Starting phenix.real_space_refine on Fri Jul 3 11:08:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10yh_75529/07_2026/10yh_75529.cif Found real_map, /net/cci-nas-00/data/ceres_data/10yh_75529/07_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_75529/07_2026/10yh_75529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10yh_75529/07_2026/10yh_75529.map" model { file = "/net/cci-nas-00/data/ceres_data/10yh_75529/07_2026/10yh_75529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10yh_75529/07_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-dev-6108/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: 2.70, per 1000 atoms: 0.20 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: 0.95 Conformation dependent library (CDL) restraints added in 437.1 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: 1.70 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: 2.80 Time building geometry restraints manager: 1.37 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 - 1.84: 19852 1.84 - 3.67: 961 3.67 - 5.51: 13 5.51 - 7.34: 8 7.34 - 9.18: 2 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: 6174 28.69 - 57.38: 1640 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 - 0.047: 1547 0.047 - 0.093: 663 0.093 - 0.140: 141 0.140 - 0.186: 7 0.186 - 0.233: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" C3' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C4' AMP L1001 " pdb=" O3' AMP L1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.36e+00 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 ... (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: 6.140 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.130 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.060 ------------------------------------------------------------------------------- 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 : 0.777 9.176 20836 Z= 0.672 Chirality : 0.050 0.233 2360 Planarity : 0.005 0.056 1617 Dihedral : 26.462 143.461 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 0.00903 / 0.75 (14496) covalent geometry : angle 0.77705 / 0.67 (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 : 0.362 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: 0.8036 time to fit residues: 216.2396 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 : 0.276 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.068444 restraints weight = 28947.711| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.44 r_work: 0.2784 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1631 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= 0.155 Angle : 0.647 10.801 20836 Z= 0.373 Chirality : 0.045 0.272 2360 Planarity : 0.005 0.053 1617 Dihedral : 30.627 142.593 4276 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.85 % Allowed : 14.91 % Favored : 81.24 % 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: 1.51 (0.27), residues: 938 helix: 2.04 (0.21), residues: 596 sheet: 0.99 (0.81), residues: 38 loop : -1.16 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 561 TYR 0.010 0.001 TYR C 57 PHE 0.018 0.002 PHE L 529 TRP 0.003 0.001 TRP L 586 HIS 0.012 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (14496) covalent geometry : angle 0.64663 / 0.37 (20836) hydrogen bonds : bond 0.04656 / 3.11 ( 838) hydrogen bonds : angle 3.43411 / 2.43 ( 2129) Misc. bond : bond 0.00061 / 0.04 ( 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 226 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9229 (t0) cc_final: 0.8878 (t0) REVERT: C 110 ASN cc_start: 0.8854 (t0) cc_final: 0.8616 (p0) REVERT: D 113 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: E 120 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7991 (mtt) REVERT: E 133 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: F 79 LYS cc_start: 0.9043 (mttm) cc_final: 0.8764 (mtpt) REVERT: G 56 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: L 397 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6904 (tpt) REVERT: L 475 LEU cc_start: 0.8173 (mm) cc_final: 0.7826 (mm) REVERT: L 534 MET cc_start: 0.6568 (ttt) cc_final: 0.5909 (tmm) REVERT: L 583 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.6483 (pttm) REVERT: L 586 TRP cc_start: 0.7741 (m100) cc_final: 0.6943 (m100) outliers start: 31 outliers final: 3 residues processed: 210 average time/residue: 0.7904 time to fit residues: 176.8682 Evaluate side-chains 185 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU 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 Chi-restraints excluded: chain L residue 583 LYS 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: 0.9980 chunk 38 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN F 93 GLN G 104 GLN H 63 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065958 restraints weight = 28928.617| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.45 r_work: 0.2717 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14497 Z= 0.186 Angle : 0.637 6.676 20836 Z= 0.367 Chirality : 0.044 0.261 2360 Planarity : 0.005 0.054 1617 Dihedral : 30.713 142.534 4274 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.78 (0.28), residues: 938 helix: 2.26 (0.21), residues: 597 sheet: 0.34 (0.77), residues: 48 loop : -1.01 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 71 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 0.011 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (14496) covalent geometry : angle 0.63742 / 0.37 (20836) hydrogen bonds : bond 0.04503 / 3.02 ( 838) hydrogen bonds : angle 3.28060 / 2.33 ( 2129) Misc. bond : bond 0.00065 / 0.04 ( 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 209 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: C 73 ASN cc_start: 0.9238 (t0) cc_final: 0.8837 (t0) REVERT: D 108 LYS cc_start: 0.8804 (pttp) cc_final: 0.8588 (ptpp) REVERT: D 113 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8554 (mp0) REVERT: F 79 LYS cc_start: 0.9123 (mttm) cc_final: 0.8827 (mtpt) REVERT: L 397 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6579 (tpt) REVERT: L 468 MET cc_start: 0.6679 (mpt) cc_final: 0.6408 (mmp) REVERT: L 534 MET cc_start: 0.6695 (ttt) cc_final: 0.5903 (tmm) REVERT: L 583 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.6594 (pttm) outliers start: 27 outliers final: 8 residues processed: 195 average time/residue: 0.8367 time to fit residues: 173.7635 Evaluate side-chains 184 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU 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 65 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 507 VAL Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 553 LEU Chi-restraints excluded: chain L residue 583 LYS 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: 0.8980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.103171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.066474 restraints weight = 28721.876| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.45 r_work: 0.2756 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14497 Z= 0.145 Angle : 0.604 7.427 20836 Z= 0.351 Chirality : 0.043 0.258 2360 Planarity : 0.004 0.050 1617 Dihedral : 30.695 143.093 4274 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 1.83 (0.28), residues: 938 helix: 2.37 (0.21), residues: 597 sheet: -0.42 (0.70), residues: 60 loop : -1.01 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 86 TYR 0.010 0.001 TYR C 57 PHE 0.015 0.001 PHE L 506 TRP 0.011 0.004 TRP L 586 HIS 0.020 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (14496) covalent geometry : angle 0.60357 / 0.35 (20836) hydrogen bonds : bond 0.03909 / 2.62 ( 838) hydrogen bonds : angle 3.17992 / 2.27 ( 2129) Misc. bond : bond 0.00036 / 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 210 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8475 (tp30) REVERT: C 73 ASN cc_start: 0.9218 (t0) cc_final: 0.8813 (t0) REVERT: D 113 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: E 120 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8141 (mtt) REVERT: F 79 LYS cc_start: 0.9101 (mttm) cc_final: 0.8826 (mtpt) REVERT: G 56 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8909 (tt0) REVERT: L 397 MET cc_start: 0.7473 (mmm) cc_final: 0.7119 (mmm) REVERT: L 468 MET cc_start: 0.6877 (mpt) cc_final: 0.6349 (mmp) REVERT: L 507 VAL cc_start: 0.7503 (OUTLIER) cc_final: 0.7094 (p) REVERT: L 534 MET cc_start: 0.6872 (ttt) cc_final: 0.6191 (tmm) REVERT: L 542 MET cc_start: 0.7385 (mmt) cc_final: 0.7035 (mmm) outliers start: 27 outliers final: 5 residues processed: 195 average time/residue: 0.7741 time to fit residues: 160.9505 Evaluate side-chains 182 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU 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 507 VAL Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 553 LEU 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: 5.9990 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.101608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.064793 restraints weight = 28779.056| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.44 r_work: 0.2711 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14497 Z= 0.188 Angle : 0.625 7.566 20836 Z= 0.357 Chirality : 0.044 0.240 2360 Planarity : 0.004 0.051 1617 Dihedral : 30.767 142.727 4274 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.98 % Allowed : 18.39 % 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: 1.76 (0.28), residues: 938 helix: 2.33 (0.21), residues: 597 sheet: -0.47 (0.69), residues: 60 loop : -1.08 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 521 TYR 0.011 0.001 TYR C 57 PHE 0.008 0.001 PHE L 513 TRP 0.005 0.001 TRP L 586 HIS 0.003 0.001 HIS L 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (14496) covalent geometry : angle 0.62534 / 0.36 (20836) hydrogen bonds : bond 0.04291 / 2.89 ( 838) hydrogen bonds : angle 3.17629 / 2.26 ( 2129) Misc. bond : bond 0.00046 / 0.03 ( 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 195 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9227 (t0) cc_final: 0.8790 (t0) REVERT: D 113 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: E 53 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8167 (ttp-110) REVERT: F 79 LYS cc_start: 0.9134 (mttm) cc_final: 0.8853 (mtpt) REVERT: G 73 ASN cc_start: 0.8717 (t0) cc_final: 0.8253 (t0) REVERT: L 397 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.6886 (tpp) REVERT: L 468 MET cc_start: 0.6770 (mpt) cc_final: 0.6340 (mmp) REVERT: L 534 MET cc_start: 0.6811 (ttt) cc_final: 0.6386 (tmm) REVERT: L 542 MET cc_start: 0.7406 (mmt) cc_final: 0.7044 (mmm) outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.7764 time to fit residues: 152.8379 Evaluate side-chains 181 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 86 SER 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 397 MET Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 507 VAL 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: 4.9990 chunk 56 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.099817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.062936 restraints weight = 28545.526| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.47 r_work: 0.2671 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14497 Z= 0.238 Angle : 0.672 9.386 20836 Z= 0.373 Chirality : 0.046 0.236 2360 Planarity : 0.005 0.053 1617 Dihedral : 30.964 143.354 4274 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.60 % Allowed : 18.51 % Favored : 77.89 % 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: 1.58 (0.27), residues: 938 helix: 2.21 (0.21), residues: 597 sheet: -0.56 (0.69), residues: 61 loop : -1.19 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.011 0.002 TYR C 57 PHE 0.010 0.002 PHE L 506 TRP 0.013 0.003 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (14496) covalent geometry : angle 0.67250 / 0.37 (20836) hydrogen bonds : bond 0.04575 / 3.09 ( 838) hydrogen bonds : angle 3.23446 / 2.29 ( 2129) Misc. bond : bond 0.00119 / 0.08 ( 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 201 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: C 73 ASN cc_start: 0.9213 (t0) cc_final: 0.8758 (t0) REVERT: D 113 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: E 53 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8186 (ttp-110) REVERT: F 79 LYS cc_start: 0.9139 (mttm) cc_final: 0.8858 (mtpt) REVERT: G 73 ASN cc_start: 0.8851 (t0) cc_final: 0.8374 (t0) REVERT: L 397 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.7128 (mmm) REVERT: L 418 SER cc_start: 0.7387 (t) cc_final: 0.6832 (m) REVERT: L 468 MET cc_start: 0.6840 (mpt) cc_final: 0.6637 (mpp) REVERT: L 534 MET cc_start: 0.6980 (ttt) cc_final: 0.6500 (tmm) REVERT: L 542 MET cc_start: 0.7391 (mmp) cc_final: 0.7009 (mmm) outliers start: 29 outliers final: 11 residues processed: 190 average time/residue: 0.7727 time to fit residues: 156.2413 Evaluate side-chains 178 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU 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 E residue 87 SER 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 507 VAL Chi-restraints excluded: chain L residue 521 ARG Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 550 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.101041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.064388 restraints weight = 28469.168| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.43 r_work: 0.2707 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14497 Z= 0.142 Angle : 0.637 10.412 20836 Z= 0.360 Chirality : 0.044 0.242 2360 Planarity : 0.006 0.169 1617 Dihedral : 30.890 143.805 4274 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.48 % Allowed : 19.13 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.28), residues: 938 helix: 2.36 (0.21), residues: 596 sheet: -0.51 (0.67), residues: 61 loop : -1.19 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 35 TYR 0.012 0.001 TYR B 51 PHE 0.026 0.001 PHE L 417 TRP 0.005 0.002 TRP L 586 HIS 0.012 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (14496) covalent geometry : angle 0.63722 / 0.36 (20836) hydrogen bonds : bond 0.04008 / 2.71 ( 838) hydrogen bonds : angle 3.19829 / 2.27 ( 2129) Misc. bond : bond 0.00012 / 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: 28 poor density : 167 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: C 73 ASN cc_start: 0.9207 (t0) cc_final: 0.8757 (t0) REVERT: D 113 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: E 53 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8200 (ttp-110) REVERT: F 79 LYS cc_start: 0.9137 (mttm) cc_final: 0.8855 (mtpt) REVERT: G 73 ASN cc_start: 0.8829 (t0) cc_final: 0.8349 (t0) REVERT: L 397 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6978 (tpp) REVERT: L 418 SER cc_start: 0.7340 (t) cc_final: 0.6942 (m) REVERT: L 468 MET cc_start: 0.6811 (mpt) cc_final: 0.6553 (mmp) REVERT: L 534 MET cc_start: 0.6929 (ttt) cc_final: 0.6469 (tmm) REVERT: L 542 MET cc_start: 0.7399 (mmp) cc_final: 0.7021 (mmm) outliers start: 28 outliers final: 12 residues processed: 181 average time/residue: 0.8015 time to fit residues: 154.5829 Evaluate side-chains 181 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 64 GLU 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 E residue 87 SER Chi-restraints excluded: chain E residue 115 LYS 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 397 MET Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 507 VAL Chi-restraints excluded: chain L residue 521 ARG 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: 0.7980 chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 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 = 0.3645 r_free = 0.3645 target = 0.101836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.065405 restraints weight = 28381.994| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.43 r_work: 0.2734 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14497 Z= 0.132 Angle : 0.609 11.167 20836 Z= 0.349 Chirality : 0.042 0.242 2360 Planarity : 0.005 0.062 1617 Dihedral : 30.705 143.742 4274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.24 % Allowed : 20.62 % 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: 1.86 (0.28), residues: 938 helix: 2.48 (0.21), residues: 597 sheet: -1.02 (0.64), residues: 67 loop : -1.05 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 35 TYR 0.010 0.001 TYR H 40 PHE 0.013 0.001 PHE L 417 TRP 0.007 0.002 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (14496) covalent geometry : angle 0.60869 / 0.35 (20836) hydrogen bonds : bond 0.03729 / 2.52 ( 838) hydrogen bonds : angle 3.11720 / 2.22 ( 2129) Misc. bond : bond 0.00011 / 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 190 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: C 73 ASN cc_start: 0.9188 (t0) cc_final: 0.8720 (t0) REVERT: F 79 LYS cc_start: 0.9150 (mttm) cc_final: 0.8883 (mtpt) REVERT: G 73 ASN cc_start: 0.8818 (t0) cc_final: 0.8334 (t0) REVERT: L 397 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7089 (tpp) REVERT: L 418 SER cc_start: 0.7284 (t) cc_final: 0.6731 (m) REVERT: L 468 MET cc_start: 0.6754 (mpt) cc_final: 0.6541 (mmp) REVERT: L 534 MET cc_start: 0.6936 (ttt) cc_final: 0.6474 (tmm) REVERT: L 542 MET cc_start: 0.7374 (mmp) cc_final: 0.7003 (mmm) outliers start: 18 outliers final: 7 residues processed: 181 average time/residue: 0.8428 time to fit residues: 162.8149 Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 65 LEU 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 475 LEU Chi-restraints excluded: chain L residue 507 VAL Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain L residue 553 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.5980 chunk 64 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 115 optimal weight: 0.0010 chunk 79 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 overall best weight: 0.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 449 HIS ** 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 = 0.3681 r_free = 0.3681 target = 0.103374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.067545 restraints weight = 28348.675| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.42 r_work: 0.2797 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.3211 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= 0.127 Angle : 0.601 12.215 20836 Z= 0.349 Chirality : 0.042 0.234 2360 Planarity : 0.004 0.060 1617 Dihedral : 30.544 144.288 4274 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.24 % Allowed : 20.25 % Favored : 77.52 % 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: 1.96 (0.28), residues: 938 helix: 2.56 (0.21), residues: 596 sheet: -1.05 (0.64), residues: 67 loop : -0.99 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 521 TYR 0.010 0.001 TYR H 40 PHE 0.011 0.001 PHE A 67 TRP 0.014 0.003 TRP L 586 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.13 (14496) covalent geometry : angle 0.60130 / 0.35 (20836) hydrogen bonds : bond 0.03581 / 2.43 ( 838) hydrogen bonds : angle 3.07087 / 2.19 ( 2129) Misc. bond : bond 0.00018 / 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 191 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8917 (tt0) REVERT: C 64 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: C 73 ASN cc_start: 0.9178 (t0) cc_final: 0.8722 (t0) REVERT: F 79 LYS cc_start: 0.9162 (mttm) cc_final: 0.8900 (mtpt) REVERT: G 73 ASN cc_start: 0.8807 (t0) cc_final: 0.8313 (t0) REVERT: L 397 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7121 (tpp) REVERT: L 418 SER cc_start: 0.7306 (t) cc_final: 0.6904 (m) REVERT: L 449 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7306 (p90) REVERT: L 507 VAL cc_start: 0.7357 (OUTLIER) cc_final: 0.6943 (p) REVERT: L 534 MET cc_start: 0.6833 (ttt) cc_final: 0.6415 (tmm) REVERT: L 542 MET cc_start: 0.7371 (mmp) cc_final: 0.6972 (mmm) outliers start: 18 outliers final: 4 residues processed: 182 average time/residue: 0.7947 time to fit residues: 154.4010 Evaluate side-chains 176 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 449 HIS Chi-restraints excluded: chain L residue 475 LEU Chi-restraints excluded: chain L residue 507 VAL 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: 0.9990 chunk 104 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 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 = 0.3670 r_free = 0.3670 target = 0.102807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.066777 restraints weight = 28302.376| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.42 r_work: 0.2777 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14497 Z= 0.147 Angle : 0.608 8.781 20836 Z= 0.350 Chirality : 0.042 0.260 2360 Planarity : 0.005 0.048 1617 Dihedral : 30.558 144.100 4274 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.86 % Allowed : 21.37 % Favored : 76.77 % 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: 1.90 (0.28), residues: 938 helix: 2.51 (0.21), residues: 596 sheet: -1.11 (0.62), residues: 67 loop : -1.01 (0.35), residues: 275 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 0.014 0.001 PHE A 67 TRP 0.014 0.003 TRP L 586 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (14496) covalent geometry : angle 0.60761 / 0.35 (20836) hydrogen bonds : bond 0.03690 / 2.49 ( 838) hydrogen bonds : angle 3.09356 / 2.21 ( 2129) Misc. bond : bond 0.00034 / 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: 15 poor density : 167 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: C 73 ASN cc_start: 0.9178 (t0) cc_final: 0.8716 (t0) REVERT: F 79 LYS cc_start: 0.9168 (mttm) cc_final: 0.8900 (mtpt) REVERT: G 73 ASN cc_start: 0.8815 (t0) cc_final: 0.8326 (t0) REVERT: L 397 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7190 (tpp) REVERT: L 418 SER cc_start: 0.7288 (t) cc_final: 0.6903 (m) REVERT: L 468 MET cc_start: 0.7298 (mmp) cc_final: 0.6278 (mmp) REVERT: L 507 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6912 (p) REVERT: L 534 MET cc_start: 0.6912 (ttt) cc_final: 0.6440 (tmm) REVERT: L 542 MET cc_start: 0.7365 (mmp) cc_final: 0.6970 (mmm) outliers start: 15 outliers final: 4 residues processed: 173 average time/residue: 0.7077 time to fit residues: 130.9406 Evaluate side-chains 175 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 507 VAL 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: 0.7980 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN F 93 GLN ** L 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 449 HIS ** 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 = 0.3676 r_free = 0.3676 target = 0.103059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.067084 restraints weight = 28370.070| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.42 r_work: 0.2785 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14497 Z= 0.136 Angle : 0.605 9.866 20836 Z= 0.349 Chirality : 0.042 0.331 2360 Planarity : 0.004 0.048 1617 Dihedral : 30.557 144.071 4274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.49 % Allowed : 21.86 % Favored : 76.65 % 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: 1.90 (0.28), residues: 938 helix: 2.52 (0.21), residues: 596 sheet: -1.16 (0.61), residues: 67 loop : -1.00 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 521 TYR 0.010 0.001 TYR H 40 PHE 0.017 0.001 PHE L 417 TRP 0.013 0.003 TRP L 586 HIS 0.017 0.001 HIS L 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (14496) covalent geometry : angle 0.60505 / 0.35 (20836) hydrogen bonds : bond 0.03632 / 2.45 ( 838) hydrogen bonds : angle 3.09595 / 2.22 ( 2129) Misc. bond : bond 0.00022 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5269.37 seconds wall clock time: 90 minutes 7.48 seconds (5407.48 seconds total)