Starting phenix.real_space_refine on Thu Aug 6 03:20:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.map" model { file = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2026/8pc6_17595.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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 293 5.49 5 S 15 5.16 5 C 7600 2.51 5 N 2518 2.21 5 O 3067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13493 Number of models: 1 Model: "" Number of chains: 12 Chain: "I" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Inner-chain residues flagged as termini: ['pdbres=" DT I -72 "'] Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 828 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 692 Classifications: {'peptide': 86} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 708 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "J" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3014 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Time building chain proxies: 2.18, per 1000 atoms: 0.16 Number of scatterers: 13493 At special positions: 0 Unit cell: (104.2, 140.045, 120.872, 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 15 16.00 P 293 15.00 O 3067 8.00 N 2518 7.00 C 7600 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=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 352.6 milliseconds 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 59.5% alpha, 6.2% beta 129 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.602A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.583A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.882A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.826A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.556A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.501A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.899A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.251A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.666A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.546A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.547A 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 72 removed outlier: 4.377A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.234A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 83 Processing helix chain 'L' and resid 76 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.649A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.464A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.155A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.424A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.223A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 49 through 53 removed outlier: 3.950A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA K 51 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE K 42 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 49 through 53 removed outlier: 3.967A pdb=" N GLU L 49 " --> pdb=" O PHE L 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA L 51 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE L 42 " --> pdb=" O ALA L 51 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 329 hydrogen bonds 654 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2773 1.33 - 1.45: 4380 1.45 - 1.57: 6591 1.57 - 1.69: 584 1.69 - 1.81: 30 Bond restraints: 14358 Sorted by residual: bond pdb=" C3' DC J -71 " pdb=" C2' DC J -71 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.62e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.40e+01 bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DT J -59 " pdb=" C2' DT J -59 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 20183 2.54 - 5.09: 419 5.09 - 7.63: 15 7.63 - 10.18: 4 10.18 - 12.72: 1 Bond angle restraints: 20622 Sorted by residual: angle pdb=" O4' DT J -72 " pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 108.00 112.00 -4.00 7.00e-01 2.04e+00 3.27e+01 angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.80 -3.80 7.00e-01 2.04e+00 2.95e+01 angle pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " pdb=" P DA I 50 " ideal model delta sigma weight residual 119.70 125.88 -6.18 1.20e+00 6.94e-01 2.65e+01 angle pdb=" O4' DA I 67 " pdb=" C4' DA I 67 " pdb=" C3' DA I 67 " ideal model delta sigma weight residual 106.00 103.08 2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 ... (remaining 20617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 6328 35.96 - 71.91: 1552 71.91 - 107.86: 27 107.86 - 143.82: 3 143.82 - 179.77: 3 Dihedral angle restraints: 7913 sinusoidal: 5194 harmonic: 2719 Sorted by residual: dihedral pdb=" C4' DT J 69 " pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sinusoidal sigma weight residual 220.00 40.23 179.77 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 68 " pdb=" C3' DC J 68 " pdb=" O3' DC J 68 " pdb=" P DT J 69 " ideal model delta sinusoidal sigma weight residual -140.00 25.50 -165.50 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DA J -73 " pdb=" C3' DA J -73 " pdb=" O3' DA J -73 " pdb=" P DT J -72 " ideal model delta sinusoidal sigma weight residual -140.00 18.32 -158.32 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1951 0.064 - 0.127: 346 0.127 - 0.191: 18 0.191 - 0.254: 5 0.254 - 0.318: 2 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CA LEU L 53 " pdb=" N LEU L 53 " pdb=" C LEU L 53 " pdb=" CB LEU L 53 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CB ILE L 58 " pdb=" CA ILE L 58 " pdb=" CG1 ILE L 58 " pdb=" CG2 ILE L 58 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" P DC J 70 " pdb=" OP1 DC J 70 " pdb=" OP2 DC J 70 " pdb=" O5' DC J 70 " both_signs ideal model delta sigma weight residual True 2.34 -2.54 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2319 not shown) Planarity restraints: 1605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C LYS F 59 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 62 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.14e+01 pdb=" C LEU F 62 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU F 62 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU F 63 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 108 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL D 108 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL D 108 " -0.021 2.00e-02 2.50e+03 pdb=" N SER D 109 " -0.019 2.00e-02 2.50e+03 ... (remaining 1602 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 454 2.69 - 3.25: 11465 3.25 - 3.80: 25026 3.80 - 4.35: 31928 4.35 - 4.90: 46216 Nonbonded interactions: 115089 Sorted by model distance: nonbonded pdb=" O TYR L 61 " pdb=" NZ LYS L 65 " model vdw 2.142 3.120 nonbonded pdb=" OG SER G 18 " pdb=" O PHE G 25 " model vdw 2.206 3.040 nonbonded pdb=" N THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.215 3.120 nonbonded pdb=" NH1 ARG A 129 " pdb=" OD1 ASP E 106 " model vdw 2.286 3.120 nonbonded pdb=" N4 DC I 51 " pdb=" O6 DG J -51 " model vdw 2.310 3.120 ... (remaining 115084 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and (resid 20 through 100 or (resid 101 and (name N or name CA or nam \ e C )))) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = (chain 'L' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name CB or name CG or name CD )) or resid 35 through 90 or (resid 91 and (na \ me N or name CA or name C or name CB or name CG or name CD or name CE or name NZ \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.480 Find NCS groups from input model: 0.160 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 0.058 14358 Z= 0.480 Angle : 0.839 12.723 20622 Z= 0.719 Chirality : 0.048 0.318 2322 Planarity : 0.007 0.074 1605 Dihedral : 28.540 179.771 6157 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % 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: 0.83 (0.27), residues: 913 helix: 1.72 (0.22), residues: 556 sheet: -3.79 (0.60), residues: 23 loop : -1.15 (0.30), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 42 TYR 0.030 0.001 TYR L 61 PHE 0.041 0.002 PHE C 25 TRP 0.012 0.002 TRP K 21 HIS 0.004 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.48 (14358) covalent geometry : angle 0.83864 / 0.72 (20622) hydrogen bonds : bond 0.19305 / 21.21 ( 753) hydrogen bonds : angle 6.21305 / 8.14 ( 1899) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.516 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 182 average time/residue: 0.1440 time to fit residues: 34.2286 Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 53 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.0370 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.082790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.054496 restraints weight = 42384.716| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.88 r_work: 0.2799 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14358 Z= 0.205 Angle : 0.718 8.536 20622 Z= 0.392 Chirality : 0.052 0.351 2322 Planarity : 0.005 0.061 1605 Dihedral : 31.777 165.841 4252 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.01 % Allowed : 7.98 % Favored : 91.00 % 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: 1.31 (0.27), residues: 913 helix: 2.12 (0.22), residues: 567 sheet: -3.63 (0.70), residues: 17 loop : -1.18 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 74 TYR 0.013 0.001 TYR C 39 PHE 0.022 0.002 PHE C 25 TRP 0.017 0.002 TRP L 21 HIS 0.005 0.001 HIS L 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (14358) covalent geometry : angle 0.71776 / 0.39 (20622) hydrogen bonds : bond 0.06373 / 6.84 ( 753) hydrogen bonds : angle 3.43944 / 4.73 ( 1899) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.307 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7910 (tm-30) REVERT: K 45 PHE cc_start: 0.6561 (m-10) cc_final: 0.6308 (m-10) REVERT: L 24 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6382 (ttt180) outliers start: 8 outliers final: 6 residues processed: 116 average time/residue: 0.1183 time to fit residues: 18.8521 Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.081121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052599 restraints weight = 42482.671| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.88 r_work: 0.2747 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9075 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 : 0.004 0.053 14358 Z= 0.208 Angle : 0.664 8.806 20622 Z= 0.370 Chirality : 0.048 0.290 2322 Planarity : 0.005 0.052 1605 Dihedral : 31.330 161.807 4252 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.89 % Allowed : 9.89 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.28), residues: 913 helix: 2.33 (0.22), residues: 568 sheet: -3.31 (0.65), residues: 31 loop : -1.05 (0.31), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 74 TYR 0.019 0.001 TYR L 61 PHE 0.027 0.002 PHE C 25 TRP 0.044 0.006 TRP K 21 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (14358) covalent geometry : angle 0.66373 / 0.37 (20622) hydrogen bonds : bond 0.06043 / 6.28 ( 753) hydrogen bonds : angle 3.27982 / 4.56 ( 1899) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.297 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 30 ARG cc_start: 0.8715 (ttm-80) cc_final: 0.8480 (ttm170) REVERT: K 45 PHE cc_start: 0.6791 (m-10) cc_final: 0.5922 (m-10) REVERT: K 89 LYS cc_start: 0.7203 (mmmt) cc_final: 0.6971 (mmmt) outliers start: 7 outliers final: 5 residues processed: 116 average time/residue: 0.1138 time to fit residues: 18.0774 Evaluate side-chains 105 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.053350 restraints weight = 42458.362| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.89 r_work: 0.2770 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14358 Z= 0.147 Angle : 0.608 8.643 20622 Z= 0.345 Chirality : 0.045 0.308 2322 Planarity : 0.004 0.043 1605 Dihedral : 31.130 162.146 4252 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.89 % Allowed : 10.90 % Favored : 88.21 % 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: 1.83 (0.28), residues: 913 helix: 2.58 (0.22), residues: 567 sheet: -3.29 (0.59), residues: 29 loop : -0.94 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 74 TYR 0.010 0.001 TYR B 51 PHE 0.012 0.001 PHE C 25 TRP 0.031 0.003 TRP K 21 HIS 0.003 0.001 HIS K 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (14358) covalent geometry : angle 0.60844 / 0.34 (20622) hydrogen bonds : bond 0.05022 / 5.29 ( 753) hydrogen bonds : angle 3.09922 / 4.32 ( 1899) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 106 time to evaluate : 0.351 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 30 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8426 (ttm170) REVERT: G 90 ASP cc_start: 0.8655 (t0) cc_final: 0.8429 (t0) REVERT: K 49 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6393 (mm-30) REVERT: K 89 LYS cc_start: 0.7063 (mmmt) cc_final: 0.6689 (mmmt) REVERT: L 24 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6622 (ttt180) REVERT: L 53 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4647 (mp) outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 0.1329 time to fit residues: 20.4909 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.080358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051905 restraints weight = 42528.594| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.87 r_work: 0.2729 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14358 Z= 0.207 Angle : 0.650 8.696 20622 Z= 0.359 Chirality : 0.047 0.294 2322 Planarity : 0.004 0.039 1605 Dihedral : 31.122 163.957 4252 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.14 % Allowed : 10.27 % Favored : 88.59 % 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: 1.80 (0.28), residues: 913 helix: 2.46 (0.22), residues: 574 sheet: -3.50 (0.64), residues: 23 loop : -0.89 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 74 TYR 0.010 0.001 TYR G 50 PHE 0.021 0.002 PHE C 25 TRP 0.047 0.005 TRP K 21 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (14358) covalent geometry : angle 0.64964 / 0.36 (20622) hydrogen bonds : bond 0.05574 / 5.87 ( 753) hydrogen bonds : angle 3.17020 / 4.40 ( 1899) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.351 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8407 (tm-30) REVERT: D 30 ARG cc_start: 0.8798 (ttm-80) cc_final: 0.8512 (ttm170) REVERT: G 90 ASP cc_start: 0.8952 (t0) cc_final: 0.8720 (t0) REVERT: K 49 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6674 (mm-30) REVERT: K 89 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6716 (mmmt) REVERT: L 24 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6759 (ttt180) REVERT: L 53 LEU cc_start: 0.5625 (OUTLIER) cc_final: 0.5148 (mp) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.1296 time to fit residues: 19.8777 Evaluate side-chains 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 81 optimal weight: 0.6980 chunk 5 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 3 optimal weight: 10.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.078035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.049655 restraints weight = 42123.468| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.85 r_work: 0.2671 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 14358 Z= 0.287 Angle : 0.740 9.484 20622 Z= 0.398 Chirality : 0.052 0.252 2322 Planarity : 0.005 0.044 1605 Dihedral : 31.206 171.488 4252 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.65 % Allowed : 12.04 % Favored : 86.31 % 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: 1.34 (0.28), residues: 913 helix: 2.10 (0.22), residues: 575 sheet: -3.06 (0.63), residues: 37 loop : -1.00 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 74 TYR 0.013 0.002 TYR G 50 PHE 0.034 0.002 PHE C 25 TRP 0.025 0.004 TRP K 21 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.29 (14358) covalent geometry : angle 0.73964 / 0.40 (20622) hydrogen bonds : bond 0.06430 / 6.84 ( 753) hydrogen bonds : angle 3.39454 / 4.73 ( 1899) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.284 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8608 (tm-30) REVERT: D 30 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8618 (ttm170) REVERT: K 11 ILE cc_start: 0.4585 (OUTLIER) cc_final: 0.4210 (mt) REVERT: K 15 MET cc_start: 0.7422 (ppp) cc_final: 0.7146 (ppp) REVERT: K 49 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6766 (mm-30) REVERT: L 24 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6827 (ttt180) REVERT: L 53 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5285 (mp) outliers start: 13 outliers final: 6 residues processed: 110 average time/residue: 0.1120 time to fit residues: 17.0939 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.079603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051437 restraints weight = 42092.075| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.86 r_work: 0.2724 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14358 Z= 0.146 Angle : 0.616 8.488 20622 Z= 0.346 Chirality : 0.045 0.275 2322 Planarity : 0.004 0.040 1605 Dihedral : 30.974 174.931 4252 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.14 % Allowed : 12.55 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.28), residues: 913 helix: 2.48 (0.22), residues: 575 sheet: -3.00 (0.57), residues: 37 loop : -0.93 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 3 TYR 0.010 0.001 TYR F 51 PHE 0.013 0.001 PHE L 52 TRP 0.018 0.002 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (14358) covalent geometry : angle 0.61643 / 0.35 (20622) hydrogen bonds : bond 0.05067 / 5.37 ( 753) hydrogen bonds : angle 3.11325 / 4.34 ( 1899) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.250 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8488 (tm-30) REVERT: D 30 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8609 (ttm170) REVERT: K 15 MET cc_start: 0.7329 (ppp) cc_final: 0.7097 (ppp) REVERT: K 49 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6645 (mm-30) REVERT: L 24 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6711 (ttt180) REVERT: L 53 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5249 (mp) outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 0.1011 time to fit residues: 14.9791 Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.079858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051743 restraints weight = 42207.474| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.87 r_work: 0.2732 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14358 Z= 0.148 Angle : 0.611 8.742 20622 Z= 0.343 Chirality : 0.045 0.284 2322 Planarity : 0.004 0.043 1605 Dihedral : 30.884 176.781 4252 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.14 % Allowed : 12.93 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.28), residues: 913 helix: 2.57 (0.22), residues: 577 sheet: -2.93 (0.55), residues: 37 loop : -0.85 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 3 TYR 0.009 0.001 TYR B 51 PHE 0.013 0.001 PHE L 52 TRP 0.015 0.002 TRP K 21 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (14358) covalent geometry : angle 0.61092 / 0.34 (20622) hydrogen bonds : bond 0.04913 / 5.22 ( 753) hydrogen bonds : angle 3.06494 / 4.26 ( 1899) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.315 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8429 (tm-30) REVERT: D 30 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8591 (ttm170) REVERT: G 90 ASP cc_start: 0.8919 (t0) cc_final: 0.8684 (t0) REVERT: K 15 MET cc_start: 0.7356 (ppp) cc_final: 0.7118 (ppp) REVERT: K 49 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6664 (mm-30) REVERT: L 24 ARG cc_start: 0.6963 (OUTLIER) cc_final: 0.6707 (ttt180) REVERT: L 53 LEU cc_start: 0.5452 (OUTLIER) cc_final: 0.5043 (mp) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.1132 time to fit residues: 16.0654 Evaluate side-chains 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.080424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052394 restraints weight = 42335.908| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.86 r_work: 0.2751 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14358 Z= 0.134 Angle : 0.594 9.659 20622 Z= 0.336 Chirality : 0.044 0.293 2322 Planarity : 0.004 0.076 1605 Dihedral : 30.802 177.460 4252 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.27 % Allowed : 12.93 % Favored : 85.80 % 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: 2.03 (0.28), residues: 913 helix: 2.69 (0.22), residues: 575 sheet: -2.84 (0.54), residues: 37 loop : -0.82 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG L 74 TYR 0.009 0.001 TYR B 51 PHE 0.010 0.001 PHE L 5 TRP 0.014 0.001 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 (14358) covalent geometry : angle 0.59428 / 0.34 (20622) hydrogen bonds : bond 0.04655 / 4.97 ( 753) hydrogen bonds : angle 2.98595 / 4.13 ( 1899) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.265 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8797 (mptp) REVERT: C 91 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 30 ARG cc_start: 0.8847 (ttm-80) cc_final: 0.8576 (ttm170) REVERT: G 90 ASP cc_start: 0.8895 (t0) cc_final: 0.8667 (t0) REVERT: K 15 MET cc_start: 0.7390 (ppp) cc_final: 0.7122 (ppp) REVERT: K 49 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6642 (mm-30) REVERT: L 24 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6748 (ttt180) REVERT: L 53 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.4968 (mp) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.1097 time to fit residues: 15.9111 Evaluate side-chains 101 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 109 optimal weight: 0.0170 chunk 61 optimal weight: 0.8980 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.079901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051783 restraints weight = 42003.363| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.85 r_work: 0.2737 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14358 Z= 0.162 Angle : 0.608 8.764 20622 Z= 0.340 Chirality : 0.044 0.297 2322 Planarity : 0.004 0.044 1605 Dihedral : 30.811 178.916 4252 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.14 % Allowed : 13.56 % Favored : 85.30 % 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: 913 helix: 2.64 (0.22), residues: 575 sheet: -2.86 (0.52), residues: 37 loop : -0.84 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 74 TYR 0.009 0.001 TYR B 51 PHE 0.012 0.001 PHE L 52 TRP 0.047 0.004 TRP K 21 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (14358) covalent geometry : angle 0.60754 / 0.34 (20622) hydrogen bonds : bond 0.04902 / 5.23 ( 753) hydrogen bonds : angle 3.04941 / 4.21 ( 1899) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.381 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8824 (mptp) REVERT: C 91 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8428 (tm-30) REVERT: D 30 ARG cc_start: 0.8867 (ttm-80) cc_final: 0.8596 (ttm170) REVERT: G 90 ASP cc_start: 0.8926 (t0) cc_final: 0.8698 (t0) REVERT: K 15 MET cc_start: 0.7544 (ppp) cc_final: 0.7229 (ppp) REVERT: K 49 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6716 (mm-30) REVERT: L 24 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6711 (ttt180) REVERT: L 53 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5087 (mp) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 0.1284 time to fit residues: 18.1946 Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.080079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052006 restraints weight = 42273.195| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.86 r_work: 0.2740 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14358 Z= 0.145 Angle : 0.598 8.692 20622 Z= 0.336 Chirality : 0.044 0.299 2322 Planarity : 0.004 0.039 1605 Dihedral : 30.800 179.147 4252 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.01 % Allowed : 13.43 % Favored : 85.55 % 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: 913 helix: 2.68 (0.22), residues: 575 sheet: -2.90 (0.51), residues: 37 loop : -0.83 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 74 TYR 0.009 0.001 TYR B 51 PHE 0.027 0.001 PHE K 77 TRP 0.067 0.005 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (14358) covalent geometry : angle 0.59827 / 0.34 (20622) hydrogen bonds : bond 0.04795 / 5.12 ( 753) hydrogen bonds : angle 3.02303 / 4.17 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.40 seconds wall clock time: 56 minutes 5.69 seconds (3365.69 seconds total)