Starting phenix.real_space_refine on Fri Jul 3 11:07:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ye_75526/07_2026/10ye_75526.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ye_75526/07_2026/10ye_75526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ye_75526/07_2026/10ye_75526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ye_75526/07_2026/10ye_75526.map" model { file = "/net/cci-nas-00/data/ceres_data/10ye_75526/07_2026/10ye_75526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ye_75526/07_2026/10ye_75526.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 295 5.49 5 S 25 5.16 5 C 7703 2.51 5 N 2539 2.21 5 O 3119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 13681 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" 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: "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: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} 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: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1573 Classifications: {'DNA': 76} Link IDs: {'rna3p': 75} Chain: "K" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1459 Classifications: {'DNA': 71} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 70} 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: 2.73, per 1000 atoms: 0.20 Number of scatterers: 13681 At special positions: 0 Unit cell: (73.676, 133.66, 121.924, 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 3119 8.00 N 2539 7.00 C 7703 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: 1.17 Conformation dependent library (CDL) restraints added in 453.3 milliseconds 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1798 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 12 sheets defined 63.3% alpha, 10.5% beta 147 base pairs and 263 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.655A 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 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.629A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.550A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.355A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.604A 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 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.125A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.324A 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 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.755A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.407A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.568A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) 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: 3.517A pdb=" N THR L 489 " --> pdb=" O PRO L 486 " (cutoff:3.500A) removed outlier: 3.821A 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: 4.312A pdb=" N MET L 558 " --> pdb=" O ASP L 554 " (cutoff:3.500A) removed outlier: 3.800A 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: 7.163A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.263A 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 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.995A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.313A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'L' and resid 398 through 401 removed outlier: 6.551A pdb=" N LEU L 398 " --> pdb=" O ARG L 584 " (cutoff:3.500A) removed outlier: 10.672A pdb=" N HIS L 585 " --> pdb=" O ASP L 574 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP L 574 " --> pdb=" O HIS L 585 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 436 through 439 removed outlier: 7.242A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 483 through 485 removed outlier: 3.791A pdb=" N LYS L 483 " --> pdb=" O ASP L 478 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU L 476 " --> pdb=" O LEU L 485 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER L 467 " --> pdb=" O TYR L 512 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYR L 512 " --> pdb=" O SER L 467 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE L 469 " --> pdb=" O CYS L 510 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N CYS L 510 " --> pdb=" O ILE L 469 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP L 471 " --> pdb=" O PHE L 508 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET L 542 " --> pdb=" O VAL L 507 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ASP L 509 " --> pdb=" O MET L 542 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 263 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2757 1.33 - 1.45: 4449 1.45 - 1.57: 6698 1.57 - 1.69: 586 1.69 - 1.81: 45 Bond restraints: 14535 Sorted by residual: bond pdb=" C3' DT I 75 " pdb=" O3' DT I 75 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.79e+01 bond pdb=" CA ILE L 458 " pdb=" CB ILE L 458 " ideal model delta sigma weight residual 1.539 1.518 0.021 5.40e-03 3.43e+04 1.58e+01 bond pdb=" C1' DT J 7 " pdb=" N1 DT J 7 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" C3' DC I 125 " pdb=" C2' DC I 125 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT J 7 " pdb=" C2' DT J 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 14530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 19956 1.81 - 3.61: 881 3.61 - 5.42: 39 5.42 - 7.22: 8 7.22 - 9.03: 2 Bond angle restraints: 20886 Sorted by residual: angle pdb=" N3 DT J 7 " pdb=" C4 DT J 7 " pdb=" O4 DT J 7 " ideal model delta sigma weight residual 119.90 123.17 -3.27 6.00e-01 2.78e+00 2.97e+01 angle pdb=" O4 DT J 7 " pdb=" C4 DT J 7 " pdb=" C5 DT J 7 " ideal model delta sigma weight residual 124.90 121.53 3.37 7.00e-01 2.04e+00 2.32e+01 angle pdb=" N3 DT K 83 " pdb=" C4 DT K 83 " pdb=" O4 DT K 83 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I 88 " pdb=" C4 DT I 88 " pdb=" O4 DT I 88 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 20881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.55: 6104 28.55 - 57.10: 1726 57.10 - 85.65: 156 85.65 - 114.20: 1 114.20 - 142.75: 3 Dihedral angle restraints: 7990 sinusoidal: 5203 harmonic: 2787 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 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 77.25 142.75 1 3.50e+01 8.16e-04 1.41e+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 78.02 141.98 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 7987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1700 0.045 - 0.089: 499 0.089 - 0.134: 153 0.134 - 0.179: 10 0.179 - 0.224: 3 Chirality restraints: 2365 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 -2.73 0.22 2.00e-01 2.50e+01 1.25e+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 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' DG J 76 " pdb=" C4' DG J 76 " pdb=" O3' DG J 76 " pdb=" C2' DG J 76 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 2362 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 112 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.75e+00 pdb=" C SER D 112 " 0.048 2.00e-02 2.50e+03 pdb=" O SER D 112 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU D 113 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU L 580 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO L 581 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO L 581 " -0.026 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=" C ARG E 42 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO E 43 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.024 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 5161 2.94 - 3.43: 12415 3.43 - 3.92: 27935 3.92 - 4.41: 30961 4.41 - 4.90: 42630 Nonbonded interactions: 119102 Sorted by model distance: nonbonded pdb=" OP1 DG J 76 " pdb=" N ARG L 426 " model vdw 2.451 3.120 nonbonded pdb=" O5' DC K 77 " pdb=" O4' DC K 77 " model vdw 2.523 2.432 nonbonded pdb=" O5' DA I 124 " pdb=" O4' DA I 124 " model vdw 2.544 2.432 nonbonded pdb=" N1 DG K 78 " pdb=" C4 DG K 78 " model vdw 2.582 2.672 nonbonded pdb=" N1 DG I 71 " pdb=" C4 DG I 71 " model vdw 2.582 2.672 ... (remaining 119097 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.300 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 0.006 0.060 14536 Z= 0.521 Angle : 0.752 9.026 20886 Z= 0.649 Chirality : 0.046 0.224 2365 Planarity : 0.005 0.050 1623 Dihedral : 26.991 142.748 6192 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.25 % Allowed : 15.72 % Favored : 84.03 % 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: 0.89 (0.26), residues: 943 helix: 1.49 (0.21), residues: 588 sheet: 0.04 (0.87), residues: 44 loop : -1.07 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 441 TYR 0.014 0.001 TYR L 579 PHE 0.012 0.001 PHE L 454 TRP 0.002 0.001 TRP L 586 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.52 (14535) covalent geometry : angle 0.75152 / 0.65 (20886) hydrogen bonds : bond 0.10968 / 7.19 ( 846) hydrogen bonds : angle 4.61798 / 3.23 ( 2147) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8203 (pm20) cc_final: 0.7921 (pm20) REVERT: A 87 SER cc_start: 0.9109 (m) cc_final: 0.8900 (p) REVERT: A 133 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8176 (mt-10) REVERT: B 79 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8560 (mttp) REVERT: C 95 LYS cc_start: 0.9284 (ttmp) cc_final: 0.8869 (tptt) REVERT: F 79 LYS cc_start: 0.9079 (mttt) cc_final: 0.8845 (mttt) REVERT: G 36 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8864 (mmmt) REVERT: G 73 ASN cc_start: 0.8375 (t0) cc_final: 0.8045 (m110) REVERT: L 473 GLU cc_start: 0.7688 (tp30) cc_final: 0.7148 (mm-30) REVERT: L 534 MET cc_start: 0.5624 (ttt) cc_final: 0.5325 (ttt) outliers start: 2 outliers final: 1 residues processed: 211 average time/residue: 0.7587 time to fit residues: 170.2381 Evaluate side-chains 187 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN E 85 GLN G 38 ASN H 84 ASN L 449 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.118364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.079590 restraints weight = 23482.405| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.63 r_work: 0.2987 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14536 Z= 0.156 Angle : 0.630 8.161 20886 Z= 0.375 Chirality : 0.044 0.189 2365 Planarity : 0.004 0.047 1623 Dihedral : 29.919 145.216 4282 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.61 % Allowed : 18.69 % Favored : 79.70 % 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: 1.42 (0.27), residues: 943 helix: 1.94 (0.21), residues: 598 sheet: 0.48 (0.81), residues: 44 loop : -1.05 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.009 0.001 TYR L 422 PHE 0.008 0.001 PHE L 454 TRP 0.005 0.001 TRP L 586 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.16 (14535) covalent geometry : angle 0.63039 / 0.37 (20886) hydrogen bonds : bond 0.04834 / 3.17 ( 846) hydrogen bonds : angle 3.70663 / 2.58 ( 2147) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8197 (pm20) cc_final: 0.7886 (pm20) REVERT: A 133 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8211 (mt-10) REVERT: B 79 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8571 (mttp) REVERT: C 15 LYS cc_start: 0.7766 (ttpp) cc_final: 0.7165 (ttmm) REVERT: C 64 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8206 (tp30) REVERT: C 95 LYS cc_start: 0.9244 (ttmp) cc_final: 0.8906 (tptt) REVERT: E 76 GLN cc_start: 0.8567 (mt0) cc_final: 0.8297 (mt0) REVERT: G 36 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8844 (mmmt) REVERT: G 73 ASN cc_start: 0.8342 (t0) cc_final: 0.8084 (m110) REVERT: G 74 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9006 (mppt) REVERT: L 473 GLU cc_start: 0.7493 (tp30) cc_final: 0.6882 (mm-30) REVERT: L 534 MET cc_start: 0.5472 (ttt) cc_final: 0.5195 (ttt) outliers start: 13 outliers final: 5 residues processed: 191 average time/residue: 0.8807 time to fit residues: 178.6118 Evaluate side-chains 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 10 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 38 ASN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.116389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077130 restraints weight = 23750.517| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.65 r_work: 0.2945 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 14536 Z= 0.176 Angle : 0.627 7.002 20886 Z= 0.365 Chirality : 0.045 0.201 2365 Planarity : 0.005 0.084 1623 Dihedral : 30.239 145.390 4282 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.10 % Allowed : 18.07 % Favored : 79.83 % 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: 1.67 (0.27), residues: 943 helix: 2.14 (0.21), residues: 598 sheet: 0.57 (0.76), residues: 48 loop : -1.00 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 86 TYR 0.011 0.001 TYR L 457 PHE 0.016 0.002 PHE L 513 TRP 0.008 0.002 TRP L 586 HIS 0.005 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (14535) covalent geometry : angle 0.62722 / 0.37 (20886) hydrogen bonds : bond 0.04320 / 2.84 ( 846) hydrogen bonds : angle 3.37212 / 2.37 ( 2147) Misc. bond : bond 0.00083 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: A 59 GLU cc_start: 0.8199 (pm20) cc_final: 0.7869 (pm20) REVERT: A 120 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8021 (mtt) REVERT: A 133 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 79 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8614 (mttp) REVERT: C 15 LYS cc_start: 0.7685 (ttpp) cc_final: 0.7081 (ttmm) REVERT: C 95 LYS cc_start: 0.9253 (ttmp) cc_final: 0.8888 (tptt) REVERT: D 71 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: E 76 GLN cc_start: 0.8534 (mt0) cc_final: 0.8310 (mt0) REVERT: F 92 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8561 (ttp80) REVERT: G 36 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8828 (mmmt) REVERT: G 73 ASN cc_start: 0.8427 (t0) cc_final: 0.8156 (m110) REVERT: G 74 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8957 (mppt) REVERT: L 534 MET cc_start: 0.5500 (ttt) cc_final: 0.5149 (ttt) REVERT: L 539 ASN cc_start: 0.6391 (m-40) cc_final: 0.6018 (m110) REVERT: L 587 LEU cc_start: 0.8531 (mt) cc_final: 0.7948 (tm) outliers start: 17 outliers final: 8 residues processed: 178 average time/residue: 0.7866 time to fit residues: 148.8837 Evaluate side-chains 183 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 39 HIS ** 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 = 0.3787 r_free = 0.3787 target = 0.115847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076609 restraints weight = 23454.754| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.61 r_work: 0.2932 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14536 Z= 0.166 Angle : 0.618 7.179 20886 Z= 0.358 Chirality : 0.044 0.217 2365 Planarity : 0.004 0.074 1623 Dihedral : 30.447 146.009 4280 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.10 % Allowed : 18.69 % Favored : 79.21 % 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: 1.75 (0.27), residues: 943 helix: 2.27 (0.21), residues: 598 sheet: -0.34 (0.68), residues: 59 loop : -0.96 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.012 0.001 TYR L 457 PHE 0.010 0.001 PHE L 506 TRP 0.005 0.002 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (14535) covalent geometry : angle 0.61770 / 0.36 (20886) hydrogen bonds : bond 0.04025 / 2.63 ( 846) hydrogen bonds : angle 3.27177 / 2.30 ( 2147) Misc. bond : bond 0.00063 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8845 (ttpp) REVERT: A 59 GLU cc_start: 0.8190 (pm20) cc_final: 0.7853 (pm20) REVERT: A 133 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8174 (mt-10) REVERT: B 79 LYS cc_start: 0.8936 (mtpp) cc_final: 0.8621 (mttp) REVERT: C 74 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8677 (mtmm) REVERT: C 95 LYS cc_start: 0.9235 (ttmp) cc_final: 0.8862 (tptt) REVERT: D 71 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: E 76 GLN cc_start: 0.8493 (tt0) cc_final: 0.8184 (mt0) REVERT: F 92 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8529 (ttp80) REVERT: G 36 LYS cc_start: 0.9046 (mmtt) cc_final: 0.8840 (mmmt) REVERT: G 73 ASN cc_start: 0.8507 (t0) cc_final: 0.8222 (m-40) REVERT: G 74 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8965 (mppt) REVERT: L 468 MET cc_start: 0.6915 (mpp) cc_final: 0.6514 (mmt) REVERT: L 534 MET cc_start: 0.5415 (ttt) cc_final: 0.5145 (ttt) REVERT: L 587 LEU cc_start: 0.8500 (mt) cc_final: 0.7976 (tm) outliers start: 17 outliers final: 7 residues processed: 182 average time/residue: 0.8226 time to fit residues: 159.3950 Evaluate side-chains 184 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.114636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.075711 restraints weight = 22830.693| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.61 r_work: 0.2875 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14536 Z= 0.163 Angle : 0.613 9.054 20886 Z= 0.353 Chirality : 0.043 0.222 2365 Planarity : 0.004 0.070 1623 Dihedral : 30.530 145.715 4280 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 18.94 % Favored : 78.84 % 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: 1.89 (0.27), residues: 943 helix: 2.33 (0.21), residues: 597 sheet: 0.10 (0.69), residues: 56 loop : -0.85 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.012 0.001 TYR L 457 PHE 0.010 0.001 PHE L 506 TRP 0.008 0.002 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (14535) covalent geometry : angle 0.61268 / 0.35 (20886) hydrogen bonds : bond 0.03929 / 2.57 ( 846) hydrogen bonds : angle 3.20229 / 2.25 ( 2147) Misc. bond : bond 0.00065 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8837 (ttpp) REVERT: A 59 GLU cc_start: 0.8198 (pm20) cc_final: 0.7913 (pm20) REVERT: A 120 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8401 (mtt) REVERT: A 133 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 79 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8606 (mttp) REVERT: C 15 LYS cc_start: 0.7691 (ttpp) cc_final: 0.7063 (tttt) REVERT: C 73 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7985 (t0) REVERT: C 74 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: C 95 LYS cc_start: 0.9182 (ttmp) cc_final: 0.8794 (tptt) REVERT: D 71 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: E 76 GLN cc_start: 0.8442 (tt0) cc_final: 0.8175 (mt0) REVERT: F 92 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8500 (ttp80) REVERT: G 73 ASN cc_start: 0.8477 (t0) cc_final: 0.8180 (m110) REVERT: G 74 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9006 (mppt) REVERT: L 468 MET cc_start: 0.7019 (mpp) cc_final: 0.6809 (mpp) REVERT: L 539 ASN cc_start: 0.6367 (m-40) cc_final: 0.6166 (m110) REVERT: L 585 HIS cc_start: 0.8415 (m-70) cc_final: 0.8127 (m-70) REVERT: L 587 LEU cc_start: 0.8423 (mt) cc_final: 0.7817 (tm) outliers start: 18 outliers final: 9 residues processed: 188 average time/residue: 0.8981 time to fit residues: 179.1085 Evaluate side-chains 187 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain L residue 527 ARG Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 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 = 0.3778 r_free = 0.3778 target = 0.115156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076152 restraints weight = 22837.974| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.63 r_work: 0.2891 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14536 Z= 0.140 Angle : 0.620 11.670 20886 Z= 0.357 Chirality : 0.043 0.229 2365 Planarity : 0.004 0.073 1623 Dihedral : 30.528 145.617 4280 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.48 % Allowed : 19.18 % Favored : 78.34 % 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: 1.95 (0.28), residues: 943 helix: 2.43 (0.21), residues: 596 sheet: -0.41 (0.65), residues: 67 loop : -0.83 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.012 0.001 TYR L 457 PHE 0.009 0.001 PHE A 67 TRP 0.002 0.001 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (14535) covalent geometry : angle 0.62011 / 0.36 (20886) hydrogen bonds : bond 0.03705 / 2.41 ( 846) hydrogen bonds : angle 3.15306 / 2.21 ( 2147) Misc. bond : bond 0.00047 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8833 (ttpp) REVERT: A 59 GLU cc_start: 0.8165 (pm20) cc_final: 0.7788 (pm20) REVERT: A 120 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: A 133 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 79 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8583 (mttp) REVERT: C 15 LYS cc_start: 0.7687 (ttpp) cc_final: 0.7067 (tttt) REVERT: C 74 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8682 (mtmm) REVERT: C 95 LYS cc_start: 0.9187 (ttmp) cc_final: 0.8800 (tptt) REVERT: D 71 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: E 76 GLN cc_start: 0.8419 (tt0) cc_final: 0.8120 (mt0) REVERT: F 92 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: G 73 ASN cc_start: 0.8477 (t0) cc_final: 0.8179 (m110) REVERT: G 74 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9012 (mppt) REVERT: L 426 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8039 (mmm-85) REVERT: L 468 MET cc_start: 0.6992 (mpp) cc_final: 0.6741 (mpp) REVERT: L 558 MET cc_start: 0.7719 (tpt) cc_final: 0.6953 (mtp) outliers start: 20 outliers final: 10 residues processed: 179 average time/residue: 0.8655 time to fit residues: 164.5907 Evaluate side-chains 186 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 527 ARG Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075656 restraints weight = 22801.112| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.61 r_work: 0.2879 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14536 Z= 0.168 Angle : 0.626 9.401 20886 Z= 0.358 Chirality : 0.043 0.226 2365 Planarity : 0.005 0.073 1623 Dihedral : 30.572 145.461 4280 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 19.68 % Favored : 78.22 % 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: 943 helix: 2.41 (0.21), residues: 596 sheet: -0.42 (0.65), residues: 67 loop : -0.87 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.012 0.001 TYR L 457 PHE 0.010 0.001 PHE L 506 TRP 0.002 0.001 TRP L 586 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (14535) covalent geometry : angle 0.62617 / 0.36 (20886) hydrogen bonds : bond 0.03953 / 2.58 ( 846) hydrogen bonds : angle 3.17464 / 2.23 ( 2147) Misc. bond : bond 0.00066 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8043 (mtp85) REVERT: A 56 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8848 (ttpp) REVERT: A 59 GLU cc_start: 0.8201 (pm20) cc_final: 0.7800 (pm20) REVERT: A 133 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8109 (mt-10) REVERT: B 79 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8594 (mttp) REVERT: C 73 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8011 (t0) REVERT: C 74 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: C 95 LYS cc_start: 0.9181 (ttmp) cc_final: 0.8797 (tptt) REVERT: D 71 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: E 76 GLN cc_start: 0.8416 (tt0) cc_final: 0.8144 (mt0) REVERT: F 92 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8493 (ttp80) REVERT: G 73 ASN cc_start: 0.8504 (t0) cc_final: 0.8196 (m110) REVERT: G 74 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9006 (mppt) REVERT: L 426 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8081 (mmm-85) REVERT: L 468 MET cc_start: 0.7044 (mpp) cc_final: 0.6780 (mpp) REVERT: L 558 MET cc_start: 0.7729 (tpt) cc_final: 0.6980 (mtp) REVERT: L 585 HIS cc_start: 0.7983 (m90) cc_final: 0.7745 (m90) outliers start: 17 outliers final: 10 residues processed: 176 average time/residue: 0.8797 time to fit residues: 164.4663 Evaluate side-chains 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain L residue 527 ARG Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.114607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075747 restraints weight = 22624.347| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.61 r_work: 0.2879 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14536 Z= 0.150 Angle : 0.628 10.238 20886 Z= 0.358 Chirality : 0.043 0.229 2365 Planarity : 0.004 0.071 1623 Dihedral : 30.580 145.398 4280 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.23 % Allowed : 19.80 % Favored : 77.97 % 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: 1.94 (0.28), residues: 943 helix: 2.42 (0.21), residues: 597 sheet: -0.38 (0.66), residues: 67 loop : -0.85 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.012 0.001 TYR L 457 PHE 0.009 0.001 PHE E 67 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 0.00280 / 0.15 (14535) covalent geometry : angle 0.62768 / 0.36 (20886) hydrogen bonds : bond 0.03806 / 2.49 ( 846) hydrogen bonds : angle 3.16883 / 2.23 ( 2147) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8612 (mmm-85) cc_final: 0.8299 (mtp-110) REVERT: A 56 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8855 (ttpp) REVERT: A 59 GLU cc_start: 0.8183 (pm20) cc_final: 0.7850 (pm20) REVERT: A 133 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8127 (mt-10) REVERT: B 79 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8583 (mttp) REVERT: C 15 LYS cc_start: 0.7726 (ttpp) cc_final: 0.7055 (tttt) REVERT: C 73 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8011 (t0) REVERT: C 74 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: C 95 LYS cc_start: 0.9181 (ttmp) cc_final: 0.8795 (tptt) REVERT: D 71 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: E 76 GLN cc_start: 0.8408 (tt0) cc_final: 0.8111 (mt0) REVERT: F 92 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8487 (ttp80) REVERT: G 73 ASN cc_start: 0.8499 (t0) cc_final: 0.8180 (m110) REVERT: L 468 MET cc_start: 0.7007 (mpp) cc_final: 0.6730 (mpp) REVERT: L 558 MET cc_start: 0.7716 (tpt) cc_final: 0.6983 (mtm) REVERT: L 585 HIS cc_start: 0.7967 (m90) cc_final: 0.7743 (m90) outliers start: 18 outliers final: 11 residues processed: 179 average time/residue: 0.8810 time to fit residues: 167.4605 Evaluate side-chains 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain L residue 527 ARG Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 539 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.114953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075960 restraints weight = 22904.320| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.64 r_work: 0.2884 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14536 Z= 0.140 Angle : 0.631 10.661 20886 Z= 0.359 Chirality : 0.043 0.230 2365 Planarity : 0.004 0.072 1623 Dihedral : 30.574 145.372 4280 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.23 % Allowed : 19.93 % Favored : 77.85 % 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: 943 helix: 2.45 (0.21), residues: 597 sheet: -0.38 (0.66), residues: 67 loop : -0.84 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 584 TYR 0.013 0.001 TYR L 457 PHE 0.009 0.001 PHE E 67 TRP 0.003 0.001 TRP L 586 HIS 0.003 0.001 HIS L 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (14535) covalent geometry : angle 0.63101 / 0.36 (20886) hydrogen bonds : bond 0.03702 / 2.42 ( 846) hydrogen bonds : angle 3.16715 / 2.23 ( 2147) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8868 (ttpp) REVERT: A 59 GLU cc_start: 0.8168 (pm20) cc_final: 0.7838 (pm20) REVERT: A 133 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8125 (mt-10) REVERT: B 79 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8587 (mttp) REVERT: C 15 LYS cc_start: 0.7720 (ttpp) cc_final: 0.7052 (tttt) REVERT: C 73 ASN cc_start: 0.8446 (OUTLIER) cc_final: 0.8013 (t0) REVERT: C 74 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8692 (mtmm) REVERT: C 95 LYS cc_start: 0.9182 (ttmp) cc_final: 0.8796 (tptt) REVERT: D 71 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: E 76 GLN cc_start: 0.8408 (tt0) cc_final: 0.8109 (mt0) REVERT: F 92 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8487 (ttp80) REVERT: G 73 ASN cc_start: 0.8499 (t0) cc_final: 0.8190 (m110) REVERT: G 74 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9013 (mppt) REVERT: L 426 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8052 (mmm-85) REVERT: L 468 MET cc_start: 0.6998 (mpp) cc_final: 0.6715 (mpp) REVERT: L 519 MET cc_start: 0.9009 (pmm) cc_final: 0.8653 (pmm) REVERT: L 558 MET cc_start: 0.7695 (tpt) cc_final: 0.6917 (mtp) REVERT: L 585 HIS cc_start: 0.7989 (m90) cc_final: 0.7723 (m90) outliers start: 18 outliers final: 12 residues processed: 177 average time/residue: 0.8067 time to fit residues: 151.7869 Evaluate side-chains 188 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain L residue 527 ARG Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN F 25 ASN G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 539 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.114942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075940 restraints weight = 22748.408| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.63 r_work: 0.2877 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14536 Z= 0.149 Angle : 0.624 11.686 20886 Z= 0.355 Chirality : 0.043 0.234 2365 Planarity : 0.004 0.068 1623 Dihedral : 30.553 145.250 4280 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.23 % Allowed : 19.93 % Favored : 77.85 % 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: 943 helix: 2.47 (0.21), residues: 597 sheet: -0.55 (0.67), residues: 66 loop : -0.85 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.014 0.001 TYR L 457 PHE 0.009 0.001 PHE A 67 TRP 0.001 0.000 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (14535) covalent geometry : angle 0.62366 / 0.35 (20886) hydrogen bonds : bond 0.03719 / 2.43 ( 846) hydrogen bonds : angle 3.13037 / 2.19 ( 2147) Misc. bond : bond 0.00043 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1886 Ramachandran restraints generated. 943 Oldfield, 0 Emsley, 943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8282 (mtp-110) REVERT: A 59 GLU cc_start: 0.8171 (pm20) cc_final: 0.7878 (pm20) REVERT: A 133 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 79 LYS cc_start: 0.8922 (mtpp) cc_final: 0.8578 (mttp) REVERT: C 15 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7109 (tttt) REVERT: C 73 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8037 (t0) REVERT: C 74 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8697 (mtmm) REVERT: C 95 LYS cc_start: 0.9186 (ttmp) cc_final: 0.8800 (tptt) REVERT: D 71 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: E 76 GLN cc_start: 0.8395 (tt0) cc_final: 0.8086 (mt0) REVERT: F 92 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8479 (ttp80) REVERT: G 73 ASN cc_start: 0.8506 (t0) cc_final: 0.8186 (m110) REVERT: G 74 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9009 (mtpt) REVERT: L 423 ASP cc_start: 0.8802 (t0) cc_final: 0.8463 (t0) REVERT: L 426 ARG cc_start: 0.8427 (tpp80) cc_final: 0.7799 (mmm-85) REVERT: L 468 MET cc_start: 0.7018 (mpp) cc_final: 0.6727 (mpp) REVERT: L 519 MET cc_start: 0.9019 (pmm) cc_final: 0.8547 (pmm) REVERT: L 558 MET cc_start: 0.7714 (tpt) cc_final: 0.6945 (mpt) REVERT: L 585 HIS cc_start: 0.8087 (m90) cc_final: 0.7797 (m90) outliers start: 18 outliers final: 10 residues processed: 177 average time/residue: 0.7991 time to fit residues: 150.2232 Evaluate side-chains 186 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 527 ARG Chi-restraints excluded: chain L residue 542 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.0060 chunk 76 optimal weight: 10.0000 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.115116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076368 restraints weight = 22781.103| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.61 r_work: 0.2894 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 14536 Z= 0.137 Angle : 0.797 50.635 20886 Z= 0.415 Chirality : 0.042 0.233 2365 Planarity : 0.004 0.067 1623 Dihedral : 30.552 145.231 4280 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.73 % Allowed : 20.42 % Favored : 77.85 % 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: 2.01 (0.28), residues: 943 helix: 2.51 (0.21), residues: 597 sheet: -0.56 (0.67), residues: 66 loop : -0.83 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.013 0.001 TYR L 457 PHE 0.010 0.001 PHE A 67 TRP 0.001 0.000 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (14535) covalent geometry : angle 0.79696 / 0.41 (20886) hydrogen bonds : bond 0.03629 / 2.37 ( 846) hydrogen bonds : angle 3.12808 / 2.19 ( 2147) Misc. bond : bond 0.00025 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6388.24 seconds wall clock time: 109 minutes 7.79 seconds (6547.79 seconds total)