Starting phenix.real_space_refine on Thu Aug 6 05:51:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yh_75529/08_2026/10yh_75529.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yh_75529/08_2026/10yh_75529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10yh_75529/08_2026/10yh_75529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yh_75529/08_2026/10yh_75529.map" model { file = "/net/cci-nas-00/data/ceres_data/10yh_75529/08_2026/10yh_75529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yh_75529/08_2026/10yh_75529.cif" } resolution = 2.9 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= 0.004 sd= 1.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 25 5.16 5 C 7679 2.51 5 N 2529 2.21 5 O 3114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13642 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 2722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2722 Classifications: {'DNA': 132} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 131} Chain: "L" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1661 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 195} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.52, per 1000 atoms: 0.18 Number of scatterers: 13642 At special positions: 0 Unit cell: (88.02, 123.88, 137.572, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 25 16.00 P 295 15.00 O 3114 8.00 N 2529 7.00 C 7679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 359.4 milliseconds 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1788 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 11 sheets defined 63.0% alpha, 10.4% beta 147 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.510A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.735A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.545A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.410A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.557A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.043A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.852A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.328A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'L' and resid 404 through 412 Processing helix chain 'L' and resid 447 through 452 Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 486 through 490 removed outlier: 3.536A pdb=" N THR L 489 " --> pdb=" O PRO L 486 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU L 490 " --> pdb=" O PHE L 487 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 486 through 490' Processing helix chain 'L' and resid 522 through 534 Processing helix chain 'L' and resid 551 through 564 removed outlier: 4.317A pdb=" N MET L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN L 564 " --> pdb=" O THR L 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.210A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.484A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.414A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.199A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.389A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 398 through 401 removed outlier: 6.519A pdb=" N LEU L 398 " --> pdb=" O ARG L 584 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N HIS L 585 " --> pdb=" O ASP L 574 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP L 574 " --> pdb=" O HIS L 585 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 436 through 439 removed outlier: 7.206A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 483 through 485 removed outlier: 3.780A pdb=" N LYS L 483 " --> pdb=" O ASP L 478 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU L 476 " --> pdb=" O LEU L 485 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N MET L 542 " --> pdb=" O VAL L 507 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N ASP L 509 " --> pdb=" O MET L 542 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2005 1.32 - 1.45: 4992 1.45 - 1.57: 6868 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14496 Sorted by residual: bond pdb=" N3 DA K 61 " pdb=" C4 DA K 61 " ideal model delta sigma weight residual 1.344 1.323 0.021 6.00e-03 2.78e+04 1.17e+01 bond pdb=" C3' DC K 81 " pdb=" O3' DC K 81 " ideal model delta sigma weight residual 1.435 1.391 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" N3 DA I 49 " pdb=" C4 DA I 49 " ideal model delta sigma weight residual 1.344 1.324 0.020 6.00e-03 2.78e+04 1.13e+01 bond pdb=" N3 DA I 61 " pdb=" C4 DA I 61 " ideal model delta sigma weight residual 1.344 1.324 0.020 6.00e-03 2.78e+04 1.11e+01 bond pdb=" N3 DA I 60 " pdb=" C4 DA I 60 " ideal model delta sigma weight residual 1.344 1.324 0.020 6.00e-03 2.78e+04 1.09e+01 ... (remaining 14491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18753 1.30 - 2.59: 1843 2.59 - 3.89: 224 3.89 - 5.19: 6 5.19 - 6.49: 10 Bond angle restraints: 20836 Sorted by residual: angle pdb=" N3 DT J 15 " pdb=" C4 DT J 15 " pdb=" O4 DT J 15 " ideal model delta sigma weight residual 119.90 122.77 -2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.23e+01 angle pdb=" N3 DT K 83 " pdb=" C4 DT K 83 " pdb=" O4 DT K 83 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" N3 DT K 50 " pdb=" C4 DT K 50 " pdb=" O4 DT K 50 " ideal model delta sigma weight residual 119.90 122.67 -2.77 6.00e-01 2.78e+00 2.13e+01 ... (remaining 20831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 6175 28.69 - 57.38: 1639 57.38 - 86.08: 145 86.08 - 114.77: 1 114.77 - 143.46: 2 Dihedral angle restraints: 7962 sinusoidal: 5190 harmonic: 2772 Sorted by residual: dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" C4' DG K 82 " pdb=" C3' DG K 82 " pdb=" O3' DG K 82 " pdb=" P DT K 83 " ideal model delta sinusoidal sigma weight residual 220.00 76.54 143.46 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DC K 126 " pdb=" C3' DC K 126 " pdb=" O3' DC K 126 " pdb=" P DC K 127 " ideal model delta sinusoidal sigma weight residual 220.00 77.79 142.21 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 7959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1370 0.039 - 0.079: 721 0.079 - 0.118: 237 0.118 - 0.157: 29 0.157 - 0.197: 3 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ILE L 420 " pdb=" N ILE L 420 " pdb=" C ILE L 420 " pdb=" CB ILE L 420 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" C3' DC K 126 " pdb=" C4' DC K 126 " pdb=" O3' DC K 126 " pdb=" C2' DC K 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CA LYS L 421 " pdb=" N LYS L 421 " pdb=" C LYS L 421 " pdb=" CB LYS L 421 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 2357 not shown) Planarity restraints: 1617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO E 43 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU L 580 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO L 581 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 581 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 581 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 61 " 0.026 2.00e-02 2.50e+03 1.14e-02 3.58e+00 pdb=" N9 DA I 61 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DA I 61 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 61 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 61 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA I 61 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 61 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I 61 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 61 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 61 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA I 61 " -0.004 2.00e-02 2.50e+03 ... (remaining 1614 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 5986 2.98 - 3.46: 12725 3.46 - 3.94: 27428 3.94 - 4.42: 30729 4.42 - 4.90: 41580 Nonbonded interactions: 118448 Sorted by model distance: nonbonded pdb=" O5' DG K 95 " pdb=" O4' DG K 95 " model vdw 2.496 2.432 nonbonded pdb=" N1 DG K 94 " pdb=" C4 DG K 94 " model vdw 2.573 2.672 nonbonded pdb=" N1 DG I 100 " pdb=" C4 DG I 100 " model vdw 2.574 2.672 nonbonded pdb=" N1 DG I 63 " pdb=" C4 DG I 63 " model vdw 2.574 2.672 nonbonded pdb=" N1 DG K 120 " pdb=" C4 DG K 120 " model vdw 2.574 2.672 ... (remaining 118443 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' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.009 0.058 14497 Z= 0.748 Angle : 0.776 6.487 20836 Z= 0.677 Chirality : 0.049 0.197 2360 Planarity : 0.005 0.056 1617 Dihedral : 26.460 143.461 6174 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.25 % Allowed : 4.60 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 938 helix: 1.65 (0.21), residues: 588 sheet: 0.29 (0.85), residues: 44 loop : -1.30 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 45 TYR 0.012 0.002 TYR L 512 PHE 0.013 0.002 PHE L 454 TRP 0.002 0.001 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00902 / 0.75 (14496) covalent geometry : angle 0.77590 / 0.68 (20836) hydrogen bonds : bond 0.12039 / 7.85 ( 838) hydrogen bonds : angle 4.24747 / 3.03 ( 2129) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8006 (mtt180) REVERT: C 24 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8926 (mm-40) REVERT: C 64 GLU cc_start: 0.8556 (tt0) cc_final: 0.8302 (tp30) REVERT: C 110 ASN cc_start: 0.8752 (t0) cc_final: 0.8377 (p0) REVERT: E 64 LYS cc_start: 0.8958 (mttt) cc_final: 0.8631 (mtmm) REVERT: F 79 LYS cc_start: 0.8684 (mttm) cc_final: 0.8238 (mtpt) REVERT: G 35 ARG cc_start: 0.8982 (mtm-85) cc_final: 0.8703 (mtt90) REVERT: G 64 GLU cc_start: 0.8548 (tt0) cc_final: 0.8277 (tp30) REVERT: H 35 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7504 (mm-30) REVERT: L 422 TYR cc_start: 0.6921 (m-80) cc_final: 0.6587 (m-80) REVERT: L 534 MET cc_start: 0.6328 (ttt) cc_final: 0.5905 (tmm) REVERT: L 537 ILE cc_start: 0.8414 (pt) cc_final: 0.8163 (mp) REVERT: L 541 ILE cc_start: 0.8817 (mp) cc_final: 0.8069 (pp) REVERT: L 545 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8436 (pt0) outliers start: 2 outliers final: 1 residues processed: 253 average time/residue: 0.7950 time to fit residues: 213.6161 Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 485 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN E 68 GLN G 73 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.105216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.068999 restraints weight = 28973.963| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.44 r_work: 0.2817 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14497 Z= 0.149 Angle : 0.645 9.982 20836 Z= 0.373 Chirality : 0.045 0.289 2360 Planarity : 0.005 0.052 1617 Dihedral : 30.527 142.444 4276 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.60 % Allowed : 15.40 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.27), residues: 938 helix: 2.05 (0.21), residues: 596 sheet: 1.04 (0.82), residues: 38 loop : -1.16 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 561 TYR 0.010 0.001 TYR C 57 PHE 0.015 0.002 PHE L 529 TRP 0.003 0.001 TRP L 586 HIS 0.011 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.15 (14496) covalent geometry : angle 0.64467 / 0.37 (20836) hydrogen bonds : bond 0.04685 / 3.13 ( 838) hydrogen bonds : angle 3.44705 / 2.44 ( 2129) Misc. bond : bond 0.00119 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8619 (mtp85) cc_final: 0.8334 (mtt180) REVERT: C 73 ASN cc_start: 0.9217 (t0) cc_final: 0.8871 (t0) REVERT: C 110 ASN cc_start: 0.8832 (t0) cc_final: 0.8627 (p0) REVERT: D 113 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: E 120 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7976 (mtt) REVERT: F 79 LYS cc_start: 0.9043 (mttm) cc_final: 0.8768 (mtpt) REVERT: G 56 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: H 63 ASN cc_start: 0.8802 (t160) cc_final: 0.8587 (m-40) REVERT: L 397 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7011 (tpt) REVERT: L 534 MET cc_start: 0.6473 (ttt) cc_final: 0.5897 (tmm) REVERT: L 586 TRP cc_start: 0.7687 (m100) cc_final: 0.6886 (m100) outliers start: 29 outliers final: 3 residues processed: 208 average time/residue: 0.6915 time to fit residues: 153.5122 Evaluate side-chains 183 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 176 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 507 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.104124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.067630 restraints weight = 29080.778| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.46 r_work: 0.2778 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 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 0.038 14497 Z= 0.155 Angle : 0.620 6.169 20836 Z= 0.361 Chirality : 0.044 0.278 2360 Planarity : 0.004 0.051 1617 Dihedral : 30.544 142.622 4274 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.35 % Allowed : 16.89 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.28), residues: 938 helix: 2.31 (0.21), residues: 597 sheet: -0.48 (0.68), residues: 60 loop : -0.90 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 29 TYR 0.018 0.002 TYR L 593 PHE 0.009 0.001 PHE L 454 TRP 0.008 0.002 TRP L 586 HIS 0.009 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (14496) covalent geometry : angle 0.61999 / 0.36 (20836) hydrogen bonds : bond 0.04187 / 2.80 ( 838) hydrogen bonds : angle 3.23829 / 2.30 ( 2129) Misc. bond : bond 0.00111 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9224 (t0) cc_final: 0.8831 (t0) REVERT: C 110 ASN cc_start: 0.8839 (t0) cc_final: 0.8579 (p0) REVERT: E 133 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7430 (mt-10) REVERT: F 79 LYS cc_start: 0.9086 (mttm) cc_final: 0.8804 (mtpt) REVERT: G 56 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8912 (tt0) REVERT: L 397 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6763 (tpt) REVERT: L 468 MET cc_start: 0.6917 (OUTLIER) cc_final: 0.5950 (mmp) REVERT: L 475 LEU cc_start: 0.8097 (mm) cc_final: 0.7807 (mm) REVERT: L 534 MET cc_start: 0.6681 (ttt) cc_final: 0.5934 (tmm) REVERT: L 541 ILE cc_start: 0.8693 (pp) cc_final: 0.8481 (pp) outliers start: 27 outliers final: 6 residues processed: 190 average time/residue: 0.8038 time to fit residues: 162.6381 Evaluate side-chains 180 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 170 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 468 MET Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 553 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 58 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN L 428 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.066812 restraints weight = 28769.068| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.45 r_work: 0.2760 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14497 Z= 0.151 Angle : 0.611 5.944 20836 Z= 0.353 Chirality : 0.043 0.259 2360 Planarity : 0.004 0.050 1617 Dihedral : 30.592 142.456 4274 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.35 % Allowed : 17.39 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.28), residues: 938 helix: 2.38 (0.21), residues: 597 sheet: -0.41 (0.70), residues: 60 loop : -0.93 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 521 TYR 0.010 0.001 TYR C 57 PHE 0.018 0.001 PHE L 506 TRP 0.003 0.001 TRP L 586 HIS 0.007 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (14496) covalent geometry : angle 0.61054 / 0.35 (20836) hydrogen bonds : bond 0.03930 / 2.64 ( 838) hydrogen bonds : angle 3.15364 / 2.25 ( 2129) Misc. bond : bond 0.00028 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: C 73 ASN cc_start: 0.9231 (t0) cc_final: 0.8827 (t0) REVERT: D 113 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: E 120 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8093 (mtt) REVERT: F 79 LYS cc_start: 0.9107 (mttm) cc_final: 0.8825 (mtpt) REVERT: G 56 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8914 (tt0) REVERT: L 397 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.7132 (tpp) REVERT: L 468 MET cc_start: 0.6928 (mpt) cc_final: 0.6279 (mmp) REVERT: L 534 MET cc_start: 0.6877 (ttt) cc_final: 0.6236 (tmm) REVERT: L 541 ILE cc_start: 0.8838 (pp) cc_final: 0.8550 (pp) REVERT: L 542 MET cc_start: 0.7472 (mmt) cc_final: 0.7047 (mmm) REVERT: L 585 HIS cc_start: 0.8309 (m90) cc_final: 0.8036 (m90) outliers start: 27 outliers final: 5 residues processed: 189 average time/residue: 0.8156 time to fit residues: 164.1535 Evaluate side-chains 176 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.102877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066256 restraints weight = 28859.614| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.45 r_work: 0.2722 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14497 Z= 0.155 Angle : 0.615 9.843 20836 Z= 0.353 Chirality : 0.043 0.249 2360 Planarity : 0.004 0.048 1617 Dihedral : 30.578 142.313 4274 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.36 % Allowed : 19.01 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.28), residues: 938 helix: 2.40 (0.21), residues: 597 sheet: -0.66 (0.68), residues: 61 loop : -0.95 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.010 0.001 TYR C 57 PHE 0.016 0.001 PHE L 508 TRP 0.005 0.002 TRP L 586 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (14496) covalent geometry : angle 0.61538 / 0.35 (20836) hydrogen bonds : bond 0.03919 / 2.63 ( 838) hydrogen bonds : angle 3.15738 / 2.23 ( 2129) Misc. bond : bond 0.00063 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9226 (t0) cc_final: 0.8797 (t0) REVERT: D 113 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: F 79 LYS cc_start: 0.9123 (mttm) cc_final: 0.8844 (mtpt) REVERT: G 73 ASN cc_start: 0.8675 (t0) cc_final: 0.8207 (t0) REVERT: H 79 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8498 (mtm-85) REVERT: L 397 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6903 (tpp) REVERT: L 468 MET cc_start: 0.6829 (mpt) cc_final: 0.6277 (mmp) REVERT: L 534 MET cc_start: 0.6863 (ttt) cc_final: 0.6300 (tmm) REVERT: L 541 ILE cc_start: 0.8887 (pp) cc_final: 0.8576 (pp) REVERT: L 542 MET cc_start: 0.7531 (mmt) cc_final: 0.7254 (mmm) outliers start: 19 outliers final: 9 residues processed: 183 average time/residue: 0.8257 time to fit residues: 160.8304 Evaluate side-chains 178 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 553 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.065330 restraints weight = 28635.161| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.46 r_work: 0.2718 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14497 Z= 0.173 Angle : 0.619 6.216 20836 Z= 0.353 Chirality : 0.043 0.235 2360 Planarity : 0.004 0.048 1617 Dihedral : 30.628 141.997 4274 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.35 % Allowed : 18.63 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.28), residues: 938 helix: 2.39 (0.21), residues: 597 sheet: -0.63 (0.73), residues: 55 loop : -1.03 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 71 TYR 0.010 0.001 TYR C 57 PHE 0.009 0.001 PHE L 506 TRP 0.012 0.003 TRP L 586 HIS 0.009 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (14496) covalent geometry : angle 0.61882 / 0.35 (20836) hydrogen bonds : bond 0.04016 / 2.70 ( 838) hydrogen bonds : angle 3.16744 / 2.25 ( 2129) Misc. bond : bond 0.00025 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8500 (tt0) REVERT: C 73 ASN cc_start: 0.9220 (t0) cc_final: 0.8776 (t0) REVERT: D 113 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: E 53 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8166 (ttp-110) REVERT: F 79 LYS cc_start: 0.9123 (mttm) cc_final: 0.8836 (mtpt) REVERT: G 73 ASN cc_start: 0.8754 (t0) cc_final: 0.8285 (t0) REVERT: L 468 MET cc_start: 0.6820 (mpt) cc_final: 0.6438 (mmp) REVERT: L 534 MET cc_start: 0.6773 (ttt) cc_final: 0.6338 (tmm) REVERT: L 541 ILE cc_start: 0.8888 (pp) cc_final: 0.8489 (pp) REVERT: L 542 MET cc_start: 0.7531 (mmt) cc_final: 0.7277 (mmm) outliers start: 27 outliers final: 8 residues processed: 186 average time/residue: 0.8626 time to fit residues: 170.7893 Evaluate side-chains 177 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.102260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.065695 restraints weight = 28669.971| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.45 r_work: 0.2714 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14497 Z= 0.144 Angle : 0.610 8.638 20836 Z= 0.349 Chirality : 0.043 0.237 2360 Planarity : 0.005 0.110 1617 Dihedral : 30.576 142.533 4274 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.11 % Allowed : 19.75 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.28), residues: 938 helix: 2.47 (0.21), residues: 597 sheet: -0.62 (0.70), residues: 55 loop : -1.04 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 548 TYR 0.009 0.001 TYR C 57 PHE 0.014 0.001 PHE L 417 TRP 0.007 0.002 TRP L 586 HIS 0.008 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (14496) covalent geometry : angle 0.61032 / 0.35 (20836) hydrogen bonds : bond 0.03782 / 2.55 ( 838) hydrogen bonds : angle 3.13454 / 2.22 ( 2129) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8485 (tt0) REVERT: C 73 ASN cc_start: 0.9210 (t0) cc_final: 0.8758 (t0) REVERT: D 113 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8595 (mp0) REVERT: E 53 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8186 (ttp-110) REVERT: E 120 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8184 (mtt) REVERT: F 79 LYS cc_start: 0.9134 (mttm) cc_final: 0.8866 (mtpt) REVERT: G 73 ASN cc_start: 0.8744 (t0) cc_final: 0.8264 (t0) REVERT: L 468 MET cc_start: 0.6856 (mpt) cc_final: 0.6483 (mmp) REVERT: L 534 MET cc_start: 0.6881 (ttt) cc_final: 0.6444 (tmm) REVERT: L 541 ILE cc_start: 0.8908 (pp) cc_final: 0.8505 (pp) REVERT: L 585 HIS cc_start: 0.8161 (m90) cc_final: 0.7942 (m90) outliers start: 25 outliers final: 7 residues processed: 182 average time/residue: 0.8512 time to fit residues: 165.0129 Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 3 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 101 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.102682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066125 restraints weight = 28526.199| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.45 r_work: 0.2746 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14497 Z= 0.132 Angle : 0.610 9.569 20836 Z= 0.348 Chirality : 0.042 0.233 2360 Planarity : 0.004 0.052 1617 Dihedral : 30.525 142.814 4274 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.11 % Allowed : 20.00 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.28), residues: 938 helix: 2.53 (0.21), residues: 596 sheet: -0.63 (0.67), residues: 61 loop : -1.02 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 521 TYR 0.009 0.001 TYR H 40 PHE 0.016 0.001 PHE L 417 TRP 0.006 0.002 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (14496) covalent geometry : angle 0.61014 / 0.35 (20836) hydrogen bonds : bond 0.03695 / 2.49 ( 838) hydrogen bonds : angle 3.10455 / 2.21 ( 2129) Misc. bond : bond 0.00009 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: C 73 ASN cc_start: 0.9192 (t0) cc_final: 0.8743 (t0) REVERT: D 113 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: E 120 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8135 (mtt) REVERT: F 79 LYS cc_start: 0.9132 (mttm) cc_final: 0.8874 (mtpt) REVERT: G 73 ASN cc_start: 0.8744 (t0) cc_final: 0.8257 (t0) REVERT: L 468 MET cc_start: 0.6853 (mpt) cc_final: 0.6571 (mmp) REVERT: L 534 MET cc_start: 0.6746 (ttt) cc_final: 0.6346 (tmm) REVERT: L 585 HIS cc_start: 0.8144 (m90) cc_final: 0.7942 (m90) outliers start: 25 outliers final: 8 residues processed: 178 average time/residue: 0.8270 time to fit residues: 156.9557 Evaluate side-chains 176 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN G 104 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.103526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.067581 restraints weight = 28344.564| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.40 r_work: 0.2793 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9105 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14497 Z= 0.135 Angle : 0.615 11.327 20836 Z= 0.350 Chirality : 0.042 0.227 2360 Planarity : 0.004 0.047 1617 Dihedral : 30.459 143.314 4274 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.99 % Allowed : 20.99 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 938 helix: 2.56 (0.21), residues: 596 sheet: -0.62 (0.66), residues: 61 loop : -0.96 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 35 TYR 0.009 0.001 TYR H 40 PHE 0.013 0.001 PHE L 506 TRP 0.010 0.003 TRP L 586 HIS 0.004 0.001 HIS L 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (14496) covalent geometry : angle 0.61550 / 0.35 (20836) hydrogen bonds : bond 0.03648 / 2.46 ( 838) hydrogen bonds : angle 3.04584 / 2.17 ( 2129) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8414 (tt0) REVERT: C 73 ASN cc_start: 0.9181 (t0) cc_final: 0.8722 (t0) REVERT: D 113 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: F 79 LYS cc_start: 0.9150 (mttm) cc_final: 0.8913 (mtpt) REVERT: G 73 ASN cc_start: 0.8760 (t0) cc_final: 0.8292 (t0) REVERT: H 63 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8650 (m-40) REVERT: L 418 SER cc_start: 0.7354 (t) cc_final: 0.6865 (m) REVERT: L 468 MET cc_start: 0.6778 (mpt) cc_final: 0.6539 (mmp) REVERT: L 512 TYR cc_start: 0.5936 (t80) cc_final: 0.5704 (t80) REVERT: L 534 MET cc_start: 0.6727 (ttt) cc_final: 0.6427 (tmm) outliers start: 16 outliers final: 8 residues processed: 178 average time/residue: 0.7982 time to fit residues: 151.8881 Evaluate side-chains 177 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 93 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.066419 restraints weight = 28278.951| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.43 r_work: 0.2745 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14497 Z= 0.152 Angle : 0.630 12.887 20836 Z= 0.354 Chirality : 0.042 0.223 2360 Planarity : 0.005 0.052 1617 Dihedral : 30.498 143.244 4274 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.74 % Allowed : 21.74 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.28), residues: 938 helix: 2.55 (0.21), residues: 596 sheet: -0.92 (0.64), residues: 67 loop : -0.93 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 35 TYR 0.010 0.001 TYR L 407 PHE 0.009 0.001 PHE L 506 TRP 0.019 0.005 TRP L 586 HIS 0.013 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (14496) covalent geometry : angle 0.62981 / 0.35 (20836) hydrogen bonds : bond 0.03799 / 2.56 ( 838) hydrogen bonds : angle 3.06449 / 2.18 ( 2129) Misc. bond : bond 0.00029 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1876 Ramachandran restraints generated. 938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: C 73 ASN cc_start: 0.9183 (t0) cc_final: 0.8727 (t0) REVERT: D 113 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: E 53 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8190 (ttp-110) REVERT: F 79 LYS cc_start: 0.9174 (mttm) cc_final: 0.8902 (mtpt) REVERT: G 73 ASN cc_start: 0.8813 (t0) cc_final: 0.8315 (t0) REVERT: L 418 SER cc_start: 0.7320 (t) cc_final: 0.6915 (m) REVERT: L 534 MET cc_start: 0.6808 (ttt) cc_final: 0.6458 (tmm) outliers start: 14 outliers final: 9 residues processed: 174 average time/residue: 0.8289 time to fit residues: 153.7132 Evaluate side-chains 179 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 535 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 30.0000 chunk 57 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 1 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.103794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.067895 restraints weight = 28485.062| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.41 r_work: 0.2764 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14497 Z= 0.134 Angle : 0.630 12.739 20836 Z= 0.355 Chirality : 0.042 0.263 2360 Planarity : 0.005 0.054 1617 Dihedral : 30.475 143.449 4274 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.86 % Allowed : 21.61 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.28), residues: 938 helix: 2.59 (0.21), residues: 596 sheet: -1.05 (0.63), residues: 67 loop : -0.91 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 35 TYR 0.010 0.001 TYR L 407 PHE 0.016 0.001 PHE L 417 TRP 0.020 0.005 TRP L 586 HIS 0.003 0.001 HIS L 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (14496) covalent geometry : angle 0.63014 / 0.35 (20836) hydrogen bonds : bond 0.03649 / 2.46 ( 838) hydrogen bonds : angle 3.05525 / 2.18 ( 2129) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5438.14 seconds wall clock time: 93 minutes 0.22 seconds (5580.22 seconds total)