Starting phenix.real_space_refine on Sun Jul 21 00:26:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/07_2024/8cbq_16549.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/07_2024/8cbq_16549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/07_2024/8cbq_16549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/07_2024/8cbq_16549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/07_2024/8cbq_16549.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/07_2024/8cbq_16549.cif" } resolution = 4.0 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= 0.001 sd= 0.021 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 300 5.49 5 S 13 5.16 5 C 7231 2.51 5 N 2421 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 24": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12959 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} 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: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 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: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Time building chain proxies: 6.85, per 1000 atoms: 0.53 Number of scatterers: 12959 At special positions: 0 Unit cell: (135.792, 81.144, 120.888, 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 13 16.00 P 300 15.00 O 2994 8.00 N 2421 7.00 C 7231 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 - 3.50 Amino acid : False - 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: 6.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 63.0% alpha, 4.2% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.520A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.791A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.646A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.515A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.541A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.585A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.735A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 102 through 122 removed outlier: 3.542A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.764A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.944A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.515A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.516A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 88 removed outlier: 3.585A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.957A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.733A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 102 through 122 removed outlier: 3.543A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 removed outlier: 5.136A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.690A 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: 3.555A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.571A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.622A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.683A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.629A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.152A 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: 6.433A 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: 7.172A 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: 7.167A 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: 7.144A 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 50 through 51 removed outlier: 3.622A pdb=" N PHE K 43 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 6.66 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: 2280 1.33 - 1.45: 4689 1.45 - 1.57: 6221 1.57 - 1.69: 598 1.69 - 1.81: 26 Bond restraints: 13814 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.761 0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.55e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.61: 1537 105.61 - 112.69: 7638 112.69 - 119.77: 4646 119.77 - 126.85: 5280 126.85 - 133.93: 842 Bond angle restraints: 19943 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 120.20 125.91 -5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.15 -5.54 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.03 -4.83 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 125.00 -4.80 1.50e+00 4.44e-01 1.03e+01 angle pdb=" CA GLU K 63 " pdb=" CB GLU K 63 " pdb=" CG GLU K 63 " ideal model delta sigma weight residual 114.10 119.63 -5.53 2.00e+00 2.50e-01 7.64e+00 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6151 34.28 - 68.56: 1376 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.39: 1 Dihedral angle restraints: 7545 sinusoidal: 5071 harmonic: 2474 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 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 48.61 171.39 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1240 0.035 - 0.070: 801 0.070 - 0.105: 162 0.105 - 0.140: 41 0.140 - 0.175: 9 Chirality restraints: 2253 Sorted by residual: chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB VAL K 90 " pdb=" CA VAL K 90 " pdb=" CG1 VAL K 90 " pdb=" CG2 VAL K 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 2250 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO E 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO C 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO G 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.037 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3125 2.81 - 3.33: 10148 3.33 - 3.85: 23925 3.85 - 4.38: 31341 4.38 - 4.90: 43637 Nonbonded interactions: 112176 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 2.440 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.330 2.520 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.359 2.520 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 2.520 nonbonded pdb=" ND2 ASN B 25 " pdb=" OE1 GLU A 73 " model vdw 2.364 2.520 ... (remaining 112171 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.570 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 : 0.008 0.077 13814 Z= 0.477 Angle : 0.724 7.992 19943 Z= 0.428 Chirality : 0.044 0.175 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.198 171.394 5947 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 7.99 % Favored : 90.18 % 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: -5.85 (0.18), residues: 831 helix: -4.46 (0.09), residues: 530 sheet: -4.09 (0.99), residues: 17 loop : -2.11 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS K 20 PHE 0.013 0.002 PHE G 25 TYR 0.012 0.002 TYR B 72 ARG 0.004 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 460 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8026 (mt) cc_final: 0.7415 (mt) REVERT: B 44 LYS cc_start: 0.8631 (tttt) cc_final: 0.8380 (mtmt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7386 (tp30) REVERT: C 32 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6706 (ttp80) REVERT: C 62 ILE cc_start: 0.9381 (mt) cc_final: 0.9068 (mm) REVERT: C 68 ASN cc_start: 0.8832 (m-40) cc_final: 0.8231 (m-40) REVERT: C 83 LEU cc_start: 0.9336 (mt) cc_final: 0.8972 (mt) REVERT: C 87 VAL cc_start: 0.9403 (m) cc_final: 0.9124 (m) REVERT: C 110 ASN cc_start: 0.7942 (t0) cc_final: 0.7375 (t0) REVERT: D 49 THR cc_start: 0.8903 (m) cc_final: 0.8702 (m) REVERT: D 59 MET cc_start: 0.8965 (mmm) cc_final: 0.8372 (tpp) REVERT: D 110 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7295 (mt-10) REVERT: F 25 ASN cc_start: 0.8290 (m-40) cc_final: 0.7814 (m110) REVERT: F 34 ILE cc_start: 0.8857 (mt) cc_final: 0.8633 (mm) REVERT: F 39 ARG cc_start: 0.9036 (mmt-90) cc_final: 0.8787 (mmt180) REVERT: F 75 HIS cc_start: 0.7838 (t70) cc_final: 0.7611 (t70) REVERT: F 88 TYR cc_start: 0.8657 (m-10) cc_final: 0.8428 (m-80) REVERT: G 20 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7420 (mtt90) REVERT: G 57 TYR cc_start: 0.8128 (t80) cc_final: 0.7804 (t80) REVERT: G 110 ASN cc_start: 0.8643 (t0) cc_final: 0.8246 (t0) REVERT: H 110 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8303 (mt-10) REVERT: H 113 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8240 (tppt) REVERT: K 40 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2391 (tp) REVERT: A 46 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 49 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7531 (mtp-110) REVERT: A 51 ILE cc_start: 0.8963 (mt) cc_final: 0.8737 (mt) REVERT: A 55 GLN cc_start: 0.8344 (mt0) cc_final: 0.7895 (mt0) REVERT: A 62 ILE cc_start: 0.8573 (mt) cc_final: 0.8240 (mt) REVERT: A 76 GLN cc_start: 0.8258 (mm110) cc_final: 0.7928 (mm-40) REVERT: A 84 PHE cc_start: 0.8420 (m-80) cc_final: 0.7629 (m-80) REVERT: A 99 TYR cc_start: 0.8300 (t80) cc_final: 0.8097 (t80) REVERT: A 120 MET cc_start: 0.7238 (mtp) cc_final: 0.6922 (mmm) REVERT: E 60 LEU cc_start: 0.8200 (mt) cc_final: 0.7431 (mp) REVERT: E 71 VAL cc_start: 0.9446 (t) cc_final: 0.9191 (t) REVERT: E 74 ILE cc_start: 0.9177 (mt) cc_final: 0.8909 (tt) REVERT: E 117 VAL cc_start: 0.9086 (t) cc_final: 0.8853 (p) REVERT: E 118 THR cc_start: 0.8515 (m) cc_final: 0.7808 (p) REVERT: E 119 ILE cc_start: 0.8810 (pt) cc_final: 0.7799 (pt) REVERT: E 120 MET cc_start: 0.7605 (mtt) cc_final: 0.6556 (mpp) outliers start: 13 outliers final: 6 residues processed: 468 average time/residue: 0.3617 time to fit residues: 215.7801 Evaluate side-chains 374 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 366 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN D 46 HIS F 18 HIS G 89 ASN H 46 HIS H 92 GLN K 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 108 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13814 Z= 0.236 Angle : 0.694 6.916 19943 Z= 0.401 Chirality : 0.038 0.204 2253 Planarity : 0.007 0.073 1485 Dihedral : 29.680 158.998 4250 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.77 % Allowed : 23.56 % Favored : 71.67 % 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: -2.80 (0.24), residues: 831 helix: -1.84 (0.18), residues: 532 sheet: -4.33 (1.25), residues: 10 loop : -1.42 (0.31), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.021 0.002 PHE H 62 TYR 0.022 0.002 TYR F 51 ARG 0.011 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 398 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8810 (m110) cc_final: 0.8565 (m110) REVERT: B 79 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8505 (mmtm) REVERT: C 32 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6738 (ttp80) REVERT: C 71 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6929 (ttp-110) REVERT: C 75 LYS cc_start: 0.8428 (mmmm) cc_final: 0.7957 (mmmm) REVERT: C 110 ASN cc_start: 0.8555 (t0) cc_final: 0.8049 (t0) REVERT: D 59 MET cc_start: 0.9464 (mmm) cc_final: 0.8825 (tpp) REVERT: D 64 ASN cc_start: 0.8604 (m110) cc_final: 0.8066 (m110) REVERT: D 110 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7352 (mt-10) REVERT: F 25 ASN cc_start: 0.8650 (m-40) cc_final: 0.8205 (m-40) REVERT: F 39 ARG cc_start: 0.8866 (mmt-90) cc_final: 0.8416 (mmt180) REVERT: F 53 GLU cc_start: 0.8225 (tp30) cc_final: 0.7454 (tp30) REVERT: F 75 HIS cc_start: 0.8442 (t70) cc_final: 0.7909 (t70) REVERT: F 88 TYR cc_start: 0.9042 (m-10) cc_final: 0.8574 (m-80) REVERT: F 92 ARG cc_start: 0.8619 (mmm160) cc_final: 0.8405 (mmm160) REVERT: F 95 ARG cc_start: 0.8312 (mpp80) cc_final: 0.8051 (mtt90) REVERT: G 17 ARG cc_start: 0.7918 (mtm180) cc_final: 0.7627 (ptp-170) REVERT: G 68 ASN cc_start: 0.8099 (p0) cc_final: 0.7680 (p0) REVERT: G 73 ASN cc_start: 0.8577 (t0) cc_final: 0.8358 (t0) REVERT: G 81 ARG cc_start: 0.8391 (tpt90) cc_final: 0.8183 (tpt90) REVERT: G 92 GLU cc_start: 0.8183 (pm20) cc_final: 0.7812 (pm20) REVERT: G 110 ASN cc_start: 0.8687 (t0) cc_final: 0.8237 (t0) REVERT: G 112 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8118 (mm110) REVERT: H 34 TYR cc_start: 0.7952 (m-80) cc_final: 0.7629 (m-80) REVERT: H 39 TYR cc_start: 0.8057 (t80) cc_final: 0.7785 (t80) REVERT: H 40 LYS cc_start: 0.8957 (tppt) cc_final: 0.8755 (tppt) REVERT: H 102 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8050 (mm-30) REVERT: K 40 LEU cc_start: 0.3621 (OUTLIER) cc_final: 0.3185 (tp) REVERT: A 40 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7936 (mtp180) REVERT: A 46 VAL cc_start: 0.9164 (t) cc_final: 0.8872 (t) REVERT: A 55 GLN cc_start: 0.8926 (mt0) cc_final: 0.8540 (tt0) REVERT: A 56 LYS cc_start: 0.7955 (pttp) cc_final: 0.7562 (pttt) REVERT: A 76 GLN cc_start: 0.8330 (mm110) cc_final: 0.7918 (mm-40) REVERT: A 79 LYS cc_start: 0.8885 (tptp) cc_final: 0.8230 (tptt) REVERT: A 129 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.8214 (mmp80) REVERT: E 41 TYR cc_start: 0.7588 (m-80) cc_final: 0.7179 (m-80) REVERT: E 49 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7595 (ptp-170) REVERT: E 50 GLU cc_start: 0.7706 (pt0) cc_final: 0.7231 (pt0) REVERT: E 71 VAL cc_start: 0.9331 (t) cc_final: 0.9099 (t) REVERT: E 117 VAL cc_start: 0.9217 (t) cc_final: 0.9009 (p) REVERT: E 119 ILE cc_start: 0.8868 (pt) cc_final: 0.7897 (pt) outliers start: 34 outliers final: 23 residues processed: 413 average time/residue: 0.3414 time to fit residues: 182.1681 Evaluate side-chains 384 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 360 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 89 ASN C 94 ASN G 89 ASN H 92 GLN H 106 HIS ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN E 55 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13814 Z= 0.213 Angle : 0.665 12.199 19943 Z= 0.376 Chirality : 0.036 0.203 2253 Planarity : 0.006 0.059 1485 Dihedral : 29.612 154.246 4248 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.61 % Allowed : 28.61 % Favored : 65.78 % 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: -1.12 (0.27), residues: 831 helix: -0.32 (0.21), residues: 542 sheet: -4.24 (1.24), residues: 10 loop : -1.22 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.014 0.001 PHE F 61 TYR 0.027 0.002 TYR D 37 ARG 0.012 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 394 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8933 (m110) cc_final: 0.8528 (m-40) REVERT: B 63 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 32 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7223 (ttp-170) REVERT: C 95 LYS cc_start: 0.8582 (pttp) cc_final: 0.8316 (pttp) REVERT: C 110 ASN cc_start: 0.8764 (t0) cc_final: 0.8353 (t0) REVERT: D 59 MET cc_start: 0.9534 (mmm) cc_final: 0.9153 (tpp) REVERT: D 64 ASN cc_start: 0.8570 (m110) cc_final: 0.8262 (m-40) REVERT: D 110 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7432 (mt-10) REVERT: D 113 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8392 (mmtm) REVERT: F 39 ARG cc_start: 0.9022 (mmt-90) cc_final: 0.8277 (mmt180) REVERT: F 51 TYR cc_start: 0.7951 (m-10) cc_final: 0.7543 (m-10) REVERT: F 79 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8499 (mmtm) REVERT: F 88 TYR cc_start: 0.9099 (m-10) cc_final: 0.8620 (m-80) REVERT: F 95 ARG cc_start: 0.8186 (mpp80) cc_final: 0.7920 (mtt90) REVERT: G 39 TYR cc_start: 0.8724 (m-80) cc_final: 0.8192 (m-80) REVERT: G 57 TYR cc_start: 0.7286 (t80) cc_final: 0.6877 (t80) REVERT: G 58 LEU cc_start: 0.8707 (mt) cc_final: 0.8415 (mp) REVERT: G 61 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7682 (mm-30) REVERT: G 68 ASN cc_start: 0.8202 (p0) cc_final: 0.7704 (p0) REVERT: G 78 ILE cc_start: 0.8520 (mt) cc_final: 0.8042 (mt) REVERT: G 95 LYS cc_start: 0.8836 (pttp) cc_final: 0.8555 (pttp) REVERT: G 110 ASN cc_start: 0.8678 (t0) cc_final: 0.8261 (t0) REVERT: H 34 TYR cc_start: 0.7915 (m-80) cc_final: 0.7512 (m-10) REVERT: H 40 LYS cc_start: 0.9444 (tppt) cc_final: 0.9118 (tptt) REVERT: H 73 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8218 (mm-30) REVERT: H 102 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7556 (mm-30) REVERT: H 113 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8311 (ptpp) REVERT: K 40 LEU cc_start: 0.4143 (OUTLIER) cc_final: 0.3864 (tp) REVERT: A 46 VAL cc_start: 0.9315 (t) cc_final: 0.9035 (t) REVERT: A 52 ARG cc_start: 0.9148 (mtm-85) cc_final: 0.8742 (ttm110) REVERT: E 41 TYR cc_start: 0.7642 (m-80) cc_final: 0.7260 (m-80) REVERT: E 49 ARG cc_start: 0.8133 (ptm160) cc_final: 0.7569 (ptp90) REVERT: E 50 GLU cc_start: 0.7192 (pt0) cc_final: 0.6906 (pt0) REVERT: E 119 ILE cc_start: 0.8434 (pt) cc_final: 0.8130 (pt) REVERT: E 120 MET cc_start: 0.6925 (mpp) cc_final: 0.6461 (mpp) REVERT: E 129 ARG cc_start: 0.8928 (mmm160) cc_final: 0.8712 (mmm160) outliers start: 40 outliers final: 24 residues processed: 410 average time/residue: 0.3540 time to fit residues: 186.3697 Evaluate side-chains 392 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 367 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.0970 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 89 optimal weight: 0.0030 chunk 60 optimal weight: 3.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 94 ASN F 75 HIS G 73 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13814 Z= 0.193 Angle : 0.643 12.753 19943 Z= 0.361 Chirality : 0.035 0.203 2253 Planarity : 0.005 0.056 1485 Dihedral : 29.492 151.852 4245 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.75 % Allowed : 30.58 % Favored : 63.67 % 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: -0.26 (0.28), residues: 831 helix: 0.39 (0.22), residues: 537 sheet: -3.93 (1.47), residues: 10 loop : -0.95 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.002 0.001 HIS D 46 PHE 0.029 0.002 PHE B 61 TYR 0.029 0.002 TYR D 37 ARG 0.010 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 388 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8696 (m110) cc_final: 0.8248 (m-40) REVERT: B 51 TYR cc_start: 0.7007 (m-80) cc_final: 0.6736 (m-80) REVERT: B 63 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 73 THR cc_start: 0.9248 (t) cc_final: 0.8987 (t) REVERT: B 95 ARG cc_start: 0.7222 (mmm-85) cc_final: 0.6998 (mmm-85) REVERT: C 24 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7874 (mm-40) REVERT: C 36 LYS cc_start: 0.8174 (pttm) cc_final: 0.7545 (pttm) REVERT: C 75 LYS cc_start: 0.8827 (mmtm) cc_final: 0.8542 (mmmm) REVERT: C 95 LYS cc_start: 0.8613 (pttp) cc_final: 0.8346 (pttp) REVERT: C 110 ASN cc_start: 0.8706 (t0) cc_final: 0.8399 (t0) REVERT: C 115 LEU cc_start: 0.8507 (mp) cc_final: 0.7894 (mp) REVERT: D 49 THR cc_start: 0.8559 (m) cc_final: 0.8259 (p) REVERT: D 59 MET cc_start: 0.9531 (mmm) cc_final: 0.9189 (tpp) REVERT: D 109 SER cc_start: 0.9036 (t) cc_final: 0.8584 (p) REVERT: D 110 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7569 (mt-10) REVERT: F 39 ARG cc_start: 0.9085 (mmt-90) cc_final: 0.8877 (mmt-90) REVERT: F 67 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8918 (ttp80) REVERT: F 70 VAL cc_start: 0.9306 (t) cc_final: 0.9053 (p) REVERT: F 78 ARG cc_start: 0.7847 (tpp80) cc_final: 0.7630 (tpp80) REVERT: F 79 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8225 (mmtm) REVERT: F 88 TYR cc_start: 0.9138 (m-10) cc_final: 0.8695 (m-80) REVERT: F 95 ARG cc_start: 0.7952 (mpp80) cc_final: 0.7728 (mtt90) REVERT: G 17 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7936 (ptp-170) REVERT: G 39 TYR cc_start: 0.8715 (m-80) cc_final: 0.8500 (m-80) REVERT: G 42 ARG cc_start: 0.8235 (mtm180) cc_final: 0.8026 (mtm180) REVERT: G 57 TYR cc_start: 0.7486 (t80) cc_final: 0.7048 (t80) REVERT: G 58 LEU cc_start: 0.8677 (mt) cc_final: 0.8310 (mp) REVERT: G 61 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7771 (mm-30) REVERT: G 68 ASN cc_start: 0.8364 (p0) cc_final: 0.8105 (p0) REVERT: G 78 ILE cc_start: 0.8783 (mt) cc_final: 0.8225 (mt) REVERT: G 81 ARG cc_start: 0.8602 (tpt90) cc_final: 0.8083 (tpt90) REVERT: G 85 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8595 (mt) REVERT: G 89 ASN cc_start: 0.8250 (m110) cc_final: 0.7888 (m110) REVERT: G 95 LYS cc_start: 0.8768 (pttp) cc_final: 0.8489 (pttp) REVERT: H 40 LYS cc_start: 0.9171 (tppt) cc_final: 0.8070 (tptt) REVERT: H 73 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8426 (mm-30) REVERT: H 102 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7458 (mm-30) REVERT: H 105 LYS cc_start: 0.8999 (ptmm) cc_final: 0.8592 (pttm) REVERT: H 113 LYS cc_start: 0.8783 (ptpt) cc_final: 0.8356 (ptpp) REVERT: A 42 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.7173 (mmm-85) REVERT: A 76 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7865 (mm-40) REVERT: E 52 ARG cc_start: 0.8876 (ttm110) cc_final: 0.8600 (ttm-80) REVERT: E 64 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7920 (mmmt) REVERT: E 68 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7735 (pp30) REVERT: E 85 GLN cc_start: 0.7921 (mt0) cc_final: 0.7694 (mt0) REVERT: E 118 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8398 (p) REVERT: E 120 MET cc_start: 0.7241 (mpp) cc_final: 0.6146 (mpp) REVERT: E 129 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8593 (mmm160) outliers start: 41 outliers final: 30 residues processed: 403 average time/residue: 0.3532 time to fit residues: 183.9299 Evaluate side-chains 404 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 372 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 89 ASN K 78 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN A 125 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13814 Z= 0.286 Angle : 0.688 13.145 19943 Z= 0.387 Chirality : 0.037 0.185 2253 Planarity : 0.005 0.053 1485 Dihedral : 29.585 149.727 4243 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 7.57 % Allowed : 29.59 % Favored : 62.83 % 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: -0.04 (0.28), residues: 831 helix: 0.56 (0.22), residues: 540 sheet: -3.06 (1.20), residues: 20 loop : -0.81 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.004 0.001 HIS E 39 PHE 0.022 0.002 PHE F 61 TYR 0.025 0.002 TYR F 51 ARG 0.010 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 373 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8926 (m110) cc_final: 0.8494 (m-40) REVERT: B 44 LYS cc_start: 0.9202 (tttt) cc_final: 0.8896 (mttt) REVERT: B 55 ARG cc_start: 0.8506 (mtt90) cc_final: 0.8244 (ttm110) REVERT: B 63 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7682 (mt-10) REVERT: C 32 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7206 (ttp-110) REVERT: C 110 ASN cc_start: 0.8961 (t0) cc_final: 0.8650 (t0) REVERT: D 39 TYR cc_start: 0.8038 (t80) cc_final: 0.7414 (t80) REVERT: D 59 MET cc_start: 0.9525 (mmm) cc_final: 0.9218 (tpp) REVERT: D 64 ASN cc_start: 0.8380 (m-40) cc_final: 0.7924 (m110) REVERT: D 92 GLN cc_start: 0.7265 (pp30) cc_final: 0.6362 (pp30) REVERT: D 108 VAL cc_start: 0.8859 (p) cc_final: 0.8619 (p) REVERT: D 109 SER cc_start: 0.8904 (t) cc_final: 0.8586 (p) REVERT: D 110 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 52 GLU cc_start: 0.9358 (tp30) cc_final: 0.9141 (tp30) REVERT: F 63 GLU cc_start: 0.7752 (pp20) cc_final: 0.7025 (pp20) REVERT: F 70 VAL cc_start: 0.9368 (t) cc_final: 0.9164 (p) REVERT: F 74 GLU cc_start: 0.7666 (tp30) cc_final: 0.7370 (tp30) REVERT: F 79 LYS cc_start: 0.9079 (mmtm) cc_final: 0.8856 (mmtm) REVERT: F 88 TYR cc_start: 0.9299 (m-10) cc_final: 0.8639 (m-80) REVERT: F 95 ARG cc_start: 0.8602 (mpp80) cc_final: 0.8212 (mtt90) REVERT: G 39 TYR cc_start: 0.8873 (m-80) cc_final: 0.8567 (m-80) REVERT: G 42 ARG cc_start: 0.8407 (mtm180) cc_final: 0.7837 (mtm180) REVERT: G 61 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8083 (mm-30) REVERT: G 78 ILE cc_start: 0.9002 (mt) cc_final: 0.8679 (mm) REVERT: G 81 ARG cc_start: 0.8720 (tpt90) cc_final: 0.8231 (tpt90) REVERT: G 84 GLN cc_start: 0.9451 (tp40) cc_final: 0.9239 (tp-100) REVERT: G 89 ASN cc_start: 0.8458 (m-40) cc_final: 0.7939 (m110) REVERT: G 95 LYS cc_start: 0.8723 (pttp) cc_final: 0.8470 (pttp) REVERT: G 108 LEU cc_start: 0.9277 (mt) cc_final: 0.9030 (mt) REVERT: H 32 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7480 (tm-30) REVERT: H 40 LYS cc_start: 0.9216 (tppt) cc_final: 0.8678 (tptp) REVERT: H 73 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8193 (mm-30) REVERT: H 113 LYS cc_start: 0.8741 (ptpt) cc_final: 0.8266 (ptpp) REVERT: A 49 ARG cc_start: 0.8489 (ttm110) cc_final: 0.8123 (mtp-110) REVERT: A 76 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7833 (mm-40) REVERT: A 79 LYS cc_start: 0.9154 (tptp) cc_final: 0.8916 (tptp) REVERT: E 39 HIS cc_start: 0.5409 (p-80) cc_final: 0.5149 (p-80) REVERT: E 63 ARG cc_start: 0.7515 (mmp80) cc_final: 0.7113 (mmp80) REVERT: E 65 LEU cc_start: 0.9082 (tt) cc_final: 0.8025 (tt) REVERT: E 67 PHE cc_start: 0.9108 (t80) cc_final: 0.8440 (t80) REVERT: E 68 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7915 (pp30) REVERT: E 70 LEU cc_start: 0.8817 (tp) cc_final: 0.8599 (tt) REVERT: E 76 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8493 (tm-30) REVERT: E 81 ASP cc_start: 0.8103 (m-30) cc_final: 0.7806 (m-30) REVERT: E 87 SER cc_start: 0.9267 (m) cc_final: 0.9005 (p) REVERT: E 99 TYR cc_start: 0.9058 (t80) cc_final: 0.8800 (t80) REVERT: E 115 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8626 (mmmm) outliers start: 54 outliers final: 44 residues processed: 395 average time/residue: 0.3558 time to fit residues: 183.1799 Evaluate side-chains 403 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 359 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 73 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.6436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13814 Z= 0.217 Angle : 0.672 12.066 19943 Z= 0.373 Chirality : 0.037 0.236 2253 Planarity : 0.005 0.050 1485 Dihedral : 29.568 149.865 4243 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.03 % Allowed : 34.08 % Favored : 59.89 % 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: 0.44 (0.28), residues: 831 helix: 0.99 (0.23), residues: 527 sheet: -2.86 (1.19), residues: 20 loop : -0.67 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.002 0.001 HIS F 75 PHE 0.028 0.002 PHE B 61 TYR 0.036 0.001 TYR F 51 ARG 0.009 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 380 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8783 (m110) cc_final: 0.8315 (m-40) REVERT: B 44 LYS cc_start: 0.9268 (tttt) cc_final: 0.8952 (mttt) REVERT: B 55 ARG cc_start: 0.8520 (mtt90) cc_final: 0.8082 (ttm110) REVERT: B 63 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 73 THR cc_start: 0.9422 (t) cc_final: 0.9206 (t) REVERT: B 78 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.8195 (mtm180) REVERT: B 88 TYR cc_start: 0.8863 (m-10) cc_final: 0.7608 (m-10) REVERT: B 95 ARG cc_start: 0.7250 (mmm-85) cc_final: 0.6999 (mmm-85) REVERT: C 17 ARG cc_start: 0.8799 (ptt180) cc_final: 0.8591 (ptt90) REVERT: C 24 GLN cc_start: 0.8651 (mm-40) cc_final: 0.7957 (mm-40) REVERT: D 39 TYR cc_start: 0.7640 (t80) cc_final: 0.7057 (t80) REVERT: D 64 ASN cc_start: 0.8637 (m-40) cc_final: 0.8180 (m110) REVERT: D 92 GLN cc_start: 0.7565 (pp30) cc_final: 0.7277 (pp30) REVERT: D 109 SER cc_start: 0.8856 (t) cc_final: 0.8396 (p) REVERT: F 63 GLU cc_start: 0.7731 (pp20) cc_final: 0.7131 (pp20) REVERT: F 70 VAL cc_start: 0.9312 (t) cc_final: 0.9101 (p) REVERT: F 74 GLU cc_start: 0.7571 (tp30) cc_final: 0.7207 (tp30) REVERT: F 79 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8593 (mmtm) REVERT: F 88 TYR cc_start: 0.9196 (m-10) cc_final: 0.8572 (m-80) REVERT: F 90 LEU cc_start: 0.9440 (mt) cc_final: 0.9239 (mp) REVERT: F 95 ARG cc_start: 0.8366 (mpp80) cc_final: 0.7937 (mtt90) REVERT: G 39 TYR cc_start: 0.8740 (m-80) cc_final: 0.8530 (m-80) REVERT: G 42 ARG cc_start: 0.8253 (mtm180) cc_final: 0.7956 (mtm180) REVERT: G 61 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7833 (mm-30) REVERT: G 78 ILE cc_start: 0.8942 (mt) cc_final: 0.8668 (mm) REVERT: G 81 ARG cc_start: 0.8633 (tpt90) cc_final: 0.8100 (tpt90) REVERT: G 95 LYS cc_start: 0.8649 (pttp) cc_final: 0.8443 (pttp) REVERT: H 40 LYS cc_start: 0.9095 (tppt) cc_final: 0.8188 (tptp) REVERT: H 113 LYS cc_start: 0.8724 (ptpt) cc_final: 0.8370 (ptpt) REVERT: H 118 TYR cc_start: 0.8041 (t80) cc_final: 0.7344 (t80) REVERT: A 49 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8284 (mtm-85) REVERT: A 79 LYS cc_start: 0.9130 (tptp) cc_final: 0.8908 (tptp) REVERT: A 120 MET cc_start: 0.7466 (mmm) cc_final: 0.7148 (mmm) REVERT: E 39 HIS cc_start: 0.5042 (p-80) cc_final: 0.4811 (p-80) REVERT: E 53 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8047 (tpt90) REVERT: E 65 LEU cc_start: 0.9027 (tt) cc_final: 0.7980 (tt) REVERT: E 67 PHE cc_start: 0.8795 (t80) cc_final: 0.8308 (t80) REVERT: E 68 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7993 (pp30) REVERT: E 73 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: E 76 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8598 (tm-30) REVERT: E 81 ASP cc_start: 0.8201 (m-30) cc_final: 0.7904 (m-30) REVERT: E 87 SER cc_start: 0.9205 (m) cc_final: 0.9001 (p) REVERT: E 97 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7713 (mt-10) REVERT: E 99 TYR cc_start: 0.9012 (t80) cc_final: 0.8684 (t80) REVERT: E 120 MET cc_start: 0.7851 (mmm) cc_final: 0.7296 (mmp) outliers start: 43 outliers final: 35 residues processed: 398 average time/residue: 0.3396 time to fit residues: 175.5893 Evaluate side-chains 404 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 367 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 73 ASN G 89 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13814 Z= 0.308 Angle : 0.716 9.078 19943 Z= 0.398 Chirality : 0.039 0.193 2253 Planarity : 0.005 0.053 1485 Dihedral : 29.615 149.190 4241 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 7.15 % Allowed : 34.08 % Favored : 58.77 % 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: 0.29 (0.28), residues: 831 helix: 0.81 (0.22), residues: 527 sheet: -2.61 (1.20), residues: 20 loop : -0.62 (0.34), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.005 0.001 HIS G 82 PHE 0.031 0.002 PHE A 67 TYR 0.056 0.003 TYR D 80 ARG 0.009 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 367 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8921 (m110) cc_final: 0.8487 (m-40) REVERT: B 55 ARG cc_start: 0.8596 (mtt90) cc_final: 0.8384 (mtt90) REVERT: B 63 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7757 (mt-10) REVERT: B 73 THR cc_start: 0.9481 (t) cc_final: 0.9265 (t) REVERT: B 78 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8264 (mtm180) REVERT: B 85 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: C 17 ARG cc_start: 0.8984 (ptt180) cc_final: 0.8669 (ptt90) REVERT: C 32 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7249 (tmm-80) REVERT: C 35 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7587 (tpm170) REVERT: C 84 GLN cc_start: 0.9090 (tp-100) cc_final: 0.8852 (tp-100) REVERT: D 39 TYR cc_start: 0.7766 (t80) cc_final: 0.7269 (t80) REVERT: D 64 ASN cc_start: 0.8754 (m-40) cc_final: 0.8321 (m110) REVERT: D 92 GLN cc_start: 0.7695 (pp30) cc_final: 0.7377 (pp30) REVERT: D 105 LYS cc_start: 0.7932 (tptp) cc_final: 0.7672 (tptp) REVERT: F 63 GLU cc_start: 0.7808 (pp20) cc_final: 0.7254 (pp20) REVERT: F 88 TYR cc_start: 0.9266 (m-10) cc_final: 0.8596 (m-80) REVERT: G 58 LEU cc_start: 0.8680 (mt) cc_final: 0.8455 (mp) REVERT: G 61 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7988 (mm-30) REVERT: G 78 ILE cc_start: 0.9034 (mt) cc_final: 0.8628 (mm) REVERT: G 81 ARG cc_start: 0.8875 (tpt90) cc_final: 0.8634 (tpt90) REVERT: G 89 ASN cc_start: 0.8221 (m-40) cc_final: 0.7966 (m110) REVERT: H 40 LYS cc_start: 0.9286 (tppt) cc_final: 0.8822 (tptp) REVERT: H 76 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8052 (mtm110) REVERT: A 42 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.7315 (mmm-85) REVERT: A 49 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8211 (mtp-110) REVERT: A 79 LYS cc_start: 0.9165 (tptp) cc_final: 0.8964 (tptp) REVERT: A 120 MET cc_start: 0.7581 (mmm) cc_final: 0.7220 (mmm) REVERT: A 123 ASP cc_start: 0.8989 (m-30) cc_final: 0.8693 (m-30) REVERT: E 53 ARG cc_start: 0.8452 (tpt90) cc_final: 0.8248 (tpt90) REVERT: E 65 LEU cc_start: 0.9193 (tt) cc_final: 0.8944 (tt) REVERT: E 68 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8145 (pp30) REVERT: E 76 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8716 (tm-30) REVERT: E 81 ASP cc_start: 0.8175 (m-30) cc_final: 0.7958 (m-30) REVERT: E 87 SER cc_start: 0.9278 (m) cc_final: 0.9074 (p) REVERT: E 97 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8190 (mt-10) REVERT: E 99 TYR cc_start: 0.9067 (t80) cc_final: 0.8776 (t80) REVERT: E 115 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8564 (mmmm) REVERT: E 122 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8299 (ptmt) outliers start: 51 outliers final: 41 residues processed: 386 average time/residue: 0.3581 time to fit residues: 179.2024 Evaluate side-chains 399 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 356 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 94 ASN G 73 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13814 Z= 0.236 Angle : 0.706 8.324 19943 Z= 0.391 Chirality : 0.038 0.221 2253 Planarity : 0.005 0.054 1485 Dihedral : 29.640 149.132 4241 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 6.03 % Allowed : 36.61 % Favored : 57.36 % 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: 0.40 (0.28), residues: 831 helix: 0.89 (0.22), residues: 529 sheet: -2.61 (1.17), residues: 20 loop : -0.58 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.002 0.001 HIS G 82 PHE 0.026 0.002 PHE B 61 TYR 0.046 0.002 TYR D 80 ARG 0.007 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 366 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8793 (m110) cc_final: 0.8272 (m-40) REVERT: B 31 LYS cc_start: 0.9022 (tptp) cc_final: 0.8821 (tptp) REVERT: B 63 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 73 THR cc_start: 0.9434 (t) cc_final: 0.9215 (t) REVERT: C 20 ARG cc_start: 0.8336 (mmt-90) cc_final: 0.7973 (mmt-90) REVERT: C 32 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7045 (tmm-80) REVERT: C 57 TYR cc_start: 0.8463 (t80) cc_final: 0.8097 (t80) REVERT: C 73 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8615 (t0) REVERT: C 84 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8872 (tp-100) REVERT: D 39 TYR cc_start: 0.7740 (t80) cc_final: 0.7128 (t80) REVERT: D 43 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8672 (tppt) REVERT: D 64 ASN cc_start: 0.8690 (m-40) cc_final: 0.8234 (m110) REVERT: D 92 GLN cc_start: 0.7628 (pp30) cc_final: 0.7363 (pp30) REVERT: D 105 LYS cc_start: 0.7809 (tptp) cc_final: 0.7588 (tptp) REVERT: F 31 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8224 (tppp) REVERT: F 63 GLU cc_start: 0.7810 (pp20) cc_final: 0.7309 (pp20) REVERT: F 88 TYR cc_start: 0.9153 (m-10) cc_final: 0.8565 (m-80) REVERT: G 61 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7872 (mm-30) REVERT: G 78 ILE cc_start: 0.9037 (mt) cc_final: 0.8661 (mm) REVERT: G 81 ARG cc_start: 0.8856 (tpt90) cc_final: 0.8551 (tpt90) REVERT: G 84 GLN cc_start: 0.9320 (tp-100) cc_final: 0.8951 (tp-100) REVERT: G 89 ASN cc_start: 0.8156 (m-40) cc_final: 0.7940 (m-40) REVERT: H 40 LYS cc_start: 0.9313 (tppt) cc_final: 0.8789 (tptp) REVERT: H 49 THR cc_start: 0.9177 (p) cc_final: 0.8945 (p) REVERT: H 92 GLN cc_start: 0.8712 (tt0) cc_final: 0.8431 (tt0) REVERT: H 113 LYS cc_start: 0.8807 (ptpt) cc_final: 0.8361 (ptpp) REVERT: A 49 ARG cc_start: 0.8529 (ttm110) cc_final: 0.8193 (mtp-110) REVERT: A 79 LYS cc_start: 0.9146 (tptp) cc_final: 0.8927 (tptp) REVERT: E 67 PHE cc_start: 0.8681 (t80) cc_final: 0.8012 (t80) REVERT: E 76 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8751 (tm-30) REVERT: E 81 ASP cc_start: 0.8213 (m-30) cc_final: 0.7976 (t0) REVERT: E 87 SER cc_start: 0.9210 (m) cc_final: 0.9005 (p) REVERT: E 99 TYR cc_start: 0.9035 (t80) cc_final: 0.8686 (t80) REVERT: E 120 MET cc_start: 0.7646 (mmm) cc_final: 0.7399 (mmm) outliers start: 43 outliers final: 37 residues processed: 385 average time/residue: 0.3449 time to fit residues: 171.9987 Evaluate side-chains 387 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 348 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 90 optimal weight: 0.0010 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.7448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13814 Z= 0.235 Angle : 0.725 12.655 19943 Z= 0.397 Chirality : 0.037 0.217 2253 Planarity : 0.005 0.053 1485 Dihedral : 29.616 148.654 4241 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 5.19 % Allowed : 39.27 % Favored : 55.54 % 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: 0.32 (0.28), residues: 831 helix: 0.81 (0.23), residues: 530 sheet: -2.51 (1.18), residues: 20 loop : -0.57 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS C 31 PHE 0.025 0.001 PHE B 61 TYR 0.041 0.002 TYR F 51 ARG 0.010 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 365 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8647 (m110) cc_final: 0.8265 (m-40) REVERT: B 39 ARG cc_start: 0.8929 (mmt90) cc_final: 0.8547 (mmt90) REVERT: B 44 LYS cc_start: 0.9345 (tttt) cc_final: 0.8845 (mttt) REVERT: B 73 THR cc_start: 0.9390 (t) cc_final: 0.9165 (t) REVERT: B 84 MET cc_start: 0.7671 (mpp) cc_final: 0.6791 (pmm) REVERT: B 95 ARG cc_start: 0.7245 (mmm-85) cc_final: 0.6999 (mmm-85) REVERT: C 20 ARG cc_start: 0.8280 (mmt-90) cc_final: 0.7932 (mmt-90) REVERT: C 25 PHE cc_start: 0.8127 (m-10) cc_final: 0.7815 (m-10) REVERT: C 32 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6708 (tmm-80) REVERT: C 35 ARG cc_start: 0.7976 (tpp80) cc_final: 0.7729 (tpm170) REVERT: C 57 TYR cc_start: 0.8466 (t80) cc_final: 0.7933 (t80) REVERT: C 115 LEU cc_start: 0.8386 (mp) cc_final: 0.7778 (tp) REVERT: D 39 TYR cc_start: 0.7573 (t80) cc_final: 0.7072 (t80) REVERT: D 43 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8769 (tppt) REVERT: D 64 ASN cc_start: 0.8728 (m-40) cc_final: 0.8233 (m110) REVERT: D 92 GLN cc_start: 0.7619 (pp30) cc_final: 0.7302 (pp30) REVERT: D 105 LYS cc_start: 0.7768 (tptp) cc_final: 0.7551 (tptp) REVERT: F 44 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8407 (mttp) REVERT: F 63 GLU cc_start: 0.7815 (pp20) cc_final: 0.7372 (pp20) REVERT: F 88 TYR cc_start: 0.9087 (m-10) cc_final: 0.8521 (m-80) REVERT: G 38 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.7608 (t0) REVERT: G 61 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7821 (mm-30) REVERT: G 78 ILE cc_start: 0.9034 (mt) cc_final: 0.8724 (mm) REVERT: G 81 ARG cc_start: 0.8966 (tpt90) cc_final: 0.8658 (tpt90) REVERT: G 84 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8891 (tp-100) REVERT: G 95 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8615 (ptpp) REVERT: H 40 LYS cc_start: 0.9228 (tppt) cc_final: 0.8384 (tptp) REVERT: H 49 THR cc_start: 0.9052 (p) cc_final: 0.8365 (m) REVERT: A 41 TYR cc_start: 0.8934 (m-80) cc_final: 0.8642 (m-80) REVERT: A 49 ARG cc_start: 0.8529 (ttm110) cc_final: 0.8176 (mtp-110) REVERT: A 79 LYS cc_start: 0.9124 (tptp) cc_final: 0.8906 (tptp) REVERT: E 67 PHE cc_start: 0.8626 (t80) cc_final: 0.8017 (t80) REVERT: E 68 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7938 (pp30) REVERT: E 76 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8746 (tm-30) REVERT: E 99 TYR cc_start: 0.8994 (t80) cc_final: 0.8637 (t80) REVERT: E 120 MET cc_start: 0.7638 (mmm) cc_final: 0.7221 (mmm) outliers start: 37 outliers final: 30 residues processed: 380 average time/residue: 0.3436 time to fit residues: 169.4779 Evaluate side-chains 386 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 354 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13814 Z= 0.299 Angle : 0.760 13.199 19943 Z= 0.417 Chirality : 0.039 0.208 2253 Planarity : 0.006 0.059 1485 Dihedral : 29.690 148.117 4241 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.77 % Allowed : 41.09 % Favored : 54.14 % 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: 0.05 (0.28), residues: 831 helix: 0.58 (0.22), residues: 529 sheet: -2.34 (1.17), residues: 20 loop : -0.66 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.004 0.001 HIS F 75 PHE 0.024 0.002 PHE B 61 TYR 0.073 0.003 TYR B 88 ARG 0.017 0.001 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 354 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8811 (m110) cc_final: 0.8296 (m-40) REVERT: B 44 LYS cc_start: 0.9368 (tttt) cc_final: 0.8811 (mttt) REVERT: B 55 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8078 (mtm-85) REVERT: B 63 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7835 (mt-10) REVERT: B 73 THR cc_start: 0.9404 (t) cc_final: 0.9169 (t) REVERT: C 20 ARG cc_start: 0.8195 (mmt-90) cc_final: 0.7771 (mmt-90) REVERT: C 32 ARG cc_start: 0.7241 (ttp80) cc_final: 0.7021 (tmm-80) REVERT: C 57 TYR cc_start: 0.8464 (t80) cc_final: 0.8117 (t80) REVERT: C 75 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8170 (mmmt) REVERT: D 39 TYR cc_start: 0.7732 (t80) cc_final: 0.7193 (t80) REVERT: D 43 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8772 (tppt) REVERT: D 64 ASN cc_start: 0.8819 (m-40) cc_final: 0.8395 (m110) REVERT: D 83 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.7031 (mmm-85) REVERT: D 92 GLN cc_start: 0.7629 (pp30) cc_final: 0.7380 (pp30) REVERT: F 63 GLU cc_start: 0.7911 (pp20) cc_final: 0.7393 (pp20) REVERT: F 88 TYR cc_start: 0.9184 (m-10) cc_final: 0.8512 (m-80) REVERT: G 38 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.7588 (t0) REVERT: G 61 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8013 (mm-30) REVERT: G 78 ILE cc_start: 0.9094 (mt) cc_final: 0.8725 (mm) REVERT: G 81 ARG cc_start: 0.8880 (tpt90) cc_final: 0.8594 (tpt90) REVERT: G 84 GLN cc_start: 0.9294 (tp-100) cc_final: 0.8964 (tp-100) REVERT: H 40 LYS cc_start: 0.9096 (tppt) cc_final: 0.8488 (tptp) REVERT: H 92 GLN cc_start: 0.8803 (tt0) cc_final: 0.8515 (tt0) REVERT: A 49 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8224 (mtp-110) REVERT: A 56 LYS cc_start: 0.8121 (pttm) cc_final: 0.7519 (ptpp) REVERT: A 79 LYS cc_start: 0.9114 (tptp) cc_final: 0.8898 (tptp) REVERT: A 99 TYR cc_start: 0.8247 (t80) cc_final: 0.7980 (t80) REVERT: A 129 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.7543 (tpt90) REVERT: E 68 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7982 (pp30) REVERT: E 76 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9004 (tm-30) REVERT: E 99 TYR cc_start: 0.9079 (t80) cc_final: 0.8729 (t80) REVERT: E 120 MET cc_start: 0.7603 (mmm) cc_final: 0.7236 (mmm) REVERT: E 122 LYS cc_start: 0.8682 (ptmt) cc_final: 0.8449 (ptmt) outliers start: 34 outliers final: 30 residues processed: 370 average time/residue: 0.3391 time to fit residues: 162.7801 Evaluate side-chains 378 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 347 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** 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 = 0.4005 r_free = 0.4005 target = 0.138760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096337 restraints weight = 31103.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099402 restraints weight = 17821.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.101416 restraints weight = 12527.174| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 13814 Z= 0.260 Angle : 0.752 13.580 19943 Z= 0.414 Chirality : 0.038 0.207 2253 Planarity : 0.006 0.059 1485 Dihedral : 29.693 147.894 4241 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.91 % Allowed : 41.80 % Favored : 53.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.28), residues: 831 helix: 0.56 (0.22), residues: 526 sheet: -2.38 (1.15), residues: 20 loop : -0.66 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.003 0.001 HIS F 75 PHE 0.026 0.002 PHE A 67 TYR 0.073 0.003 TYR B 88 ARG 0.013 0.001 ARG E 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.69 seconds wall clock time: 60 minutes 59.58 seconds (3659.58 seconds total)