 80 optimal weight: 0.3980 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 568 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.093611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.060688 restraints weight = 31070.620| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.91 r_work: 0.2471 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2484 r_free = 0.2484 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 11933 Z= 0.196 Angle : 0.652 14.044 16329 Z= 0.301 Chirality : 0.041 0.142 1730 Planarity : 0.004 0.063 2023 Dihedral : 7.693 84.925 1766 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.67 % Rotamer: Outliers : 2.33 % Allowed : 16.95 % Favored : 80.72 % 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: 2.14 (0.23), residues: 1419 helix: 2.27 (0.17), residues: 998 sheet: -2.48 (0.69), residues: 20 loop : -0.58 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 267 TYR 0.016 0.001 TYR B 324 PHE 0.018 0.001 PHE A 635 TRP 0.020 0.002 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.19 (11929) covalent geometry : angle 0.65197 / 0.30 (16329) hydrogen bonds : bond 0.05758 / 3.90 ( 783) hydrogen bonds : angle 4.13541 / 3.02 ( 2271) Misc. bond : bond 0.13964 / 6.85 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.303 Fit side-chains REVERT: A 126 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8573 (tt0) REVERT: A 467 PHE cc_start: 0.7443 (m-80) cc_final: 0.7023 (m-80) REVERT: A 508 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8390 (mp) REVERT: B 362 TYR cc_start: 0.8251 (m-80) cc_final: 0.7992 (m-80) REVERT: B 494 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 508 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8341 (mp) REVERT: B 584 GLU cc_start: 0.8666 (pp20) cc_final: 0.8072 (tm-30) outliers start: 26 outliers final: 12 residues processed: 109 average time/residue: 0.5335 time to fit residues: 63.6295 Evaluate side-chains 113 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 133 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.063032 restraints weight = 37385.464| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 3.16 r_work: 0.2521 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 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 = 0.2517 r_free = 0.2517 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: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 11933 Z= 0.125 Angle : 0.602 12.252 16329 Z= 0.277 Chirality : 0.038 0.136 1730 Planarity : 0.004 0.059 2023 Dihedral : 7.499 86.367 1766 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.33 % Favored : 96.46 % Rotamer: Outliers : 1.79 % Allowed : 17.40 % Favored : 80.81 % 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: 2.28 (0.23), residues: 1419 helix: 2.38 (0.17), residues: 1001 sheet: -2.52 (0.70), residues: 20 loop : -0.57 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 267 TYR 0.019 0.001 TYR A 30 PHE 0.011 0.001 PHE A 635 TRP 0.023 0.001 TRP B 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (11929) covalent geometry : angle 0.60174 / 0.28 (16329) hydrogen bonds : bond 0.04601 / 3.13 ( 783) hydrogen bonds : angle 3.95860 / 2.89 ( 2271) Misc. bond : bond 0.06614 / 3.35 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.454 Fit side-chains REVERT: A 126 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: A 467 PHE cc_start: 0.7351 (m-80) cc_final: 0.6886 (m-80) REVERT: A 508 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8402 (mp) REVERT: A 584 GLU cc_start: 0.8404 (pm20) cc_final: 0.8006 (mm-30) REVERT: B 123 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8224 (tp) REVERT: B 494 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7959 (mm-30) REVERT: B 508 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8327 (mp) REVERT: B 584 GLU cc_start: 0.8640 (pp20) cc_final: 0.8015 (tm-30) outliers start: 20 outliers final: 11 residues processed: 105 average time/residue: 0.5694 time to fit residues: 65.4790 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 136 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.096669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.063407 restraints weight = 36617.824| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.14 r_work: 0.2529 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 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: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 11933 Z= 0.126 Angle : 0.598 12.669 16329 Z= 0.274 Chirality : 0.038 0.136 1730 Planarity : 0.004 0.064 2023 Dihedral : 7.463 87.061 1766 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.67 % Rotamer: Outliers : 1.88 % Allowed : 17.76 % Favored : 80.36 % 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: 2.39 (0.23), residues: 1419 helix: 2.50 (0.17), residues: 989 sheet: -2.44 (0.72), residues: 20 loop : -0.53 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 267 TYR 0.013 0.001 TYR B 362 PHE 0.014 0.001 PHE A 635 TRP 0.022 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11929) covalent geometry : angle 0.59776 / 0.27 (16329) hydrogen bonds : bond 0.04506 / 3.07 ( 783) hydrogen bonds : angle 3.91102 / 2.86 ( 2271) Misc. bond : bond 0.06828 / 3.42 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.443 Fit side-chains REVERT: A 126 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: A 467 PHE cc_start: 0.7282 (m-80) cc_final: 0.6805 (m-80) REVERT: A 508 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 584 GLU cc_start: 0.8375 (pm20) cc_final: 0.8020 (mm-30) REVERT: B 494 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7984 (mm-30) REVERT: B 508 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 584 GLU cc_start: 0.8619 (pp20) cc_final: 0.8037 (tm-30) outliers start: 21 outliers final: 11 residues processed: 104 average time/residue: 0.5973 time to fit residues: 67.7791 Evaluate side-chains 109 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.095799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.062108 restraints weight = 42739.694| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.33 r_work: 0.2479 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 11933 Z= 0.147 Angle : 0.615 13.273 16329 Z= 0.281 Chirality : 0.039 0.138 1730 Planarity : 0.004 0.061 2023 Dihedral : 7.514 85.411 1766 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.26 % Favored : 96.53 % Rotamer: Outliers : 1.97 % Allowed : 17.58 % Favored : 80.45 % 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: 2.35 (0.23), residues: 1419 helix: 2.47 (0.17), residues: 989 sheet: -2.50 (0.71), residues: 20 loop : -0.54 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 267 TYR 0.021 0.001 TYR A 30 PHE 0.015 0.001 PHE A 635 TRP 0.019 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (11929) covalent geometry : angle 0.61512 / 0.28 (16329) hydrogen bonds : bond 0.04878 / 3.31 ( 783) hydrogen bonds : angle 3.95690 / 2.89 ( 2271) Misc. bond : bond 0.09572 / 4.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.364 Fit side-chains REVERT: A 126 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: A 467 PHE cc_start: 0.7301 (m-80) cc_final: 0.6813 (m-80) REVERT: A 508 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8349 (mp) REVERT: A 584 GLU cc_start: 0.8393 (pm20) cc_final: 0.8051 (mm-30) REVERT: B 126 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: B 494 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7951 (mm-30) REVERT: B 508 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8314 (mp) REVERT: B 584 GLU cc_start: 0.8629 (pp20) cc_final: 0.8017 (tm-30) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.5748 time to fit residues: 66.5534 Evaluate side-chains 110 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.0170 chunk 64 optimal weight: 0.1980 chunk 109 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 568 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.065498 restraints weight = 52689.463| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.64 r_work: 0.2551 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11933 Z= 0.108 Angle : 0.570 10.687 16329 Z= 0.264 Chirality : 0.037 0.134 1730 Planarity : 0.004 0.061 2023 Dihedral : 7.305 88.597 1766 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.90 % Favored : 96.89 % Rotamer: Outliers : 1.08 % Allowed : 18.57 % Favored : 80.36 % 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: 2.55 (0.23), residues: 1419 helix: 2.60 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.55 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 267 TYR 0.013 0.001 TYR B 362 PHE 0.012 0.001 PHE A 492 TRP 0.024 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11929) covalent geometry : angle 0.57023 / 0.26 (16329) hydrogen bonds : bond 0.03786 / 2.58 ( 783) hydrogen bonds : angle 3.81360 / 2.78 ( 2271) Misc. bond : bond 0.01498 / 0.77 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 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: 12 poor density : 102 time to evaluate : 0.424 Fit side-chains REVERT: A 126 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: A 302 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7451 (t80) REVERT: A 467 PHE cc_start: 0.7260 (m-80) cc_final: 0.6790 (m-80) REVERT: A 508 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 584 GLU cc_start: 0.8388 (pm20) cc_final: 0.8013 (mm-30) REVERT: B 302 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7469 (t80) REVERT: B 494 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 508 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8311 (mp) REVERT: B 584 GLU cc_start: 0.8584 (pp20) cc_final: 0.7995 (tm-30) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 0.5704 time to fit residues: 65.6184 Evaluate side-chains 106 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 45 optimal weight: 0.8980 chunk 97 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.0670 overall best weight: 0.4530 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.098762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.065235 restraints weight = 45066.034| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 3.42 r_work: 0.2549 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11933 Z= 0.110 Angle : 0.576 11.728 16329 Z= 0.263 Chirality : 0.037 0.134 1730 Planarity : 0.004 0.063 2023 Dihedral : 7.328 89.130 1766 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.04 % Favored : 96.74 % Rotamer: Outliers : 1.08 % Allowed : 18.65 % Favored : 80.27 % 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: 2.56 (0.23), residues: 1419 helix: 2.59 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.48 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 267 TYR 0.022 0.001 TYR A 30 PHE 0.013 0.001 PHE A 635 TRP 0.023 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (11929) covalent geometry : angle 0.57572 / 0.26 (16329) hydrogen bonds : bond 0.03947 / 2.69 ( 783) hydrogen bonds : angle 3.80148 / 2.77 ( 2271) Misc. bond : bond 0.03666 / 1.84 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.467 Fit side-chains REVERT: A 302 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7498 (t80) REVERT: A 467 PHE cc_start: 0.7266 (m-80) cc_final: 0.6753 (m-80) REVERT: A 508 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8410 (mp) REVERT: A 584 GLU cc_start: 0.8373 (pm20) cc_final: 0.8008 (mm-30) REVERT: B 302 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 494 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 508 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 584 GLU cc_start: 0.8608 (pp20) cc_final: 0.8007 (tm-30) outliers start: 12 outliers final: 3 residues processed: 103 average time/residue: 0.5562 time to fit residues: 62.8935 Evaluate side-chains 105 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 PHE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 302 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 582 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 9 optimal weight: 0.0370 chunk 136 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 0.0970 chunk 26 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 overall best weight: 0.1634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 GLN B 621 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.069458 restraints weight = 37821.072| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.20 r_work: 0.2652 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11933 Z= 0.102 Angle : 0.556 8.969 16329 Z= 0.259 Chirality : 0.037 0.133 1730 Planarity : 0.004 0.063 2023 Dihedral : 7.075 88.532 1766 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.62 % Favored : 97.17 % Rotamer: Outliers : 0.54 % Allowed : 19.73 % Favored : 79.73 % 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: 2.63 (0.24), residues: 1419 helix: 2.63 (0.17), residues: 991 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 267 TYR 0.012 0.001 TYR B 362 PHE 0.021 0.001 PHE A 492 TRP 0.027 0.001 TRP A 338 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (11929) covalent geometry : angle 0.55607 / 0.26 (16329) hydrogen bonds : bond 0.03318 / 2.27 ( 783) hydrogen bonds : angle 3.73492 / 2.72 ( 2271) Misc. bond : bond 0.01908 / 0.93 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.61 seconds wall clock time: 74 minutes 33.84 seconds (4473.84 seconds total)