Starting phenix.real_space_refine on Thu Sep 26 17:14:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/09_2024/7yi1_33848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/09_2024/7yi1_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/09_2024/7yi1_33848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/09_2024/7yi1_33848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/09_2024/7yi1_33848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi1_33848/09_2024/7yi1_33848.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 8.14, per 1000 atoms: 0.58 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: 3.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.80 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: 5.24 Time building geometry restraints manager: 3.96 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=" C GLY K 19 " pdb=" N PRO K 20 " ideal model delta sigma weight residual 1.331 1.344 -0.012 7.90e-03 1.60e+04 2.34e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" CD M3L A 36 " pdb=" CE M3L A 36 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" N M3L A 36 " pdb=" CA M3L A 36 " ideal model delta sigma weight residual 1.458 1.441 0.017 1.90e-02 2.77e+03 8.47e-01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 7.99e-01 ... (remaining 14798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 21113 2.29 - 4.57: 153 4.57 - 6.86: 10 6.86 - 9.14: 1 9.14 - 11.43: 1 Bond angle restraints: 21278 Sorted by residual: angle pdb=" CB MET K 37 " pdb=" CG MET K 37 " pdb=" SD MET K 37 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA MET K 37 " pdb=" CB MET K 37 " pdb=" CG MET K 37 " ideal model delta sigma weight residual 114.10 120.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" C THR F 30 " pdb=" N LYS F 31 " pdb=" CA LYS F 31 " ideal model delta sigma weight residual 120.09 123.79 -3.70 1.25e+00 6.40e-01 8.78e+00 angle pdb=" CA GLU K 24 " pdb=" CB GLU K 24 " pdb=" CG GLU K 24 " ideal model delta sigma weight residual 114.10 119.14 -5.04 2.00e+00 2.50e-01 6.34e+00 angle pdb=" CG MET L 22 " pdb=" SD MET L 22 " pdb=" CE MET L 22 " ideal model delta sigma weight residual 100.90 95.78 5.12 2.20e+00 2.07e-01 5.41e+00 ... (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 - 0.027: 1532 0.027 - 0.055: 598 0.055 - 0.082: 184 0.082 - 0.110: 62 0.110 - 0.137: 12 Chirality restraints: 2388 Sorted by residual: 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=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE L 67 " pdb=" N ILE L 67 " pdb=" C ILE L 67 " pdb=" CB ILE L 67 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-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: 2.000 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.003 0.038 14803 Z= 0.183 Angle : 0.567 11.427 21278 Z= 0.338 Chirality : 0.034 0.137 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.018 0.002 TRP K 88 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE D 67 TYR 0.021 0.001 TYR L 23 ARG 0.005 0.000 ARG A 42 *********************** 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 fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.116 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: 1.9413 time to fit residues: 228.8643 Evaluate side-chains 102 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 103 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 81 ASN K 80 HIS ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14803 Z= 0.228 Angle : 0.577 8.111 21278 Z= 0.343 Chirality : 0.036 0.128 2388 Planarity : 0.005 0.046 1642 Dihedral : 30.009 156.166 4384 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.98 % Allowed : 13.75 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 940 helix: 1.62 (0.20), residues: 596 sheet: 0.69 (1.23), residues: 20 loop : -1.39 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 91 HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE D 67 TYR 0.014 0.002 TYR L 23 ARG 0.007 0.001 ARG A 42 *********************** 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 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 44 GLN cc_start: 0.8105 (mt0) cc_final: 0.7852 (mt0) REVERT: K 37 MET cc_start: 0.2874 (ppp) cc_final: 0.1980 (tmm) REVERT: L 22 MET cc_start: 0.1389 (pmm) cc_final: 0.1062 (pmm) REVERT: E 120 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8422 (mtt) outliers start: 16 outliers final: 6 residues processed: 111 average time/residue: 1.9044 time to fit residues: 224.4759 Evaluate side-chains 102 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR 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 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14803 Z= 0.285 Angle : 0.604 7.572 21278 Z= 0.357 Chirality : 0.038 0.133 2388 Planarity : 0.005 0.049 1642 Dihedral : 30.284 158.056 4384 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.97 % Allowed : 14.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 940 helix: 1.79 (0.21), residues: 596 sheet: 0.89 (1.19), residues: 20 loop : -1.32 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 91 HIS 0.005 0.001 HIS E 39 PHE 0.009 0.002 PHE D 67 TYR 0.013 0.002 TYR D 118 ARG 0.006 0.001 ARG A 42 *********************** 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 122 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.6963 (tttp) REVERT: H 44 GLN cc_start: 0.8078 (mt0) cc_final: 0.7823 (mt0) REVERT: K 108 LYS cc_start: 0.1301 (OUTLIER) cc_final: 0.0603 (mtmm) REVERT: L 22 MET cc_start: 0.1638 (pmm) cc_final: 0.1222 (pmm) REVERT: L 94 TYR cc_start: 0.2640 (OUTLIER) cc_final: 0.1958 (t80) outliers start: 24 outliers final: 11 residues processed: 112 average time/residue: 1.8755 time to fit residues: 223.5035 Evaluate side-chains 111 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 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 83 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 31 optimal weight: 0.0770 chunk 98 optimal weight: 10.0000 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0960 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= 0.219 Angle : 0.578 7.373 21278 Z= 0.345 Chirality : 0.036 0.185 2388 Planarity : 0.004 0.048 1642 Dihedral : 30.252 157.843 4384 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.85 % Allowed : 15.99 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.26), residues: 940 helix: 1.96 (0.21), residues: 596 sheet: 1.04 (1.21), residues: 20 loop : -1.25 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 91 HIS 0.003 0.001 HIS E 39 PHE 0.009 0.001 PHE D 67 TYR 0.011 0.002 TYR D 118 ARG 0.005 0.000 ARG A 42 *********************** 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 120 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6966 (tttp) REVERT: H 44 GLN cc_start: 0.8063 (mt0) cc_final: 0.7750 (mt0) REVERT: K 108 LYS cc_start: 0.1305 (OUTLIER) cc_final: 0.0607 (mtmm) REVERT: L 22 MET cc_start: 0.1476 (pmm) cc_final: 0.1079 (pmm) REVERT: L 94 TYR cc_start: 0.2629 (OUTLIER) cc_final: 0.1956 (t80) outliers start: 23 outliers final: 14 residues processed: 112 average time/residue: 1.8501 time to fit residues: 220.7583 Evaluate side-chains 114 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 62 ILE 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14803 Z= 0.179 Angle : 0.564 6.990 21278 Z= 0.338 Chirality : 0.035 0.157 2388 Planarity : 0.004 0.047 1642 Dihedral : 30.207 157.639 4384 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.85 % Allowed : 16.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 940 helix: 2.15 (0.21), residues: 596 sheet: 0.80 (0.78), residues: 40 loop : -1.18 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 91 HIS 0.003 0.001 HIS H 79 PHE 0.008 0.001 PHE K 17 TYR 0.010 0.001 TYR L 38 ARG 0.010 0.000 ARG A 42 *********************** 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 122 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.6967 (tttp) REVERT: H 44 GLN cc_start: 0.8044 (mt0) cc_final: 0.7666 (mt0) REVERT: H 110 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7985 (mm-30) REVERT: K 108 LYS cc_start: 0.1302 (OUTLIER) cc_final: 0.0610 (mtmm) REVERT: L 22 MET cc_start: 0.1352 (pmm) cc_final: 0.0920 (pmm) REVERT: L 94 TYR cc_start: 0.2621 (OUTLIER) cc_final: 0.1957 (t80) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 1.9226 time to fit residues: 230.9607 Evaluate side-chains 113 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 41 GLU 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 30 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 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 106 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14803 Z= 0.205 Angle : 0.550 6.677 21278 Z= 0.331 Chirality : 0.035 0.132 2388 Planarity : 0.004 0.049 1642 Dihedral : 30.054 157.426 4384 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.10 % Allowed : 16.73 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.27), residues: 940 helix: 2.27 (0.21), residues: 596 sheet: 1.11 (1.19), residues: 20 loop : -1.06 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 91 HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE D 67 TYR 0.013 0.001 TYR L 23 ARG 0.008 0.000 ARG A 42 *********************** 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 124 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7808 (mtt-85) REVERT: F 84 MET cc_start: 0.9068 (tpp) cc_final: 0.8711 (mmm) REVERT: H 31 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.6963 (tttp) REVERT: H 44 GLN cc_start: 0.8098 (mt0) cc_final: 0.7786 (mt0) REVERT: H 110 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7998 (mm-30) REVERT: K 104 ASN cc_start: 0.4045 (OUTLIER) cc_final: 0.3491 (t0) REVERT: K 108 LYS cc_start: 0.1349 (OUTLIER) cc_final: 0.0606 (mtmm) REVERT: L 22 MET cc_start: 0.1644 (pmm) cc_final: 0.1208 (pmm) REVERT: L 94 TYR cc_start: 0.2579 (OUTLIER) cc_final: 0.1950 (t80) outliers start: 25 outliers final: 12 residues processed: 114 average time/residue: 1.9770 time to fit residues: 241.0914 Evaluate side-chains 114 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 14803 Z= 0.456 Angle : 0.708 8.432 21278 Z= 0.408 Chirality : 0.046 0.165 2388 Planarity : 0.006 0.067 1642 Dihedral : 30.723 158.295 4384 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.22 % Allowed : 17.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 940 helix: 1.61 (0.20), residues: 596 sheet: -0.43 (0.71), residues: 50 loop : -1.14 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 91 HIS 0.009 0.002 HIS E 39 PHE 0.013 0.002 PHE K 77 TYR 0.019 0.003 TYR D 118 ARG 0.007 0.001 ARG A 42 *********************** 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 121 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7935 (mtt-85) REVERT: H 31 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.6976 (mmpt) REVERT: H 44 GLN cc_start: 0.8203 (mt0) cc_final: 0.7874 (mt0) REVERT: H 110 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8070 (mm-30) REVERT: H 113 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8421 (tttt) REVERT: K 104 ASN cc_start: 0.4072 (OUTLIER) cc_final: 0.3232 (t0) REVERT: K 108 LYS cc_start: 0.1356 (OUTLIER) cc_final: 0.0502 (mtmm) REVERT: L 22 MET cc_start: 0.1503 (pmm) cc_final: -0.0336 (tmm) REVERT: L 94 TYR cc_start: 0.2818 (OUTLIER) cc_final: 0.2355 (t80) REVERT: A 64 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.7589 (mmtp) outliers start: 26 outliers final: 14 residues processed: 111 average time/residue: 1.8807 time to fit residues: 222.1851 Evaluate side-chains 115 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 62 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 30 ARG 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 30 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 64 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14803 Z= 0.222 Angle : 0.574 7.435 21278 Z= 0.342 Chirality : 0.036 0.129 2388 Planarity : 0.004 0.050 1642 Dihedral : 30.184 157.961 4384 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.97 % Allowed : 17.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.27), residues: 940 helix: 2.04 (0.21), residues: 596 sheet: -0.48 (0.71), residues: 50 loop : -0.93 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 91 HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE D 67 TYR 0.013 0.001 TYR D 118 ARG 0.009 0.000 ARG A 42 *********************** 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 122 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8425 (ptm160) REVERT: B 95 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7823 (mtt-85) REVERT: H 31 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.6974 (mmpt) REVERT: H 44 GLN cc_start: 0.8129 (mt0) cc_final: 0.7829 (mt0) REVERT: H 110 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8015 (mm-30) REVERT: H 113 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8360 (tttt) REVERT: K 22 MET cc_start: 0.2104 (ttm) cc_final: 0.1789 (mtm) REVERT: K 104 ASN cc_start: 0.3981 (OUTLIER) cc_final: 0.3211 (t0) REVERT: K 108 LYS cc_start: 0.1595 (OUTLIER) cc_final: 0.0506 (mtmm) REVERT: L 22 MET cc_start: 0.1598 (pmm) cc_final: -0.0366 (tmm) REVERT: L 94 TYR cc_start: 0.2742 (OUTLIER) cc_final: 0.2301 (t80) outliers start: 24 outliers final: 11 residues processed: 114 average time/residue: 1.8795 time to fit residues: 227.9825 Evaluate side-chains 114 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG 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 77 ASP Chi-restraints excluded: chain E residue 65 LEU 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 112 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14803 Z= 0.196 Angle : 0.569 8.250 21278 Z= 0.339 Chirality : 0.035 0.126 2388 Planarity : 0.004 0.048 1642 Dihedral : 30.189 157.634 4384 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.27), residues: 940 helix: 2.19 (0.21), residues: 596 sheet: -0.46 (0.71), residues: 50 loop : -0.88 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 91 HIS 0.003 0.001 HIS H 79 PHE 0.008 0.001 PHE K 77 TYR 0.012 0.001 TYR D 118 ARG 0.009 0.000 ARG A 42 *********************** 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 116 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8415 (ptm160) REVERT: B 95 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7813 (mtt-85) REVERT: H 31 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.6965 (mmpt) REVERT: H 44 GLN cc_start: 0.8115 (mt0) cc_final: 0.7798 (mt0) REVERT: H 110 GLU cc_start: 0.8260 (mm-30) cc_final: 0.8028 (mm-30) REVERT: K 22 MET cc_start: 0.2070 (ttm) cc_final: 0.1772 (mtm) REVERT: K 104 ASN cc_start: 0.3987 (OUTLIER) cc_final: 0.3217 (t0) REVERT: K 108 LYS cc_start: 0.1594 (OUTLIER) cc_final: 0.0506 (mtmm) REVERT: L 22 MET cc_start: 0.1582 (pmm) cc_final: -0.0355 (tmm) REVERT: L 94 TYR cc_start: 0.2740 (OUTLIER) cc_final: 0.2255 (t80) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 1.9610 time to fit residues: 226.9089 Evaluate side-chains 114 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG 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 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 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 121 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1242 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= 0.246 Angle : 0.584 7.740 21278 Z= 0.346 Chirality : 0.037 0.139 2388 Planarity : 0.005 0.049 1642 Dihedral : 30.211 157.530 4384 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.60 % Allowed : 18.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.27), residues: 940 helix: 2.10 (0.21), residues: 596 sheet: 0.70 (0.77), residues: 40 loop : -0.97 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 91 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE F 100 TYR 0.016 0.002 TYR D 118 ARG 0.009 0.000 ARG A 42 ********************** 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 118 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8431 (ptm160) REVERT: B 95 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7821 (mtt-85) REVERT: D 105 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8159 (mttm) REVERT: F 77 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8387 (mmmt) REVERT: H 31 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.6954 (mmpt) REVERT: H 44 GLN cc_start: 0.8112 (mt0) cc_final: 0.7894 (mt0) REVERT: H 110 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8032 (mm-30) REVERT: K 22 MET cc_start: 0.2164 (ttm) cc_final: 0.1850 (mtm) REVERT: K 104 ASN cc_start: 0.4040 (OUTLIER) cc_final: 0.3350 (t0) REVERT: K 108 LYS cc_start: 0.1625 (OUTLIER) cc_final: 0.0544 (mtmm) REVERT: L 94 TYR cc_start: 0.2738 (OUTLIER) cc_final: 0.2302 (t80) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 1.8608 time to fit residues: 219.8062 Evaluate side-chains 117 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 ARG 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 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3797 r_free = 0.3797 target = 0.136273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094876 restraints weight = 19632.930| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.02 r_work: 0.2905 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1239 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= 0.190 Angle : 0.573 7.459 21278 Z= 0.341 Chirality : 0.035 0.135 2388 Planarity : 0.004 0.048 1642 Dihedral : 30.209 157.224 4384 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.48 % Allowed : 18.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.27), residues: 940 helix: 2.19 (0.21), residues: 596 sheet: 0.65 (0.77), residues: 40 loop : -0.94 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 91 HIS 0.003 0.001 HIS H 79 PHE 0.006 0.001 PHE H 67 TYR 0.014 0.001 TYR D 118 ARG 0.010 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4344.63 seconds wall clock time: 76 minutes 26.11 seconds (4586.11 seconds total)