Starting phenix.real_space_refine on Thu Sep 26 09:14:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/09_2024/6s01_10069.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/09_2024/6s01_10069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/09_2024/6s01_10069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/09_2024/6s01_10069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/09_2024/6s01_10069.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s01_10069/09_2024/6s01_10069.cif" } resolution = 3.2 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= 0.007 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. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12959 Number of models: 1 Model: "" Number of chains: 11 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: "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: "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} 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 Time building chain proxies: 7.01, per 1000 atoms: 0.54 Number of scatterers: 12959 At special positions: 0 Unit cell: (90.3, 120.75, 135.45, 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 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 'A' and resid 44 through 55 removed outlier: 3.689A 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: 3.554A 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 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.521A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.789A 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: 3.632A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.647A 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: 3.542A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.586A 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: 3.552A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.734A 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: 3.713A 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: 3.543A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.621A 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 helix chain 'F' and resid 24 through 29 removed outlier: 3.766A 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: 3.943A 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: 3.748A 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: 3.655A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.516A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.515A 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: 3.586A 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: 3.734A 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: 3.542A 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: 3.523A 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: 5.137A 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 sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.021A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.435A 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: 7.173A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.996A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.144A 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: 4.21 Time building geometry restraints manager: 3.16 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: 2251 1.33 - 1.45: 4697 1.45 - 1.57: 6242 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 1.756 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.762 0.055 2.00e-02 2.50e+03 7.53e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.498 -0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.99e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 18956 1.59 - 3.19: 921 3.19 - 4.78: 47 4.78 - 6.37: 12 6.37 - 7.97: 7 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 120.20 125.90 -5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.12 -5.51 1.56e+00 4.11e-01 1.25e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.04 -4.84 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 120.20 124.93 -4.73 1.50e+00 4.44e-01 9.96e+00 angle pdb=" CA GLU K 63 " pdb=" CB GLU K 63 " pdb=" CG GLU K 63 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.66e+00 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6150 34.28 - 68.56: 1377 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.40: 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 180.00 160.07 19.93 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 48.60 171.40 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 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1250 0.035 - 0.071: 810 0.071 - 0.106: 147 0.106 - 0.142: 38 0.142 - 0.177: 8 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 7.83e-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 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-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 6.87e-02 7.55e+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 6.70e-02 7.19e+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: 3130 2.81 - 3.33: 10159 3.33 - 3.85: 23914 3.85 - 4.38: 31356 4.38 - 4.90: 43625 Nonbonded interactions: 112184 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 3.040 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.331 3.120 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 3.120 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.361 3.120 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.364 3.120 ... (remaining 112179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.090 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.076 13814 Z= 0.470 Angle : 0.723 7.969 19943 Z= 0.427 Chirality : 0.044 0.177 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.197 171.395 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 G 31 PHE 0.013 0.002 PHE K 45 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 212 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7389 (mtp-110) REVERT: A 79 LYS cc_start: 0.8426 (tttm) cc_final: 0.7851 (tptp) REVERT: A 90 MET cc_start: 0.7852 (mmm) cc_final: 0.7324 (mmp) REVERT: A 120 MET cc_start: 0.7789 (mtp) cc_final: 0.7237 (mtp) REVERT: A 123 ASP cc_start: 0.8686 (m-30) cc_final: 0.8411 (m-30) REVERT: B 31 LYS cc_start: 0.8548 (tttt) cc_final: 0.8195 (ttmm) REVERT: B 59 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7857 (tttt) REVERT: B 63 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 84 MET cc_start: 0.8015 (mmt) cc_final: 0.7727 (mmp) REVERT: C 42 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7464 (mtp85) REVERT: C 61 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 113 SER cc_start: 0.8026 (m) cc_final: 0.7674 (t) REVERT: D 54 LYS cc_start: 0.8103 (tptp) cc_final: 0.7614 (tptp) REVERT: D 105 LYS cc_start: 0.8895 (mttt) cc_final: 0.8017 (tmmt) REVERT: E 42 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7407 (mmt-90) REVERT: E 56 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7477 (tptp) REVERT: E 64 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7661 (mmtm) REVERT: E 81 ASP cc_start: 0.7992 (m-30) cc_final: 0.7484 (t0) REVERT: E 94 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 105 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: F 31 LYS cc_start: 0.8631 (tttt) cc_final: 0.8401 (tttm) REVERT: F 63 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7735 (mt-10) REVERT: F 74 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7467 (tp30) REVERT: G 99 ARG cc_start: 0.7727 (mmt180) cc_final: 0.7498 (mmm160) REVERT: G 110 ASN cc_start: 0.8282 (t0) cc_final: 0.8035 (t0) REVERT: H 32 GLU cc_start: 0.8597 (pt0) cc_final: 0.8298 (pt0) REVERT: H 56 MET cc_start: 0.8759 (tpp) cc_final: 0.7899 (tpt) REVERT: H 65 ASP cc_start: 0.8179 (t70) cc_final: 0.7786 (t0) REVERT: H 69 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7844 (mtt180) REVERT: H 105 LYS cc_start: 0.8532 (mttt) cc_final: 0.8131 (mtpp) REVERT: H 109 SER cc_start: 0.8616 (t) cc_final: 0.8059 (p) REVERT: K 52 PHE cc_start: 0.7905 (m-80) cc_final: 0.7648 (m-80) REVERT: K 74 ARG cc_start: 0.4404 (mtt90) cc_final: 0.4158 (mtm110) outliers start: 13 outliers final: 6 residues processed: 206 average time/residue: 0.3517 time to fit residues: 94.4680 Evaluate side-chains 163 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 0.0270 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS B 75 HIS E 68 GLN E 76 GLN E 93 GLN F 25 ASN F 75 HIS ** K 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 ASN K 86 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13814 Z= 0.179 Angle : 0.579 5.503 19943 Z= 0.352 Chirality : 0.035 0.139 2253 Planarity : 0.005 0.056 1485 Dihedral : 29.793 157.343 4244 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.26 % Allowed : 11.64 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.64 (0.25), residues: 831 helix: -1.61 (0.19), residues: 540 sheet: -3.69 (1.00), residues: 17 loop : -1.51 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 82 HIS 0.007 0.001 HIS K 20 PHE 0.018 0.001 PHE K 45 TYR 0.019 0.001 TYR K 61 ARG 0.006 0.000 ARG C 71 *********************** 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 180 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7633 (mtp-110) cc_final: 0.7276 (mtp-110) REVERT: A 79 LYS cc_start: 0.8484 (tttm) cc_final: 0.7922 (tptp) REVERT: A 106 ASP cc_start: 0.7457 (m-30) cc_final: 0.7200 (m-30) REVERT: A 120 MET cc_start: 0.7438 (mtp) cc_final: 0.6817 (mtm) REVERT: A 123 ASP cc_start: 0.8684 (m-30) cc_final: 0.8207 (m-30) REVERT: A 131 ARG cc_start: 0.8058 (mtt180) cc_final: 0.7742 (mtm180) REVERT: B 31 LYS cc_start: 0.8230 (tttt) cc_final: 0.7860 (ttmm) REVERT: B 63 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7986 (mt-10) REVERT: C 42 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7444 (mtp85) REVERT: C 61 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6949 (mm-30) REVERT: C 92 GLU cc_start: 0.6962 (pm20) cc_final: 0.6717 (pm20) REVERT: C 113 SER cc_start: 0.8131 (m) cc_final: 0.7730 (t) REVERT: D 54 LYS cc_start: 0.7974 (tptp) cc_final: 0.7528 (tptp) REVERT: D 105 LYS cc_start: 0.8933 (mttt) cc_final: 0.8117 (tmmt) REVERT: D 116 THR cc_start: 0.8582 (OUTLIER) cc_final: 0.8352 (p) REVERT: E 42 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7473 (mpt180) REVERT: E 56 LYS cc_start: 0.8067 (mtpt) cc_final: 0.7500 (tptp) REVERT: E 64 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7447 (mmtm) REVERT: E 81 ASP cc_start: 0.8107 (m-30) cc_final: 0.7506 (t0) REVERT: E 94 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 120 MET cc_start: 0.7851 (mtp) cc_final: 0.7626 (mtp) REVERT: E 133 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6718 (mt-10) REVERT: F 63 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7519 (mt-10) REVERT: F 74 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7581 (tp30) REVERT: G 110 ASN cc_start: 0.8252 (t0) cc_final: 0.8046 (t0) REVERT: H 56 MET cc_start: 0.8453 (tpp) cc_final: 0.7903 (tpt) REVERT: H 65 ASP cc_start: 0.7932 (t70) cc_final: 0.7594 (t0) REVERT: H 82 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8048 (mttp) REVERT: H 105 LYS cc_start: 0.8544 (mttt) cc_final: 0.8168 (mtpp) REVERT: K 40 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.4912 (mm) REVERT: K 87 ASN cc_start: 0.7426 (t0) cc_final: 0.6950 (p0) outliers start: 9 outliers final: 3 residues processed: 174 average time/residue: 0.3516 time to fit residues: 79.7424 Evaluate side-chains 158 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 152 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain K residue 40 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13814 Z= 0.298 Angle : 0.599 8.326 19943 Z= 0.356 Chirality : 0.038 0.137 2253 Planarity : 0.005 0.048 1485 Dihedral : 30.038 153.368 4235 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.24 % Allowed : 11.78 % Favored : 85.97 % 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: -1.04 (0.28), residues: 831 helix: -0.15 (0.22), residues: 538 sheet: -3.33 (1.03), residues: 17 loop : -1.39 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.009 0.001 HIS K 20 PHE 0.018 0.002 PHE K 59 TYR 0.013 0.001 TYR B 51 ARG 0.005 0.001 ARG E 116 *********************** 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 167 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7324 (mtp-110) REVERT: A 79 LYS cc_start: 0.8385 (tttm) cc_final: 0.7915 (tptp) REVERT: A 120 MET cc_start: 0.7465 (mtp) cc_final: 0.6906 (mtt) REVERT: A 123 ASP cc_start: 0.8679 (m-30) cc_final: 0.8250 (m-30) REVERT: B 31 LYS cc_start: 0.8198 (tttt) cc_final: 0.7929 (ttmm) REVERT: B 63 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8070 (mt-10) REVERT: C 42 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7463 (mtp85) REVERT: C 61 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7089 (mm-30) REVERT: D 54 LYS cc_start: 0.7935 (tptp) cc_final: 0.7470 (tptp) REVERT: D 105 LYS cc_start: 0.9009 (mttt) cc_final: 0.8111 (tmmt) REVERT: E 42 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7401 (mmt-90) REVERT: E 56 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7599 (tptp) REVERT: E 59 GLU cc_start: 0.7834 (pm20) cc_final: 0.7584 (pm20) REVERT: E 64 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7538 (mmtm) REVERT: E 81 ASP cc_start: 0.8085 (m-30) cc_final: 0.7549 (t0) REVERT: E 133 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6826 (mt-10) REVERT: F 63 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7609 (mt-10) REVERT: F 74 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7482 (tp30) REVERT: H 56 MET cc_start: 0.8563 (tpp) cc_final: 0.7964 (tpt) REVERT: H 105 LYS cc_start: 0.8551 (mttt) cc_final: 0.7915 (mmtt) REVERT: K 40 LEU cc_start: 0.5744 (OUTLIER) cc_final: 0.5261 (mm) REVERT: K 87 ASN cc_start: 0.7477 (t0) cc_final: 0.6903 (p0) outliers start: 16 outliers final: 12 residues processed: 159 average time/residue: 0.3321 time to fit residues: 70.2593 Evaluate side-chains 155 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13814 Z= 0.278 Angle : 0.584 7.810 19943 Z= 0.348 Chirality : 0.037 0.131 2253 Planarity : 0.004 0.046 1485 Dihedral : 30.052 152.428 4235 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.24 % Allowed : 13.32 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.29), residues: 831 helix: 0.40 (0.23), residues: 538 sheet: -3.17 (1.05), residues: 17 loop : -1.19 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 21 HIS 0.006 0.001 HIS K 20 PHE 0.013 0.002 PHE K 59 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.000 ARG E 116 *********************** 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 163 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7312 (mtp-110) REVERT: A 79 LYS cc_start: 0.8410 (tttm) cc_final: 0.7958 (tptp) REVERT: A 120 MET cc_start: 0.7536 (mtp) cc_final: 0.6980 (mtt) REVERT: A 123 ASP cc_start: 0.8676 (m-30) cc_final: 0.8241 (m-30) REVERT: B 31 LYS cc_start: 0.8168 (tttt) cc_final: 0.7898 (ttmm) REVERT: B 63 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 42 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7441 (mtp85) REVERT: D 54 LYS cc_start: 0.7950 (tptp) cc_final: 0.7429 (tptp) REVERT: D 105 LYS cc_start: 0.9010 (mttt) cc_final: 0.8110 (tmmt) REVERT: E 42 ARG cc_start: 0.7760 (mtm180) cc_final: 0.7400 (mmt-90) REVERT: E 56 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7609 (tptp) REVERT: E 59 GLU cc_start: 0.7837 (pm20) cc_final: 0.7592 (pm20) REVERT: E 81 ASP cc_start: 0.8070 (m-30) cc_final: 0.7514 (t0) REVERT: E 115 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7485 (mmtp) REVERT: E 133 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6931 (mt-10) REVERT: F 63 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7589 (mt-10) REVERT: F 74 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7492 (tp30) REVERT: H 56 MET cc_start: 0.8555 (tpp) cc_final: 0.7952 (tpt) REVERT: H 105 LYS cc_start: 0.8549 (mttt) cc_final: 0.7968 (mmtt) REVERT: K 40 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5389 (mm) REVERT: K 87 ASN cc_start: 0.7523 (t0) cc_final: 0.6948 (p0) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.3302 time to fit residues: 68.8021 Evaluate side-chains 156 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13814 Z= 0.279 Angle : 0.580 8.046 19943 Z= 0.344 Chirality : 0.037 0.158 2253 Planarity : 0.004 0.046 1485 Dihedral : 30.162 147.619 4235 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.38 % Allowed : 13.60 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.29), residues: 831 helix: 0.74 (0.23), residues: 534 sheet: -3.00 (1.07), residues: 17 loop : -1.01 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.005 0.001 HIS K 20 PHE 0.011 0.002 PHE C 25 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.001 ARG E 116 *********************** 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 168 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6860 (t70) REVERT: A 42 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7273 (mtp-110) REVERT: A 79 LYS cc_start: 0.8316 (tttm) cc_final: 0.7526 (tppt) REVERT: A 120 MET cc_start: 0.7446 (mtp) cc_final: 0.6897 (mtm) REVERT: A 123 ASP cc_start: 0.8641 (m-30) cc_final: 0.8198 (m-30) REVERT: B 31 LYS cc_start: 0.8089 (tttt) cc_final: 0.7870 (ttmm) REVERT: C 42 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7330 (mtp85) REVERT: D 54 LYS cc_start: 0.7985 (tptp) cc_final: 0.7464 (tptp) REVERT: D 105 LYS cc_start: 0.8981 (mttt) cc_final: 0.8157 (ttpt) REVERT: E 42 ARG cc_start: 0.7647 (mtm180) cc_final: 0.7368 (mmt-90) REVERT: E 56 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7631 (tptp) REVERT: E 81 ASP cc_start: 0.7972 (m-30) cc_final: 0.7364 (t0) REVERT: E 94 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7471 (mm-30) REVERT: E 115 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7471 (mmtm) REVERT: E 133 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7024 (mt-10) REVERT: F 63 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7562 (mt-10) REVERT: F 74 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7272 (tp30) REVERT: H 56 MET cc_start: 0.8588 (tpp) cc_final: 0.7895 (tpt) REVERT: H 105 LYS cc_start: 0.8529 (mttt) cc_final: 0.7828 (mmtt) REVERT: H 109 SER cc_start: 0.8323 (t) cc_final: 0.7737 (p) outliers start: 17 outliers final: 14 residues processed: 160 average time/residue: 0.3167 time to fit residues: 67.7066 Evaluate side-chains 159 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN E 68 GLN ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13814 Z= 0.178 Angle : 0.550 9.246 19943 Z= 0.332 Chirality : 0.034 0.153 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.142 148.263 4233 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.66 % Allowed : 14.45 % Favored : 82.89 % 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: 0.48 (0.29), residues: 831 helix: 1.03 (0.23), residues: 539 sheet: -2.96 (1.08), residues: 17 loop : -0.78 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 21 HIS 0.005 0.001 HIS K 20 PHE 0.011 0.001 PHE K 45 TYR 0.009 0.001 TYR B 51 ARG 0.003 0.000 ARG K 74 *********************** 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 168 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.6859 (t70) REVERT: A 42 ARG cc_start: 0.7629 (mtp-110) cc_final: 0.7244 (mtp-110) REVERT: A 79 LYS cc_start: 0.8314 (tttm) cc_final: 0.7531 (tppt) REVERT: A 120 MET cc_start: 0.7427 (mtp) cc_final: 0.6891 (mtm) REVERT: A 123 ASP cc_start: 0.8628 (m-30) cc_final: 0.8203 (m-30) REVERT: B 31 LYS cc_start: 0.8182 (tttt) cc_final: 0.7957 (ttmm) REVERT: D 105 LYS cc_start: 0.8960 (mttt) cc_final: 0.8138 (ttpt) REVERT: E 42 ARG cc_start: 0.7639 (mtm180) cc_final: 0.7368 (mmt-90) REVERT: E 65 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7872 (mp) REVERT: E 68 GLN cc_start: 0.7831 (tt0) cc_final: 0.7555 (tt0) REVERT: E 81 ASP cc_start: 0.7949 (m-30) cc_final: 0.7336 (t0) REVERT: E 94 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7366 (mm-30) REVERT: E 115 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7448 (mmtm) REVERT: E 133 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6936 (mt-10) REVERT: F 63 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7523 (mt-10) REVERT: F 74 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7275 (tp30) REVERT: H 56 MET cc_start: 0.8505 (tpp) cc_final: 0.7887 (tpt) REVERT: H 105 LYS cc_start: 0.8506 (mttt) cc_final: 0.7813 (mmtt) REVERT: H 109 SER cc_start: 0.8335 (t) cc_final: 0.7744 (p) outliers start: 19 outliers final: 15 residues processed: 159 average time/residue: 0.3199 time to fit residues: 68.1646 Evaluate side-chains 161 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.0040 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 44 GLN D 81 ASN F 18 HIS ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13814 Z= 0.181 Angle : 0.546 6.366 19943 Z= 0.329 Chirality : 0.034 0.177 2253 Planarity : 0.004 0.048 1485 Dihedral : 30.083 147.629 4233 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.24 % Allowed : 14.87 % Favored : 82.89 % 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: 0.74 (0.29), residues: 831 helix: 1.19 (0.23), residues: 542 sheet: -2.85 (1.09), residues: 17 loop : -0.60 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 21 HIS 0.005 0.001 HIS K 20 PHE 0.012 0.001 PHE K 59 TYR 0.009 0.001 TYR B 51 ARG 0.008 0.000 ARG G 77 *********************** 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 164 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7539 (OUTLIER) cc_final: 0.6860 (t70) REVERT: A 42 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7232 (mtp-110) REVERT: A 79 LYS cc_start: 0.8317 (tttm) cc_final: 0.7530 (tppt) REVERT: A 120 MET cc_start: 0.7474 (mtp) cc_final: 0.6952 (mtm) REVERT: A 123 ASP cc_start: 0.8641 (m-30) cc_final: 0.8226 (m-30) REVERT: B 31 LYS cc_start: 0.8133 (tttt) cc_final: 0.7902 (ttmm) REVERT: D 105 LYS cc_start: 0.8942 (mttt) cc_final: 0.8128 (ttpt) REVERT: E 42 ARG cc_start: 0.7628 (mtm180) cc_final: 0.7365 (mmt-90) REVERT: E 65 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7872 (mp) REVERT: E 68 GLN cc_start: 0.7848 (tt0) cc_final: 0.7586 (tt0) REVERT: E 81 ASP cc_start: 0.7957 (m-30) cc_final: 0.7341 (t0) REVERT: E 94 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7382 (mm-30) REVERT: E 115 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7443 (mmtm) REVERT: E 133 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6914 (mt-10) REVERT: F 63 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7516 (mt-10) REVERT: F 74 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: H 56 MET cc_start: 0.8501 (tpp) cc_final: 0.7875 (tpt) REVERT: H 105 LYS cc_start: 0.8492 (mttt) cc_final: 0.7893 (mmtt) outliers start: 16 outliers final: 13 residues processed: 156 average time/residue: 0.3182 time to fit residues: 66.8172 Evaluate side-chains 160 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS D 44 GLN D 81 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13814 Z= 0.181 Angle : 0.534 5.964 19943 Z= 0.323 Chirality : 0.034 0.133 2253 Planarity : 0.004 0.049 1485 Dihedral : 29.925 145.911 4233 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 15.15 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.29), residues: 831 helix: 1.45 (0.23), residues: 545 sheet: -2.75 (1.11), residues: 17 loop : -0.40 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 21 HIS 0.003 0.001 HIS E 113 PHE 0.011 0.001 PHE K 59 TYR 0.008 0.001 TYR B 51 ARG 0.002 0.000 ARG C 71 *********************** 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 165 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7562 (mtp-110) cc_final: 0.7208 (mtp-110) REVERT: A 79 LYS cc_start: 0.8356 (tttm) cc_final: 0.7586 (tppt) REVERT: A 120 MET cc_start: 0.7530 (mtp) cc_final: 0.6973 (mtm) REVERT: A 123 ASP cc_start: 0.8626 (m-30) cc_final: 0.8171 (m-30) REVERT: B 31 LYS cc_start: 0.8139 (tttt) cc_final: 0.7804 (ttmm) REVERT: B 63 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7924 (mt-10) REVERT: C 92 GLU cc_start: 0.7342 (pm20) cc_final: 0.6997 (pm20) REVERT: D 105 LYS cc_start: 0.8908 (mttt) cc_final: 0.8096 (ttpt) REVERT: E 42 ARG cc_start: 0.7628 (mtm180) cc_final: 0.7360 (mmt-90) REVERT: E 57 SER cc_start: 0.8435 (m) cc_final: 0.7995 (p) REVERT: E 65 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7824 (mp) REVERT: E 68 GLN cc_start: 0.7814 (tt0) cc_final: 0.7568 (tt0) REVERT: E 81 ASP cc_start: 0.7966 (m-30) cc_final: 0.7369 (t0) REVERT: E 94 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7318 (mm-30) REVERT: E 115 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7443 (mmtm) REVERT: E 133 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7038 (mt-10) REVERT: F 63 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7586 (mt-10) REVERT: F 74 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: H 36 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8748 (pt) REVERT: H 56 MET cc_start: 0.8486 (tpp) cc_final: 0.7821 (tpt) REVERT: H 105 LYS cc_start: 0.8473 (mttt) cc_final: 0.7822 (mmtt) outliers start: 17 outliers final: 12 residues processed: 155 average time/residue: 0.3129 time to fit residues: 65.1419 Evaluate side-chains 159 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13814 Z= 0.271 Angle : 0.570 7.140 19943 Z= 0.338 Chirality : 0.036 0.160 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.055 144.387 4233 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.10 % Allowed : 15.85 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.29), residues: 831 helix: 1.29 (0.23), residues: 544 sheet: -2.56 (1.17), residues: 17 loop : -0.48 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 21 HIS 0.003 0.001 HIS K 20 PHE 0.011 0.002 PHE C 25 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.001 ARG E 116 *********************** 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 165 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7610 (mtp-110) cc_final: 0.7223 (mtp-110) REVERT: A 79 LYS cc_start: 0.8360 (tttm) cc_final: 0.7598 (tppt) REVERT: A 120 MET cc_start: 0.7562 (mtp) cc_final: 0.7004 (mtm) REVERT: A 123 ASP cc_start: 0.8626 (m-30) cc_final: 0.8194 (m-30) REVERT: B 31 LYS cc_start: 0.8194 (tttt) cc_final: 0.7916 (ttmm) REVERT: D 54 LYS cc_start: 0.7981 (tptp) cc_final: 0.7420 (tptp) REVERT: D 105 LYS cc_start: 0.8950 (mttt) cc_final: 0.8133 (ttpt) REVERT: D 117 LYS cc_start: 0.8457 (tttm) cc_final: 0.8255 (tttp) REVERT: E 42 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7363 (mmt-90) REVERT: E 64 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7587 (mmtm) REVERT: E 65 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7877 (mp) REVERT: E 81 ASP cc_start: 0.7999 (m-30) cc_final: 0.7388 (t0) REVERT: E 94 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7357 (mm-30) REVERT: E 115 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7461 (mmtm) REVERT: E 133 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7027 (mt-10) REVERT: F 63 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7558 (mt-10) REVERT: F 74 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7224 (tp30) REVERT: H 56 MET cc_start: 0.8550 (tpp) cc_final: 0.7800 (tpt) REVERT: H 105 LYS cc_start: 0.8497 (mttt) cc_final: 0.7881 (mmtt) REVERT: H 109 SER cc_start: 0.8294 (t) cc_final: 0.7896 (p) outliers start: 15 outliers final: 14 residues processed: 158 average time/residue: 0.3312 time to fit residues: 70.0037 Evaluate side-chains 162 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 50 THR 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: 9.9990 chunk 110 optimal weight: 0.0670 chunk 101 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3069 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= 0.163 Angle : 0.557 13.885 19943 Z= 0.332 Chirality : 0.034 0.177 2253 Planarity : 0.004 0.050 1485 Dihedral : 30.071 145.199 4233 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.10 % Allowed : 15.85 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.29), residues: 831 helix: 1.48 (0.23), residues: 542 sheet: -2.54 (1.17), residues: 17 loop : -0.37 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE K 45 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG B 36 ********************** 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 164 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7607 (mtp-110) cc_final: 0.7227 (mtp-110) REVERT: A 79 LYS cc_start: 0.8331 (tttm) cc_final: 0.7560 (tppt) REVERT: A 120 MET cc_start: 0.7544 (mtp) cc_final: 0.6997 (mtm) REVERT: A 123 ASP cc_start: 0.8586 (m-30) cc_final: 0.8114 (m-30) REVERT: B 31 LYS cc_start: 0.8179 (tttt) cc_final: 0.7905 (ttmm) REVERT: B 63 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7970 (mt-10) REVERT: D 105 LYS cc_start: 0.8930 (mttt) cc_final: 0.8081 (ttpt) REVERT: D 117 LYS cc_start: 0.8456 (tttm) cc_final: 0.8251 (tttp) REVERT: E 42 ARG cc_start: 0.7611 (mtm180) cc_final: 0.7361 (mmt-90) REVERT: E 65 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7859 (mp) REVERT: E 68 GLN cc_start: 0.7816 (tt0) cc_final: 0.7559 (tt0) REVERT: E 81 ASP cc_start: 0.7980 (m-30) cc_final: 0.7363 (t0) REVERT: E 94 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7325 (mm-30) REVERT: E 115 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7494 (mmtm) REVERT: E 133 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7024 (mt-10) REVERT: F 63 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7558 (mt-10) REVERT: F 74 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: H 56 MET cc_start: 0.8498 (tpp) cc_final: 0.7810 (tpt) REVERT: H 105 LYS cc_start: 0.8426 (mttt) cc_final: 0.7792 (mmtt) outliers start: 15 outliers final: 13 residues processed: 156 average time/residue: 0.3123 time to fit residues: 65.6323 Evaluate side-chains 161 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 50 THR 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: 3.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.103676 restraints weight = 20029.830| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 0.99 r_work: 0.3200 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13814 Z= 0.188 Angle : 0.549 12.217 19943 Z= 0.329 Chirality : 0.035 0.172 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.050 145.026 4233 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.10 % Allowed : 15.99 % Favored : 81.91 % 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: 1.15 (0.29), residues: 831 helix: 1.47 (0.23), residues: 543 sheet: -2.54 (1.17), residues: 17 loop : -0.36 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.009 0.001 PHE K 45 TYR 0.010 0.001 TYR B 51 ARG 0.002 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2513.11 seconds wall clock time: 45 minutes 22.30 seconds (2722.30 seconds total)