Starting phenix.real_space_refine on Sat Sep 12 04:10:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi1_33848/09_2026/7yi1_33848.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 302 5.49 5 S 21 5.16 5 C 7843 2.51 5 N 2576 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13926 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3076 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3115 Classifications: {'DNA': 151} Link IDs: {'rna3p': 150} Chain: "K" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 853 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "A" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 830 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 822 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.18 Number of scatterers: 13926 At special positions: 0 Unit cell: (139.643, 141.808, 106.085, 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 21 16.00 P 302 15.00 O 3184 8.00 N 2576 7.00 C 7843 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: 0.87 Conformation dependent library (CDL) restraints added in 389.1 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 63.0% alpha, 11.6% beta 146 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.633A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.756A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.074A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 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 removed outlier: 3.536A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.699A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 4.203A pdb=" N ASN K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 4.156A pdb=" N ASP K 89 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 124 Processing helix chain 'L' and resid 101 through 124 Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.654A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.537A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.608A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.521A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.414A pdb=" N ARG B 45 " --> pdb=" O ILE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.577A 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: 7.308A 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 'F' and resid 45 through 46 removed outlier: 7.339A pdb=" N ARG F 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 80 through 81 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.270A 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 58 through 60 removed outlier: 5.534A pdb=" N ILE K 27 " --> pdb=" O HIS K 80 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS K 80 " --> pdb=" O ILE K 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.574A pdb=" N LEU K 15 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.410A pdb=" N PHE L 78 " --> pdb=" O LEU L 28 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE L 30 " --> pdb=" O CYS L 76 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS L 76 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.621A pdb=" N LEU L 21 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU L 15 " --> pdb=" O ARG L 98 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2586 1.33 - 1.45: 4718 1.45 - 1.57: 6860 1.57 - 1.69: 602 1.69 - 1.81: 37 Bond restraints: 14803 Sorted by residual: bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J -24 " pdb=" C2' DT J -24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J 73 " pdb=" C2' DG J 73 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DA I 61 " pdb=" C2' DA I 61 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG J -22 " pdb=" C2' DG J -22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.87e+00 ... (remaining 14798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 20835 2.29 - 4.57: 431 4.57 - 6.86: 10 6.86 - 9.14: 1 9.14 - 11.43: 1 Bond angle restraints: 21278 Sorted by residual: angle pdb=" O4' DA J 16 " pdb=" C1' DA J 16 " pdb=" N9 DA J 16 " ideal model delta sigma weight residual 108.00 111.30 -3.30 7.00e-01 2.04e+00 2.22e+01 angle pdb=" O4' DA I -54 " pdb=" C4' DA I -54 " pdb=" C3' DA I -54 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT I 68 " pdb=" C4 DT I 68 " pdb=" O4 DT I 68 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 21273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.03: 6354 31.03 - 62.05: 1732 62.05 - 93.08: 41 93.08 - 124.10: 0 124.10 - 155.13: 1 Dihedral angle restraints: 8128 sinusoidal: 5321 harmonic: 2807 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 64.87 155.13 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CB GLU L 124 " pdb=" CG GLU L 124 " pdb=" CD GLU L 124 " pdb=" OE1 GLU L 124 " ideal model delta sinusoidal sigma weight residual 0.00 -88.34 88.34 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA PHE L 17 " pdb=" C PHE L 17 " pdb=" N HIS L 18 " pdb=" CA HIS L 18 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1274 0.029 - 0.058: 701 0.058 - 0.087: 265 0.087 - 0.115: 132 0.115 - 0.144: 16 Chirality restraints: 2388 Sorted by residual: chirality pdb=" C3' DC J 49 " pdb=" C4' DC J 49 " pdb=" O3' DC J 49 " pdb=" C2' DC J 49 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" C3' DA I -66 " pdb=" C4' DA I -66 " pdb=" O3' DA I -66 " pdb=" C2' DA I -66 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2385 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C GLU B 63 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.15e+00 pdb=" N9 DA I -35 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.024 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 556 2.70 - 3.25: 11891 3.25 - 3.80: 26384 3.80 - 4.35: 33394 4.35 - 4.90: 47488 Nonbonded interactions: 119713 Sorted by model distance: nonbonded pdb=" O2 DC I 70 " pdb=" N2 DG J -70 " model vdw 2.155 2.496 nonbonded pdb=" OH TYR L 81 " pdb=" OE1 GLU L 90 " model vdw 2.175 3.040 nonbonded pdb=" O2 DC I -50 " pdb=" N2 DG J 50 " model vdw 2.194 2.496 nonbonded pdb=" O ALA K 99 " pdb=" ND2 ASN K 104 " model vdw 2.210 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.213 3.040 ... (remaining 119708 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 36 through 109 or (resid 110 through 111 and (name N or na \ me CA or name C or name O or name CB )) or resid 112 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.770 Find NCS groups from input model: 0.150 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:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 0.039 14803 Z= 0.490 Angle : 0.722 11.427 21278 Z= 0.632 Chirality : 0.043 0.144 2388 Planarity : 0.005 0.042 1642 Dihedral : 26.984 155.126 6316 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.37 % Allowed : 14.62 % Favored : 85.01 % 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: 0.11 (0.26), residues: 940 helix: 1.01 (0.21), residues: 586 sheet: 0.29 (1.30), residues: 20 loop : -1.63 (0.28), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 42 TYR 0.021 0.001 TYR L 23 PHE 0.008 0.001 PHE D 67 TRP 0.018 0.002 TRP K 88 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.49 (14803) covalent geometry : angle 0.72224 / 0.63 (21278) hydrogen bonds : bond 0.11448 / 7.95 ( 855) hydrogen bonds : angle 4.07865 / 2.90 ( 2155) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8329 (tttp) cc_final: 0.8125 (tttt) REVERT: D 105 LYS cc_start: 0.8014 (mtpm) cc_final: 0.7791 (mtpp) REVERT: H 44 GLN cc_start: 0.8067 (mt0) cc_final: 0.7730 (mt0) REVERT: K 37 MET cc_start: 0.3006 (ppp) cc_final: 0.2134 (tmm) REVERT: K 103 GLU cc_start: 0.3359 (pp20) cc_final: 0.2243 (tp30) REVERT: L 22 MET cc_start: 0.1646 (pmm) cc_final: 0.1049 (pmm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.8557 time to fit residues: 100.6763 Evaluate side-chains 102 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain K residue 67 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN H 81 ASN K 80 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095172 restraints weight = 19825.854| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.08 r_work: 0.2895 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14803 Z= 0.156 Angle : 0.635 8.265 21278 Z= 0.371 Chirality : 0.045 0.241 2388 Planarity : 0.005 0.046 1642 Dihedral : 30.095 157.907 4384 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.61 % Allowed : 13.88 % Favored : 84.51 % 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: 0.87 (0.26), residues: 940 helix: 1.62 (0.21), residues: 593 sheet: 0.64 (1.22), residues: 20 loop : -1.44 (0.29), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 42 TYR 0.013 0.002 TYR L 23 PHE 0.008 0.001 PHE D 67 TRP 0.011 0.001 TRP K 91 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (14803) covalent geometry : angle 0.63475 / 0.37 (21278) hydrogen bonds : bond 0.05948 / 4.04 ( 855) hydrogen bonds : angle 3.24812 / 2.32 ( 2155) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: D 105 LYS cc_start: 0.8179 (mtpm) cc_final: 0.7970 (mtpp) REVERT: H 44 GLN cc_start: 0.8133 (mt0) cc_final: 0.7799 (mt0) REVERT: K 37 MET cc_start: 0.3702 (ppp) cc_final: 0.2613 (tmm) REVERT: L 22 MET cc_start: 0.1463 (pmm) cc_final: 0.0625 (pmm) REVERT: E 120 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8379 (mtt) outliers start: 13 outliers final: 6 residues processed: 106 average time/residue: 0.8558 time to fit residues: 96.4668 Evaluate side-chains 100 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.094838 restraints weight = 20100.305| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.06 r_work: 0.2885 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14803 Z= 0.161 Angle : 0.631 7.299 21278 Z= 0.365 Chirality : 0.046 0.263 2388 Planarity : 0.004 0.049 1642 Dihedral : 30.271 158.670 4384 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.35 % Allowed : 15.12 % Favored : 82.53 % 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: 1.22 (0.27), residues: 940 helix: 1.88 (0.21), residues: 596 sheet: -0.35 (0.88), residues: 42 loop : -1.23 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 96 TYR 0.012 0.002 TYR L 23 PHE 0.026 0.002 PHE K 77 TRP 0.014 0.001 TRP K 91 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (14803) covalent geometry : angle 0.63110 / 0.36 (21278) hydrogen bonds : bond 0.05763 / 3.89 ( 855) hydrogen bonds : angle 3.17087 / 2.26 ( 2155) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 44 GLN cc_start: 0.8102 (mt0) cc_final: 0.7835 (mt0) REVERT: K 108 LYS cc_start: 0.0901 (OUTLIER) cc_final: 0.0324 (mtmm) REVERT: L 22 MET cc_start: 0.1352 (pmm) cc_final: 0.0516 (pmm) REVERT: L 94 TYR cc_start: 0.3632 (OUTLIER) cc_final: 0.3122 (t80) REVERT: A 64 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7678 (mmtp) REVERT: E 90 MET cc_start: 0.7900 (mmm) cc_final: 0.7659 (mmm) outliers start: 19 outliers final: 10 residues processed: 108 average time/residue: 0.8284 time to fit residues: 95.0900 Evaluate side-chains 107 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094501 restraints weight = 19847.250| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.10 r_work: 0.2872 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14803 Z= 0.165 Angle : 0.642 7.301 21278 Z= 0.365 Chirality : 0.046 0.270 2388 Planarity : 0.005 0.054 1642 Dihedral : 30.412 159.624 4384 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.22 % Allowed : 14.62 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 940 helix: 1.99 (0.21), residues: 596 sheet: 0.72 (1.14), residues: 20 loop : -1.23 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.013 0.002 TYR L 23 PHE 0.008 0.001 PHE D 67 TRP 0.012 0.001 TRP K 91 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 (14803) covalent geometry : angle 0.64232 / 0.37 (21278) hydrogen bonds : bond 0.05764 / 3.88 ( 855) hydrogen bonds : angle 3.11689 / 2.23 ( 2155) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7047 (mmpt) REVERT: H 44 GLN cc_start: 0.8151 (mt0) cc_final: 0.7788 (mt0) REVERT: K 108 LYS cc_start: 0.0793 (OUTLIER) cc_final: 0.0344 (mtmm) REVERT: L 22 MET cc_start: 0.1313 (pmm) cc_final: 0.0451 (pmm) REVERT: L 94 TYR cc_start: 0.3596 (OUTLIER) cc_final: 0.3060 (t80) REVERT: A 64 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7779 (mmtp) REVERT: E 90 MET cc_start: 0.7949 (mmm) cc_final: 0.7736 (mmm) outliers start: 26 outliers final: 12 residues processed: 114 average time/residue: 0.8231 time to fit residues: 99.8815 Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094713 restraints weight = 19983.439| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.08 r_work: 0.2875 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14803 Z= 0.159 Angle : 0.635 7.349 21278 Z= 0.362 Chirality : 0.046 0.267 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.436 159.918 4384 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.10 % Allowed : 16.23 % Favored : 80.67 % 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: 1.44 (0.26), residues: 940 helix: 2.05 (0.21), residues: 596 sheet: 0.78 (1.14), residues: 20 loop : -1.18 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.013 0.002 TYR D 118 PHE 0.009 0.001 PHE D 67 TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (14803) covalent geometry : angle 0.63533 / 0.36 (21278) hydrogen bonds : bond 0.05671 / 3.82 ( 855) hydrogen bonds : angle 3.09551 / 2.21 ( 2155) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 44 GLN cc_start: 0.8167 (mt0) cc_final: 0.7896 (mt0) REVERT: K 104 ASN cc_start: 0.3093 (OUTLIER) cc_final: 0.2442 (t0) REVERT: K 108 LYS cc_start: 0.0764 (OUTLIER) cc_final: 0.0339 (mtmm) REVERT: L 22 MET cc_start: 0.1295 (pmm) cc_final: 0.0505 (pmm) REVERT: L 94 TYR cc_start: 0.3627 (OUTLIER) cc_final: 0.3126 (t80) REVERT: E 90 MET cc_start: 0.7988 (mmm) cc_final: 0.7775 (mmm) outliers start: 25 outliers final: 13 residues processed: 114 average time/residue: 0.8603 time to fit residues: 104.0231 Evaluate side-chains 113 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 111 optimal weight: 0.6980 chunk 100 optimal weight: 0.0570 chunk 84 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095335 restraints weight = 19837.701| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.09 r_work: 0.2885 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14803 Z= 0.131 Angle : 0.617 7.122 21278 Z= 0.354 Chirality : 0.045 0.264 2388 Planarity : 0.004 0.047 1642 Dihedral : 30.412 159.543 4384 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.60 % Allowed : 17.35 % Favored : 80.05 % 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: 1.64 (0.27), residues: 940 helix: 2.22 (0.21), residues: 596 sheet: 0.82 (1.13), residues: 20 loop : -1.13 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 42 TYR 0.010 0.001 TYR D 118 PHE 0.009 0.001 PHE K 17 TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (14803) covalent geometry : angle 0.61700 / 0.35 (21278) hydrogen bonds : bond 0.05410 / 3.64 ( 855) hydrogen bonds : angle 3.07247 / 2.19 ( 2155) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.6867 (tttp) REVERT: H 44 GLN cc_start: 0.8201 (mt0) cc_final: 0.7877 (mt0) REVERT: H 110 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7964 (mm-30) REVERT: K 104 ASN cc_start: 0.3160 (OUTLIER) cc_final: 0.2507 (t0) REVERT: K 108 LYS cc_start: 0.0797 (OUTLIER) cc_final: 0.0346 (mtmm) REVERT: L 22 MET cc_start: 0.1187 (pmm) cc_final: 0.0427 (pmm) REVERT: L 94 TYR cc_start: 0.3569 (OUTLIER) cc_final: 0.3037 (t80) REVERT: E 90 MET cc_start: 0.7991 (mmm) cc_final: 0.7759 (mmm) outliers start: 21 outliers final: 12 residues processed: 113 average time/residue: 0.8213 time to fit residues: 98.8449 Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 110 ARG Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 99 optimal weight: 0.0980 chunk 93 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.136403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094530 restraints weight = 19764.581| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.08 r_work: 0.2885 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14803 Z= 0.156 Angle : 0.629 7.139 21278 Z= 0.358 Chirality : 0.046 0.268 2388 Planarity : 0.005 0.051 1642 Dihedral : 30.440 160.067 4384 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.97 % Allowed : 17.60 % Favored : 79.43 % 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: 1.62 (0.27), residues: 940 helix: 2.18 (0.21), residues: 596 sheet: 0.85 (1.13), residues: 20 loop : -1.07 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.013 0.002 TYR D 118 PHE 0.008 0.001 PHE D 67 TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (14803) covalent geometry : angle 0.62879 / 0.36 (21278) hydrogen bonds : bond 0.05587 / 3.77 ( 855) hydrogen bonds : angle 3.04720 / 2.17 ( 2155) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: F 84 MET cc_start: 0.9032 (tpp) cc_final: 0.8676 (mmm) REVERT: H 31 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6955 (mmpt) REVERT: H 44 GLN cc_start: 0.8148 (mt0) cc_final: 0.7855 (mt0) REVERT: K 104 ASN cc_start: 0.3172 (OUTLIER) cc_final: 0.2485 (t0) REVERT: K 108 LYS cc_start: 0.0841 (OUTLIER) cc_final: 0.0375 (mtmm) REVERT: L 22 MET cc_start: 0.1144 (pmm) cc_final: 0.0386 (pmm) REVERT: L 94 TYR cc_start: 0.3528 (OUTLIER) cc_final: 0.2997 (t80) REVERT: E 90 MET cc_start: 0.7975 (mmm) cc_final: 0.7737 (mmm) outliers start: 24 outliers final: 15 residues processed: 108 average time/residue: 0.8571 time to fit residues: 98.5769 Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain K residue 110 ARG Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093663 restraints weight = 19799.081| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.05 r_work: 0.2872 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14803 Z= 0.169 Angle : 0.652 8.380 21278 Z= 0.366 Chirality : 0.047 0.271 2388 Planarity : 0.005 0.053 1642 Dihedral : 30.501 160.298 4384 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.97 % Allowed : 17.84 % Favored : 79.18 % 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: 1.56 (0.26), residues: 940 helix: 2.09 (0.21), residues: 596 sheet: 0.90 (1.13), residues: 20 loop : -1.02 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.015 0.002 TYR D 118 PHE 0.008 0.001 PHE D 67 TRP 0.010 0.001 TRP K 91 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (14803) covalent geometry : angle 0.65158 / 0.37 (21278) hydrogen bonds : bond 0.05740 / 3.87 ( 855) hydrogen bonds : angle 3.06667 / 2.19 ( 2155) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7762 (mtt-85) REVERT: H 31 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.6993 (mmpt) REVERT: H 44 GLN cc_start: 0.8163 (mt0) cc_final: 0.7877 (mt0) REVERT: K 104 ASN cc_start: 0.3177 (OUTLIER) cc_final: 0.2481 (t0) REVERT: K 108 LYS cc_start: 0.0840 (OUTLIER) cc_final: 0.0448 (mtmm) REVERT: L 22 MET cc_start: 0.1771 (pmm) cc_final: 0.1110 (pmm) REVERT: L 94 TYR cc_start: 0.3549 (OUTLIER) cc_final: 0.3023 (t80) REVERT: E 90 MET cc_start: 0.7972 (mmm) cc_final: 0.7761 (mmm) outliers start: 24 outliers final: 14 residues processed: 110 average time/residue: 0.8263 time to fit residues: 96.4870 Evaluate side-chains 113 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 108 LYS Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093970 restraints weight = 19899.767| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.07 r_work: 0.2879 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14803 Z= 0.162 Angle : 0.647 7.596 21278 Z= 0.364 Chirality : 0.046 0.270 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.496 160.386 4384 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.48 % Allowed : 18.34 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.26), residues: 940 helix: 2.10 (0.21), residues: 596 sheet: 0.95 (1.13), residues: 20 loop : -1.00 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.015 0.002 TYR D 118 PHE 0.007 0.001 PHE D 67 TRP 0.011 0.001 TRP K 91 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (14803) covalent geometry : angle 0.64717 / 0.36 (21278) hydrogen bonds : bond 0.05665 / 3.81 ( 855) hydrogen bonds : angle 3.06339 / 2.19 ( 2155) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7757 (mtt-85) REVERT: H 31 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.6999 (mmpt) REVERT: H 44 GLN cc_start: 0.8175 (mt0) cc_final: 0.7893 (mt0) REVERT: L 94 TYR cc_start: 0.3620 (OUTLIER) cc_final: 0.3141 (t80) REVERT: E 90 MET cc_start: 0.7977 (mmm) cc_final: 0.7752 (mmm) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.8505 time to fit residues: 95.1434 Evaluate side-chains 112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094150 restraints weight = 19852.747| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.05 r_work: 0.2880 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14803 Z= 0.159 Angle : 0.645 8.141 21278 Z= 0.363 Chirality : 0.046 0.269 2388 Planarity : 0.005 0.054 1642 Dihedral : 30.486 160.394 4384 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.23 % Allowed : 18.71 % Favored : 79.06 % 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: 1.64 (0.27), residues: 940 helix: 2.14 (0.21), residues: 596 sheet: 1.07 (1.16), residues: 20 loop : -0.97 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 42 TYR 0.015 0.002 TYR D 118 PHE 0.007 0.001 PHE H 67 TRP 0.010 0.001 TRP K 91 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (14803) covalent geometry : angle 0.64460 / 0.36 (21278) hydrogen bonds : bond 0.05600 / 3.77 ( 855) hydrogen bonds : angle 3.05288 / 2.18 ( 2155) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.6991 (mmpt) REVERT: H 44 GLN cc_start: 0.8173 (mt0) cc_final: 0.7893 (mt0) REVERT: L 22 MET cc_start: 0.1292 (pmm) cc_final: -0.0416 (tmm) REVERT: L 94 TYR cc_start: 0.3574 (OUTLIER) cc_final: 0.3058 (t80) REVERT: L 107 MET cc_start: 0.0963 (ppp) cc_final: 0.0692 (ppp) REVERT: E 90 MET cc_start: 0.7939 (mmm) cc_final: 0.7716 (mmm) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.8294 time to fit residues: 91.8530 Evaluate side-chains 110 residues out of total 808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 94 TYR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.135521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093644 restraints weight = 19753.809| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.11 r_work: 0.2863 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14803 Z= 0.183 Angle : 0.671 7.539 21278 Z= 0.374 Chirality : 0.048 0.276 2388 Planarity : 0.005 0.050 1642 Dihedral : 30.562 160.477 4384 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.35 % Allowed : 18.59 % Favored : 79.06 % 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: 1.54 (0.27), residues: 940 helix: 2.03 (0.21), residues: 596 sheet: 0.71 (0.76), residues: 40 loop : -1.01 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.017 0.002 TYR D 118 PHE 0.009 0.002 PHE H 67 TRP 0.012 0.002 TRP K 84 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 (14803) covalent geometry : angle 0.67149 / 0.37 (21278) hydrogen bonds : bond 0.05902 / 3.97 ( 855) hydrogen bonds : angle 3.10934 / 2.22 ( 2155) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4834.88 seconds wall clock time: 82 minutes 42.64 seconds (4962.64 seconds total)