Starting phenix.real_space_refine on Sun Apr 5 21:56:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ye_75526/04_2026/10ye_75526.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ye_75526/04_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_75526/04_2026/10ye_75526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ye_75526/04_2026/10ye_75526.map" model { file = "/net/cci-nas-00/data/ceres_data/10ye_75526/04_2026/10ye_75526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ye_75526/04_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-2.1rc1-6017/lib/python3.9/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: 3.38, per 1000 atoms: 0.25 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: 1.09 Conformation dependent library (CDL) restraints added in 422.9 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: 2.03 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: 3.40 Time building geometry restraints manager: 1.49 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=" 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=" CA TYR L 422 " pdb=" C TYR L 422 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.29e-02 6.01e+03 8.28e+00 bond pdb=" N ILE L 420 " pdb=" CA ILE L 420 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.32e-02 5.74e+03 7.52e+00 bond pdb=" N TYR L 593 " pdb=" CA TYR L 593 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.34e+00 bond pdb=" N LEU D 101 " pdb=" CA LEU D 101 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.97e+00 ... (remaining 14530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 20416 1.81 - 3.61: 428 3.61 - 5.42: 32 5.42 - 7.22: 8 7.22 - 9.03: 2 Bond angle restraints: 20886 Sorted by residual: angle pdb=" N LEU D 101 " pdb=" CA LEU D 101 " pdb=" CB LEU D 101 " ideal model delta sigma weight residual 110.16 105.37 4.79 1.48e+00 4.57e-01 1.05e+01 angle pdb=" CA ILE L 420 " pdb=" C ILE L 420 " pdb=" O ILE L 420 " ideal model delta sigma weight residual 121.59 118.26 3.33 1.03e+00 9.43e-01 1.04e+01 angle pdb=" C1' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " ideal model delta sigma weight residual 111.00 101.97 9.03 3.00e+00 1.11e-01 9.05e+00 angle pdb=" CA LYS L 421 " pdb=" C LYS L 421 " pdb=" O LYS L 421 " ideal model delta sigma weight residual 121.58 118.31 3.27 1.12e+00 7.97e-01 8.51e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 120.02 -6.84 2.37e+00 1.78e-01 8.33e+00 ... (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: 1890 0.045 - 0.089: 389 0.089 - 0.134: 79 0.134 - 0.179: 5 0.179 - 0.224: 2 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=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-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: 5.770 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: 0.390 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.990 Find NCS groups from input model: 0.140 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:9.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14536 Z= 0.220 Angle : 0.605 9.026 20886 Z= 0.355 Chirality : 0.038 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 covalent geometry : bond 0.00473 (14535) covalent geometry : angle 0.60466 (20886) hydrogen bonds : bond 0.10968 ( 846) hydrogen bonds : angle 4.61798 ( 2147) Misc. bond : bond 0.00002 ( 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 : 0.326 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: 0.9165 time to fit residues: 204.8563 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 : 0.345 ------------------------------------------------------------------------------- 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: 4.9990 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: 1.9990 chunk 62 optimal weight: 1.9990 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... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 85 GLN G 38 ASN H 84 ASN L 449 HIS ** L 539 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 = 0.3824 r_free = 0.3824 target = 0.118387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079742 restraints weight = 23478.271| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.63 r_work: 0.2990 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14536 Z= 0.167 Angle : 0.586 8.781 20886 Z= 0.345 Chirality : 0.035 0.186 2365 Planarity : 0.005 0.051 1623 Dihedral : 29.720 143.650 4282 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.53 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: 0.49 (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 0.008 0.001 TYR C 57 PHE 0.008 0.001 PHE L 454 TRP 0.004 0.001 TRP L 586 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00363 (14535) covalent geometry : angle 0.58592 (20886) hydrogen bonds : bond 0.04185 ( 846) hydrogen bonds : angle 3.65316 ( 2147) Misc. bond : bond 0.00016 ( 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 : 0.383 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: 0.8201 (pm20) cc_final: 0.7890 (pm20) REVERT: A 133 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 79 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8568 (mttp) REVERT: C 15 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7155 (ttmm) REVERT: C 64 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: C 95 LYS cc_start: 0.9244 (ttmp) cc_final: 0.8906 (tptt) REVERT: E 76 GLN cc_start: 0.8580 (mt0) cc_final: 0.8299 (mt0) REVERT: G 36 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8849 (mmmt) REVERT: G 73 ASN cc_start: 0.8340 (t0) cc_final: 0.8081 (m110) REVERT: G 74 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9004 (mppt) REVERT: L 473 GLU cc_start: 0.7476 (tp30) cc_final: 0.6848 (mm-30) REVERT: L 534 MET cc_start: 0.5478 (ttt) cc_final: 0.5198 (ttt) outliers start: 13 outliers final: 5 residues processed: 191 average time/residue: 0.9169 time to fit residues: 185.5286 Evaluate side-chains 184 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 39 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.114734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075424 restraints weight = 23578.741| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.62 r_work: 0.2909 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14536 Z= 0.236 Angle : 0.594 7.095 20886 Z= 0.352 Chirality : 0.038 0.149 2365 Planarity : 0.005 0.069 1623 Dihedral : 30.057 147.896 4282 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.10 % Allowed : 18.56 % Favored : 79.33 % 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: 597 sheet: 0.73 (0.77), residues: 48 loop : -1.02 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 86 TYR 0.011 0.002 TYR L 457 PHE 0.010 0.002 PHE C 25 TRP 0.011 0.003 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00534 (14535) covalent geometry : angle 0.59434 (20886) hydrogen bonds : bond 0.04060 ( 846) hydrogen bonds : angle 3.28011 ( 2147) Misc. bond : bond 0.00094 ( 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 : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8855 (ttpp) REVERT: A 59 GLU cc_start: 0.8240 (pm20) cc_final: 0.7964 (pm20) REVERT: A 133 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8133 (mt-10) REVERT: B 79 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8604 (mttp) REVERT: C 95 LYS cc_start: 0.9236 (ttmp) cc_final: 0.8877 (tptt) REVERT: D 71 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: E 76 GLN cc_start: 0.8513 (mt0) cc_final: 0.8301 (mt0) REVERT: F 92 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8523 (ttp80) REVERT: G 73 ASN cc_start: 0.8559 (t0) cc_final: 0.8251 (m110) REVERT: L 391 MET cc_start: 0.8368 (mpm) cc_final: 0.8164 (mpm) REVERT: L 534 MET cc_start: 0.5413 (ttt) cc_final: 0.5190 (ttt) REVERT: L 542 MET cc_start: 0.5879 (mpp) cc_final: 0.5675 (mpp) REVERT: L 587 LEU cc_start: 0.8544 (mt) cc_final: 0.8036 (tm) outliers start: 17 outliers final: 9 residues processed: 178 average time/residue: 0.8998 time to fit residues: 169.6353 Evaluate side-chains 178 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 73 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 112 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 109 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN ** 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 = 0.3800 r_free = 0.3800 target = 0.116689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.077734 restraints weight = 23528.046| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.62 r_work: 0.2955 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14536 Z= 0.146 Angle : 0.563 8.760 20886 Z= 0.333 Chirality : 0.035 0.148 2365 Planarity : 0.004 0.069 1623 Dihedral : 29.973 145.460 4280 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.98 % Allowed : 19.18 % 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: 1.84 (0.27), residues: 943 helix: 2.28 (0.21), residues: 598 sheet: 0.07 (0.71), residues: 56 loop : -0.84 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.011 0.001 TYR L 457 PHE 0.009 0.001 PHE A 67 TRP 0.006 0.002 TRP L 586 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00311 (14535) covalent geometry : angle 0.56292 (20886) hydrogen bonds : bond 0.03298 ( 846) hydrogen bonds : angle 3.18649 ( 2147) Misc. bond : bond 0.00024 ( 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 203 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8805 (ttpp) REVERT: A 59 GLU cc_start: 0.8125 (pm20) cc_final: 0.7846 (pm20) REVERT: A 133 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 79 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8577 (mttp) REVERT: C 15 LYS cc_start: 0.7643 (ttpp) cc_final: 0.6997 (tttt) REVERT: C 73 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8011 (t0) REVERT: C 74 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8674 (mtmm) REVERT: C 95 LYS cc_start: 0.9229 (ttmp) cc_final: 0.8865 (tptt) REVERT: D 71 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: E 76 GLN cc_start: 0.8457 (mt0) cc_final: 0.8214 (mt0) REVERT: F 92 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8505 (ttp80) REVERT: G 73 ASN cc_start: 0.8510 (t0) cc_final: 0.8229 (m110) REVERT: G 74 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8957 (mppt) REVERT: L 391 MET cc_start: 0.8389 (mpm) cc_final: 0.8188 (mpm) REVERT: L 468 MET cc_start: 0.6659 (mpp) cc_final: 0.6126 (mmt) REVERT: L 534 MET cc_start: 0.5395 (ttt) cc_final: 0.5179 (ttt) REVERT: L 539 ASN cc_start: 0.6485 (m-40) cc_final: 0.6197 (m110) REVERT: L 580 GLU cc_start: 0.9093 (pt0) cc_final: 0.8877 (pp20) REVERT: L 587 LEU cc_start: 0.8372 (mt) cc_final: 0.7834 (tm) outliers start: 16 outliers final: 7 residues processed: 189 average time/residue: 0.9397 time to fit residues: 187.8140 Evaluate side-chains 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP 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 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: 0.7980 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 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 = 0.3770 r_free = 0.3770 target = 0.114658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.075394 restraints weight = 23524.089| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.62 r_work: 0.2905 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14536 Z= 0.218 Angle : 0.587 7.287 20886 Z= 0.346 Chirality : 0.037 0.147 2365 Planarity : 0.004 0.070 1623 Dihedral : 30.078 146.336 4280 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.48 % Allowed : 19.06 % Favored : 78.47 % 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: 1.85 (0.27), residues: 943 helix: 2.31 (0.21), residues: 596 sheet: 0.12 (0.69), residues: 56 loop : -0.87 (0.33), residues: 291 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 0.002 0.001 TRP L 586 HIS 0.008 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00491 (14535) covalent geometry : angle 0.58680 (20886) hydrogen bonds : bond 0.03873 ( 846) hydrogen bonds : angle 3.16979 ( 2147) Misc. bond : bond 0.00074 ( 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 200 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.373 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: 0.8259 (pm20) cc_final: 0.7989 (pm20) REVERT: A 133 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8132 (mt-10) REVERT: B 79 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8589 (mttp) REVERT: C 73 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8075 (t0) REVERT: C 74 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8696 (mtmm) REVERT: C 95 LYS cc_start: 0.9228 (ttmp) cc_final: 0.8855 (tptt) REVERT: D 71 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: E 76 GLN cc_start: 0.8462 (mt0) cc_final: 0.8212 (mt0) REVERT: F 92 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8497 (ttp80) REVERT: G 73 ASN cc_start: 0.8575 (t0) cc_final: 0.8241 (m110) REVERT: G 74 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8931 (mppt) REVERT: L 391 MET cc_start: 0.8327 (mpm) cc_final: 0.8125 (mpm) REVERT: L 404 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7669 (p) REVERT: L 426 ARG cc_start: 0.8349 (tpp80) cc_final: 0.7833 (mmm-85) REVERT: L 534 MET cc_start: 0.5308 (ttt) cc_final: 0.5084 (ttt) REVERT: L 536 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8262 (tp30) REVERT: L 539 ASN cc_start: 0.6655 (m-40) cc_final: 0.6366 (m110) REVERT: L 558 MET cc_start: 0.7713 (tpt) cc_final: 0.7065 (mtm) outliers start: 20 outliers final: 12 residues processed: 187 average time/residue: 0.9323 time to fit residues: 184.3605 Evaluate side-chains 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 ILE 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 24 ASP 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 51 ASP Chi-restraints excluded: chain L residue 404 SER 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: 1.9990 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 105 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076497 restraints weight = 23517.816| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.61 r_work: 0.2927 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14536 Z= 0.165 Angle : 0.576 9.273 20886 Z= 0.339 Chirality : 0.035 0.149 2365 Planarity : 0.004 0.067 1623 Dihedral : 30.051 145.745 4280 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.23 % Allowed : 19.18 % Favored : 78.59 % 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 (0.27), residues: 943 helix: 2.38 (0.21), residues: 596 sheet: 0.20 (0.71), residues: 56 loop : -0.81 (0.33), residues: 291 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 0.004 0.002 TRP L 586 HIS 0.006 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00363 (14535) covalent geometry : angle 0.57584 (20886) hydrogen bonds : bond 0.03434 ( 846) hydrogen bonds : angle 3.14812 ( 2147) Misc. bond : bond 0.00051 ( 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 199 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8184 (pm20) cc_final: 0.7892 (pm20) REVERT: A 133 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 79 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8593 (mttp) REVERT: C 15 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7025 (tttt) REVERT: C 73 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8076 (t0) REVERT: C 74 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8690 (mtmm) REVERT: C 95 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8861 (tptt) REVERT: D 71 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: E 76 GLN cc_start: 0.8444 (tt0) cc_final: 0.8154 (mt0) REVERT: F 92 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8497 (ttp80) REVERT: G 73 ASN cc_start: 0.8567 (t0) cc_final: 0.8237 (m110) REVERT: L 534 MET cc_start: 0.5342 (ttt) cc_final: 0.5132 (ttt) REVERT: L 536 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8343 (tp30) REVERT: L 539 ASN cc_start: 0.6720 (m-40) cc_final: 0.6469 (m110) REVERT: L 558 MET cc_start: 0.7710 (tpt) cc_final: 0.6940 (mpt) REVERT: L 580 GLU cc_start: 0.7677 (pp20) cc_final: 0.7386 (pm20) REVERT: L 585 HIS cc_start: 0.7754 (m170) cc_final: 0.7542 (m90) outliers start: 18 outliers final: 9 residues processed: 187 average time/residue: 0.9320 time to fit residues: 184.2009 Evaluate side-chains 184 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 95 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL 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: 0.6980 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 54 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 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 = 0.3788 r_free = 0.3788 target = 0.115999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.076975 restraints weight = 23500.005| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.61 r_work: 0.2942 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2047 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= 0.154 Angle : 0.586 9.861 20886 Z= 0.342 Chirality : 0.035 0.180 2365 Planarity : 0.004 0.064 1623 Dihedral : 30.015 145.217 4280 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.35 % Allowed : 19.31 % 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: 2.04 (0.27), residues: 943 helix: 2.43 (0.21), residues: 596 sheet: 0.28 (0.73), residues: 56 loop : -0.76 (0.34), residues: 291 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 0.009 0.001 PHE A 67 TRP 0.003 0.001 TRP L 586 HIS 0.012 0.001 HIS L 585 Details of bonding type rmsd covalent geometry : bond 0.00335 (14535) covalent geometry : angle 0.58644 (20886) hydrogen bonds : bond 0.03319 ( 846) hydrogen bonds : angle 3.13960 ( 2147) Misc. bond : bond 0.00022 ( 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 200 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8313 (mtp-110) REVERT: A 59 GLU cc_start: 0.8161 (pm20) cc_final: 0.7893 (pm20) REVERT: A 133 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8145 (mt-10) REVERT: B 79 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8580 (mttp) REVERT: C 73 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8071 (t0) REVERT: C 74 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8684 (mtmm) REVERT: C 95 LYS cc_start: 0.9233 (ttmp) cc_final: 0.8861 (tptt) REVERT: D 71 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7880 (mp0) REVERT: E 76 GLN cc_start: 0.8435 (tt0) cc_final: 0.8164 (mt0) REVERT: F 92 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8488 (ttp80) REVERT: G 73 ASN cc_start: 0.8561 (t0) cc_final: 0.8242 (m110) REVERT: G 74 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8982 (mppt) REVERT: L 397 MET cc_start: 0.8331 (mtp) cc_final: 0.7926 (mtm) REVERT: L 534 MET cc_start: 0.5338 (ttt) cc_final: 0.5124 (ttt) REVERT: L 536 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8337 (tp30) REVERT: L 558 MET cc_start: 0.7740 (tpt) cc_final: 0.7094 (mtm) outliers start: 19 outliers final: 10 residues processed: 188 average time/residue: 0.9194 time to fit residues: 182.7388 Evaluate side-chains 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 71 GLU Chi-restraints excluded: chain F residue 24 ASP 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: 4.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 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 = 0.3754 r_free = 0.3754 target = 0.113667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.074508 restraints weight = 22657.516| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.62 r_work: 0.2853 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14536 Z= 0.211 Angle : 0.601 9.266 20886 Z= 0.350 Chirality : 0.036 0.151 2365 Planarity : 0.005 0.064 1623 Dihedral : 30.023 146.001 4280 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 19.68 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.27), residues: 943 helix: 2.40 (0.21), residues: 596 sheet: 0.24 (0.75), residues: 55 loop : -0.82 (0.34), residues: 292 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 0.010 0.001 PHE L 506 TRP 0.001 0.000 TRP L 586 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00475 (14535) covalent geometry : angle 0.60138 (20886) hydrogen bonds : bond 0.03848 ( 846) hydrogen bonds : angle 3.12300 ( 2147) Misc. bond : bond 0.00090 ( 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 193 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8198 (pm20) cc_final: 0.7890 (pm20) REVERT: A 133 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8087 (mt-10) REVERT: B 79 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8590 (mttp) REVERT: C 15 LYS cc_start: 0.7604 (ttmm) cc_final: 0.7299 (ttpp) REVERT: C 73 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8075 (t0) REVERT: C 74 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8717 (mtmm) REVERT: C 95 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8804 (tptt) REVERT: D 71 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: E 76 GLN cc_start: 0.8413 (tt0) cc_final: 0.8126 (mt0) REVERT: F 92 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8477 (ttp80) REVERT: G 73 ASN cc_start: 0.8557 (t0) cc_final: 0.8213 (m110) REVERT: G 74 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8990 (mppt) REVERT: L 397 MET cc_start: 0.8205 (mtp) cc_final: 0.7602 (mtm) REVERT: L 426 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8101 (mmm-85) REVERT: L 519 MET cc_start: 0.9015 (pmm) cc_final: 0.8643 (pmm) REVERT: L 558 MET cc_start: 0.7686 (tpt) cc_final: 0.6902 (mpt) REVERT: L 585 HIS cc_start: 0.8123 (m90) cc_final: 0.7822 (m90) outliers start: 18 outliers final: 9 residues processed: 180 average time/residue: 0.8921 time to fit residues: 170.1467 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 : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS 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 C residue 95 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 20.0000 chunk 51 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 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 = 0.3759 r_free = 0.3759 target = 0.114008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.075216 restraints weight = 22789.747| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.60 r_work: 0.2865 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14536 Z= 0.182 Angle : 0.604 10.467 20886 Z= 0.349 Chirality : 0.036 0.191 2365 Planarity : 0.004 0.061 1623 Dihedral : 30.037 145.990 4280 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 20.17 % 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: 1.98 (0.28), residues: 943 helix: 2.41 (0.21), residues: 597 sheet: 0.09 (0.75), residues: 55 loop : -0.83 (0.34), residues: 291 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 0.012 0.002 PHE L 462 TRP 0.000 0.000 TRP L 586 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00403 (14535) covalent geometry : angle 0.60363 (20886) hydrogen bonds : bond 0.03680 ( 846) hydrogen bonds : angle 3.12494 ( 2147) Misc. bond : bond 0.00082 ( 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 187 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8309 (mtp-110) REVERT: A 59 GLU cc_start: 0.8182 (pm20) cc_final: 0.7891 (pm20) REVERT: A 133 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 79 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8586 (mttp) REVERT: C 15 LYS cc_start: 0.7621 (ttmm) cc_final: 0.7352 (ttpp) REVERT: C 73 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8063 (t0) REVERT: C 74 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8712 (mtmm) REVERT: C 95 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8802 (tptt) REVERT: D 71 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: E 76 GLN cc_start: 0.8402 (tt0) cc_final: 0.8121 (mt0) REVERT: F 92 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8468 (ttp80) REVERT: G 73 ASN cc_start: 0.8551 (t0) cc_final: 0.8223 (m110) REVERT: G 74 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8991 (mppt) REVERT: L 397 MET cc_start: 0.8232 (mtp) cc_final: 0.7632 (mtm) REVERT: L 426 ARG cc_start: 0.8469 (tpp80) cc_final: 0.8112 (mmm-85) REVERT: L 519 MET cc_start: 0.9035 (pmm) cc_final: 0.8685 (pmm) REVERT: L 539 ASN cc_start: 0.6830 (m-40) cc_final: 0.6622 (m110) REVERT: L 558 MET cc_start: 0.7682 (tpt) cc_final: 0.6900 (mpt) REVERT: L 585 HIS cc_start: 0.8122 (m90) cc_final: 0.7822 (m90) outliers start: 16 outliers final: 10 residues processed: 177 average time/residue: 0.9203 time to fit residues: 172.5151 Evaluate side-chains 187 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS 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 C residue 95 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 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 = 0.3735 r_free = 0.3735 target = 0.112365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.073445 restraints weight = 22660.055| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.60 r_work: 0.2835 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14536 Z= 0.279 Angle : 0.632 10.716 20886 Z= 0.365 Chirality : 0.039 0.152 2365 Planarity : 0.005 0.059 1623 Dihedral : 30.229 147.659 4280 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 20.17 % Favored : 77.72 % 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: 1.68 (0.27), residues: 943 helix: 2.25 (0.21), residues: 597 sheet: -0.72 (0.66), residues: 64 loop : -0.95 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.014 0.002 TYR L 457 PHE 0.011 0.002 PHE L 506 TRP 0.006 0.001 TRP L 586 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00637 (14535) covalent geometry : angle 0.63203 (20886) hydrogen bonds : bond 0.04182 ( 846) hydrogen bonds : angle 3.19727 ( 2147) Misc. bond : bond 0.00141 ( 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 185 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.8188 (mtp-110) REVERT: A 59 GLU cc_start: 0.8324 (pm20) cc_final: 0.8004 (pm20) REVERT: A 133 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8088 (mt-10) REVERT: B 79 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8623 (mttp) REVERT: C 73 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8100 (t0) REVERT: C 74 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8732 (mtmm) REVERT: C 95 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8805 (tptt) REVERT: D 71 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: E 76 GLN cc_start: 0.8421 (tt0) cc_final: 0.8171 (mt0) REVERT: F 92 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8470 (ttp80) REVERT: G 73 ASN cc_start: 0.8612 (t0) cc_final: 0.8296 (m110) REVERT: G 74 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8928 (mppt) REVERT: L 397 MET cc_start: 0.8160 (mtp) cc_final: 0.7758 (mtm) REVERT: L 519 MET cc_start: 0.9034 (pmm) cc_final: 0.8676 (pmm) REVERT: L 558 MET cc_start: 0.7603 (tpt) cc_final: 0.6842 (mpt) REVERT: L 585 HIS cc_start: 0.8228 (m90) cc_final: 0.8028 (m-70) outliers start: 17 outliers final: 10 residues processed: 174 average time/residue: 0.9250 time to fit residues: 170.3936 Evaluate side-chains 184 residues out of total 810 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 119 optimal weight: 0.0010 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS 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 = 0.3755 r_free = 0.3755 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.075023 restraints weight = 22685.736| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.60 r_work: 0.2867 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14536 Z= 0.151 Angle : 0.600 10.783 20886 Z= 0.350 Chirality : 0.035 0.152 2365 Planarity : 0.004 0.058 1623 Dihedral : 30.228 147.750 4280 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.98 % Allowed : 19.93 % Favored : 78.09 % 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: 1.79 (0.28), residues: 943 helix: 2.34 (0.21), residues: 597 sheet: -0.72 (0.67), residues: 64 loop : -0.91 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 86 TYR 0.015 0.001 TYR L 457 PHE 0.011 0.001 PHE E 67 TRP 0.004 0.001 TRP L 586 HIS 0.002 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00321 (14535) covalent geometry : angle 0.60039 (20886) hydrogen bonds : bond 0.03540 ( 846) hydrogen bonds : angle 3.15414 ( 2147) Misc. bond : bond 0.00053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6636.15 seconds wall clock time: 113 minutes 4.78 seconds (6784.78 seconds total)