Starting phenix.real_space_refine on Sat Aug 23 16:08:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pc6_17595/08_2025/8pc6_17595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pc6_17595/08_2025/8pc6_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2025/8pc6_17595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2025/8pc6_17595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2025/8pc6_17595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pc6_17595/08_2025/8pc6_17595.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.23, per 1000 atoms: 0.24 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: 1.25 Conformation dependent library (CDL) restraints added in 392.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.32 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: 2.60 Time building geometry restraints manager: 1.66 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=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.35e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.766 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" N LEU L 53 " pdb=" CA LEU L 53 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.29e-02 6.01e+03 4.99e+00 bond pdb=" C3' DG J 64 " pdb=" O3' DG J 64 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.98e+00 bond pdb=" C3' DT J -72 " pdb=" O3' DT J -72 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.44e+00 ... (remaining 14353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 20408 2.54 - 5.09: 194 5.09 - 7.63: 15 7.63 - 10.18: 4 10.18 - 12.72: 1 Bond angle restraints: 20622 Sorted by residual: angle pdb=" CB MET L 1 " pdb=" CG MET L 1 " pdb=" SD MET L 1 " ideal model delta sigma weight residual 112.70 125.42 -12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C3' DC I 49 " pdb=" O3' DC I 49 " pdb=" P DA I 50 " ideal model delta sigma weight residual 120.20 125.88 -5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" N LEU L 53 " pdb=" CA LEU L 53 " pdb=" CB LEU L 53 " ideal model delta sigma weight residual 111.55 105.15 6.40 1.74e+00 3.30e-01 1.35e+01 angle pdb=" CA TYR L 61 " pdb=" CB TYR L 61 " pdb=" CG TYR L 61 " ideal model delta sigma weight residual 113.90 120.41 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" N MET L 1 " pdb=" CA MET L 1 " pdb=" C MET L 1 " ideal model delta sigma weight residual 111.00 101.39 9.61 2.80e+00 1.28e-01 1.18e+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: 2023 0.064 - 0.127: 278 0.127 - 0.191: 14 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=" C1' DT J -72 " pdb=" O4' DT J -72 " pdb=" C2' DT J -72 " pdb=" N1 DT J -72 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 1.02e+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: 0.010 Normalize map: mean=0, sd=1: 6.560 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.360 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.004 0.058 14358 Z= 0.173 Angle : 0.682 12.723 20622 Z= 0.402 Chirality : 0.044 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 aren 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 covalent geometry : bond 0.00373 (14358) covalent geometry : angle 0.68243 (20622) hydrogen bonds : bond 0.19305 ( 753) hydrogen bonds : angle 6.21305 ( 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 : 0.391 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: 0.1954 time to fit residues: 45.7792 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 : 0.398 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.0370 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 2.9990 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: 4.9990 overall best weight: 1.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 93 GLN K 20 HIS K 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.081510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.052942 restraints weight = 42262.413| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.91 r_work: 0.2758 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14358 Z= 0.238 Angle : 0.604 8.225 20622 Z= 0.353 Chirality : 0.039 0.159 2322 Planarity : 0.005 0.047 1605 Dihedral : 31.051 164.767 4252 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.01 % Allowed : 7.35 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.28), residues: 913 helix: 2.22 (0.22), residues: 568 sheet: -3.53 (0.65), residues: 23 loop : -1.03 (0.30), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 74 TYR 0.012 0.001 TYR G 50 PHE 0.026 0.002 PHE C 25 TRP 0.016 0.002 TRP L 21 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00546 (14358) covalent geometry : angle 0.60446 (20622) hydrogen bonds : bond 0.05420 ( 753) hydrogen bonds : angle 3.26569 ( 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 : 0.397 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: 0.8575 (tm-30) cc_final: 0.8209 (tm-30) REVERT: K 45 PHE cc_start: 0.6392 (m-10) cc_final: 0.6047 (m-10) REVERT: L 24 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6554 (ttt180) outliers start: 8 outliers final: 5 residues processed: 117 average time/residue: 0.1572 time to fit residues: 25.0760 Evaluate side-chains 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU 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: 6.9990 chunk 16 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 0.0010 chunk 96 optimal weight: 4.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.081951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053885 restraints weight = 42369.988| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.88 r_work: 0.2786 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14358 Z= 0.170 Angle : 0.539 6.939 20622 Z= 0.317 Chirality : 0.035 0.161 2322 Planarity : 0.004 0.038 1605 Dihedral : 30.549 166.858 4252 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.14 % Allowed : 8.49 % Favored : 90.37 % 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 aren not related in a simple way. whole: 1.76 (0.28), residues: 913 helix: 2.49 (0.22), residues: 575 sheet: -3.16 (0.61), residues: 38 loop : -0.92 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 74 TYR 0.015 0.001 TYR L 61 PHE 0.015 0.001 PHE C 25 TRP 0.010 0.002 TRP K 21 HIS 0.005 0.001 HIS K 48 Details of bonding type rmsd covalent geometry : bond 0.00381 (14358) covalent geometry : angle 0.53856 (20622) hydrogen bonds : bond 0.04516 ( 753) hydrogen bonds : angle 2.96258 ( 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 116 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.385 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: 0.8565 (tm-30) cc_final: 0.8111 (tm-30) REVERT: K 15 MET cc_start: 0.7011 (ppp) cc_final: 0.6779 (ppp) REVERT: K 45 PHE cc_start: 0.6523 (m-10) cc_final: 0.6054 (m-10) REVERT: L 53 LEU cc_start: 0.5224 (OUTLIER) cc_final: 0.4718 (mp) outliers start: 9 outliers final: 4 residues processed: 114 average time/residue: 0.1594 time to fit residues: 24.7134 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 : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 77 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.079831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051674 restraints weight = 42110.286| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.87 r_work: 0.2728 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14358 Z= 0.219 Angle : 0.557 6.616 20622 Z= 0.327 Chirality : 0.037 0.171 2322 Planarity : 0.004 0.040 1605 Dihedral : 30.581 178.449 4252 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.27 % Allowed : 9.13 % Favored : 89.61 % 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 aren not related in a simple way. whole: 1.80 (0.28), residues: 913 helix: 2.51 (0.22), residues: 575 sheet: -3.24 (0.60), residues: 38 loop : -0.87 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.011 0.001 TYR B 51 PHE 0.022 0.002 PHE C 25 TRP 0.014 0.002 TRP K 21 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00501 (14358) covalent geometry : angle 0.55722 (20622) hydrogen bonds : bond 0.04940 ( 753) hydrogen bonds : angle 3.03245 ( 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 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.252 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: 0.8860 (tm-30) cc_final: 0.8455 (tm-30) REVERT: K 15 MET cc_start: 0.7257 (ppp) cc_final: 0.6829 (ppp) REVERT: L 24 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6636 (ttt180) REVERT: L 53 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.5011 (mp) outliers start: 10 outliers final: 4 residues processed: 107 average time/residue: 0.1427 time to fit residues: 20.8203 Evaluate side-chains 98 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 82 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 38 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.080642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052627 restraints weight = 42430.961| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.88 r_work: 0.2755 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14358 Z= 0.176 Angle : 0.528 8.909 20622 Z= 0.311 Chirality : 0.035 0.150 2322 Planarity : 0.004 0.041 1605 Dihedral : 30.342 178.988 4252 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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 aren not related in a simple way. whole: 2.01 (0.28), residues: 913 helix: 2.67 (0.22), residues: 577 sheet: -3.17 (0.59), residues: 38 loop : -0.79 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 3 TYR 0.009 0.001 TYR B 51 PHE 0.015 0.001 PHE C 25 TRP 0.009 0.001 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00397 (14358) covalent geometry : angle 0.52774 (20622) hydrogen bonds : bond 0.04339 ( 753) hydrogen bonds : angle 2.91231 ( 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 110 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.324 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: C 56 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: C 91 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8353 (tm-30) REVERT: K 15 MET cc_start: 0.7404 (ppp) cc_final: 0.7032 (ppp) REVERT: L 24 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6706 (ttt180) REVERT: L 53 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.4862 (mp) outliers start: 7 outliers final: 2 residues processed: 109 average time/residue: 0.1431 time to fit residues: 21.1293 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 1 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 72 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.081332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053486 restraints weight = 42083.372| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.86 r_work: 0.2781 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14358 Z= 0.152 Angle : 0.512 7.181 20622 Z= 0.303 Chirality : 0.034 0.149 2322 Planarity : 0.004 0.041 1605 Dihedral : 30.231 177.050 4252 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.63 % Allowed : 10.27 % Favored : 89.10 % 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 aren not related in a simple way. whole: 2.15 (0.28), residues: 913 helix: 2.78 (0.22), residues: 577 sheet: -3.17 (0.56), residues: 38 loop : -0.72 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 3 TYR 0.008 0.001 TYR B 51 PHE 0.016 0.001 PHE K 77 TRP 0.030 0.003 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00336 (14358) covalent geometry : angle 0.51241 (20622) hydrogen bonds : bond 0.04072 ( 753) hydrogen bonds : angle 2.86446 ( 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 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.325 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: C 56 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: K 15 MET cc_start: 0.7433 (ppp) cc_final: 0.7066 (ppp) REVERT: L 24 ARG cc_start: 0.6899 (OUTLIER) cc_final: 0.6652 (ttt180) REVERT: L 53 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4764 (mp) outliers start: 5 outliers final: 2 residues processed: 101 average time/residue: 0.1373 time to fit residues: 19.0228 Evaluate side-chains 97 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 15 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052240 restraints weight = 41862.342| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.84 r_work: 0.2746 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14358 Z= 0.186 Angle : 0.531 7.617 20622 Z= 0.313 Chirality : 0.035 0.133 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.280 174.480 4252 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.51 % Allowed : 10.77 % Favored : 88.72 % 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 aren not related in a simple way. whole: 2.06 (0.28), residues: 913 helix: 2.73 (0.22), residues: 575 sheet: -3.51 (0.64), residues: 26 loop : -0.88 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 3 TYR 0.010 0.001 TYR B 51 PHE 0.016 0.001 PHE C 25 TRP 0.041 0.003 TRP K 21 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00423 (14358) covalent geometry : angle 0.53150 (20622) hydrogen bonds : bond 0.04520 ( 753) hydrogen bonds : angle 2.94101 ( 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 99 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.410 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8820 (tt0) REVERT: C 91 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8554 (tm-30) REVERT: K 89 LYS cc_start: 0.7255 (mmmt) cc_final: 0.7029 (mmmt) REVERT: L 24 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6731 (ttt180) REVERT: L 53 LEU cc_start: 0.5530 (OUTLIER) cc_final: 0.4996 (mp) outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.1494 time to fit residues: 20.0450 Evaluate side-chains 96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.079496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.051616 restraints weight = 41940.347| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 1.84 r_work: 0.2733 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14358 Z= 0.198 Angle : 0.541 9.380 20622 Z= 0.317 Chirality : 0.036 0.131 2322 Planarity : 0.004 0.043 1605 Dihedral : 30.270 173.213 4252 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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 aren not related in a simple way. whole: 2.00 (0.28), residues: 913 helix: 2.66 (0.22), residues: 575 sheet: -3.64 (0.62), residues: 26 loop : -0.86 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 74 TYR 0.010 0.001 TYR B 51 PHE 0.023 0.002 PHE K 77 TRP 0.050 0.004 TRP K 21 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00450 (14358) covalent geometry : angle 0.54125 (20622) hydrogen bonds : bond 0.04593 ( 753) hydrogen bonds : angle 2.96287 ( 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 106 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.414 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: 0.8834 (tm-30) cc_final: 0.8508 (tm-30) REVERT: K 11 ILE cc_start: 0.4454 (OUTLIER) cc_final: 0.4157 (mt) REVERT: K 89 LYS cc_start: 0.7102 (mmmt) cc_final: 0.6704 (mmmt) REVERT: L 24 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6815 (ttt180) REVERT: L 53 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.5026 (mp) outliers start: 7 outliers final: 3 residues processed: 103 average time/residue: 0.1488 time to fit residues: 20.9766 Evaluate side-chains 100 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 53 LEU 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: 0.8980 chunk 102 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.079725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051898 restraints weight = 42077.218| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.84 r_work: 0.2741 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14358 Z= 0.170 Angle : 0.529 8.502 20622 Z= 0.312 Chirality : 0.035 0.133 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.271 173.398 4252 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.89 % Allowed : 10.65 % Favored : 88.47 % 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 aren not related in a simple way. whole: 2.05 (0.28), residues: 913 helix: 2.71 (0.22), residues: 576 sheet: -3.69 (0.62), residues: 26 loop : -0.85 (0.32), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 74 TYR 0.010 0.001 TYR B 51 PHE 0.023 0.001 PHE L 52 TRP 0.035 0.003 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00381 (14358) covalent geometry : angle 0.52940 (20622) hydrogen bonds : bond 0.04467 ( 753) hydrogen bonds : angle 2.92421 ( 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 102 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.379 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: 0.8824 (tm-30) cc_final: 0.8483 (tm-30) REVERT: K 15 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7334 (ppp) REVERT: K 89 LYS cc_start: 0.7098 (mmmt) cc_final: 0.6678 (mmmt) REVERT: L 24 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6794 (ttt180) REVERT: L 53 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5057 (mp) outliers start: 7 outliers final: 4 residues processed: 99 average time/residue: 0.1571 time to fit residues: 21.2217 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 : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 15 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 109 optimal weight: 0.0570 chunk 61 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.080102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052276 restraints weight = 41758.131| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.84 r_work: 0.2751 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14358 Z= 0.149 Angle : 0.531 13.548 20622 Z= 0.311 Chirality : 0.034 0.133 2322 Planarity : 0.004 0.042 1605 Dihedral : 30.266 173.661 4252 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.01 % Allowed : 10.65 % Favored : 88.34 % 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 aren not related in a simple way. whole: 2.09 (0.28), residues: 913 helix: 2.77 (0.22), residues: 574 sheet: -3.73 (0.62), residues: 26 loop : -0.87 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 74 TYR 0.010 0.001 TYR F 51 PHE 0.028 0.001 PHE K 77 TRP 0.047 0.004 TRP K 21 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00330 (14358) covalent geometry : angle 0.53071 (20622) hydrogen bonds : bond 0.04336 ( 753) hydrogen bonds : angle 2.90851 ( 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: 8 poor density : 95 time to evaluate : 0.337 Fit side-chains TARDY: cannot create tardy model for: "LYS G 118 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7711 (p0) cc_final: 0.7499 (p0) REVERT: C 91 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8446 (tm-30) REVERT: K 11 ILE cc_start: 0.4485 (OUTLIER) cc_final: 0.4191 (mt) REVERT: K 15 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7302 (ppp) REVERT: K 89 LYS cc_start: 0.7142 (mmmt) cc_final: 0.6734 (mmmt) REVERT: L 24 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6784 (ttt180) REVERT: L 53 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5126 (mp) outliers start: 8 outliers final: 4 residues processed: 100 average time/residue: 0.1495 time to fit residues: 20.4935 Evaluate side-chains 103 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 12 PHE Chi-restraints excluded: chain K residue 15 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 85 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.080173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052400 restraints weight = 41950.380| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.84 r_work: 0.2756 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14358 Z= 0.155 Angle : 0.531 15.176 20622 Z= 0.310 Chirality : 0.034 0.134 2322 Planarity : 0.004 0.041 1605 Dihedral : 30.225 173.962 4252 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.89 % Allowed : 10.52 % 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 aren not related in a simple way. whole: 2.13 (0.28), residues: 913 helix: 2.78 (0.22), residues: 575 sheet: -3.72 (0.62), residues: 26 loop : -0.83 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 3 TYR 0.009 0.001 TYR B 51 PHE 0.013 0.001 PHE L 52 TRP 0.033 0.003 TRP K 21 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00344 (14358) covalent geometry : angle 0.53056 (20622) hydrogen bonds : bond 0.04281 ( 753) hydrogen bonds : angle 2.89564 ( 1899) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3951.85 seconds wall clock time: 68 minutes 4.20 seconds (4084.20 seconds total)