Starting phenix.real_space_refine on Wed Jul 30 20:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s01_10069/07_2025/6s01_10069.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s01_10069/07_2025/6s01_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/cci-nas-00/data/ceres_data/6s01_10069/07_2025/6s01_10069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s01_10069/07_2025/6s01_10069.map" model { file = "/net/cci-nas-00/data/ceres_data/6s01_10069/07_2025/6s01_10069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s01_10069/07_2025/6s01_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-5711/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: 7.59, per 1000 atoms: 0.59 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: 3.26 Conformation dependent library (CDL) restraints added in 934.8 milliseconds 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: 6.54 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: 4.87 Time building geometry restraints manager: 3.86 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: 1.150 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.320 Find NCS groups from input model: 0.290 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- 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= 0.367 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 Details of bonding type rmsd hydrogen bonds : bond 0.31408 ( 658) hydrogen bonds : angle 10.64414 ( 1637) covalent geometry : bond 0.00831 (13814) covalent geometry : angle 0.72269 (19943) *********************** 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 to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 1.033 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: 0.3851 time to fit residues: 103.5013 Evaluate side-chains 163 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105189 restraints weight = 20259.613| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.02 r_work: 0.3228 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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= 0.157 Angle : 0.579 5.504 19943 Z= 0.352 Chirality : 0.035 0.139 2253 Planarity : 0.005 0.056 1485 Dihedral : 29.793 157.346 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 Details of bonding type rmsd hydrogen bonds : bond 0.05838 ( 658) hydrogen bonds : angle 3.20918 ( 1637) covalent geometry : bond 0.00334 (13814) covalent geometry : angle 0.57878 (19943) *********************** 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 to be fit. rotamer outliers: 9 poor density : 171 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8081 (mtp) cc_final: 0.7856 (mtm) REVERT: A 123 ASP cc_start: 0.8852 (m-30) cc_final: 0.8593 (m-30) REVERT: A 131 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8283 (mtm180) REVERT: C 113 SER cc_start: 0.8465 (m) cc_final: 0.8142 (t) REVERT: E 94 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8135 (mm-30) REVERT: E 133 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6622 (mt-10) REVERT: F 59 LYS cc_start: 0.8953 (tppp) cc_final: 0.8653 (ttmm) REVERT: F 63 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7826 (mt-10) REVERT: H 56 MET cc_start: 0.8896 (tpp) cc_final: 0.8447 (tpt) REVERT: H 82 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8409 (mttp) REVERT: K 40 LEU cc_start: 0.5459 (OUTLIER) cc_final: 0.4963 (mm) REVERT: K 87 ASN cc_start: 0.7333 (t0) cc_final: 0.6930 (p0) outliers start: 9 outliers final: 3 residues processed: 174 average time/residue: 0.3624 time to fit residues: 82.4785 Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 85 THR 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 4 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.137807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104276 restraints weight = 20248.781| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.02 r_work: 0.3204 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13814 Z= 0.178 Angle : 0.558 6.843 19943 Z= 0.336 Chirality : 0.035 0.135 2253 Planarity : 0.004 0.049 1485 Dihedral : 29.887 152.758 4235 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.24 % Allowed : 10.80 % Favored : 86.96 % 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: -0.83 (0.28), residues: 831 helix: -0.00 (0.22), residues: 543 sheet: -3.36 (1.02), residues: 17 loop : -1.28 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 82 HIS 0.009 0.001 HIS K 20 PHE 0.017 0.002 PHE K 59 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG B 36 Details of bonding type rmsd hydrogen bonds : bond 0.05361 ( 658) hydrogen bonds : angle 2.88521 ( 1637) covalent geometry : bond 0.00396 (13814) covalent geometry : angle 0.55788 (19943) *********************** 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 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.992 Fit side-chains REVERT: A 123 ASP cc_start: 0.8898 (m-30) cc_final: 0.8642 (m-30) REVERT: A 131 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8505 (mtt90) REVERT: E 133 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6682 (mt-10) REVERT: F 63 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7853 (mt-10) REVERT: H 105 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8431 (mmtt) REVERT: K 40 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5494 (mm) REVERT: K 87 ASN cc_start: 0.7289 (t0) cc_final: 0.6894 (p0) outliers start: 16 outliers final: 14 residues processed: 154 average time/residue: 0.3069 time to fit residues: 63.9947 Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 19 ARG 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 29 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.101019 restraints weight = 20162.938| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.02 r_work: 0.3147 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13814 Z= 0.325 Angle : 0.662 10.127 19943 Z= 0.383 Chirality : 0.042 0.146 2253 Planarity : 0.005 0.045 1485 Dihedral : 30.376 149.408 4235 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.66 % Allowed : 13.60 % Favored : 83.73 % 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: -0.63 (0.28), residues: 831 helix: 0.20 (0.22), residues: 537 sheet: -3.13 (1.08), residues: 17 loop : -1.30 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP K 82 HIS 0.006 0.001 HIS K 20 PHE 0.016 0.002 PHE C 25 TYR 0.014 0.002 TYR B 51 ARG 0.007 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.06087 ( 658) hydrogen bonds : angle 3.16886 ( 1637) covalent geometry : bond 0.00746 (13814) covalent geometry : angle 0.66189 (19943) *********************** 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 162 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.636 Fit side-chains REVERT: A 39 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7002 (t70) REVERT: A 123 ASP cc_start: 0.8902 (m-30) cc_final: 0.8616 (m-30) REVERT: E 56 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8729 (ttmm) REVERT: E 133 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7110 (mt-10) REVERT: F 63 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7860 (mt-10) REVERT: H 105 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8408 (mmtt) REVERT: H 109 SER cc_start: 0.8776 (t) cc_final: 0.8557 (p) REVERT: K 87 ASN cc_start: 0.7525 (t0) cc_final: 0.7008 (p0) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 0.3726 time to fit residues: 76.8659 Evaluate side-chains 157 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 86 SER 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 110 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 44 optimal weight: 0.0070 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 44 GLN D 81 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.103476 restraints weight = 20134.467| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 0.97 r_work: 0.3197 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13814 Z= 0.150 Angle : 0.564 7.132 19943 Z= 0.340 Chirality : 0.036 0.153 2253 Planarity : 0.004 0.048 1485 Dihedral : 30.295 151.065 4233 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 15.57 % 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: 0.13 (0.29), residues: 831 helix: 0.80 (0.23), residues: 539 sheet: -3.11 (1.08), residues: 17 loop : -1.02 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.012 0.001 PHE K 45 TYR 0.011 0.001 TYR B 51 ARG 0.003 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 658) hydrogen bonds : angle 2.83936 ( 1637) covalent geometry : bond 0.00324 (13814) covalent geometry : angle 0.56355 (19943) *********************** 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 161 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.091 Fit side-chains REVERT: A 123 ASP cc_start: 0.8894 (m-30) cc_final: 0.8599 (m-30) REVERT: E 56 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8707 (ttmm) REVERT: E 133 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6936 (mt-10) REVERT: F 63 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7855 (mt-10) REVERT: H 105 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8467 (mmtt) REVERT: K 87 ASN cc_start: 0.7492 (t0) cc_final: 0.7004 (p0) outliers start: 14 outliers final: 9 residues processed: 155 average time/residue: 0.3106 time to fit residues: 65.6121 Evaluate side-chains 146 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107156 restraints weight = 20332.693| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.00 r_work: 0.3243 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3208 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= 0.147 Angle : 0.528 5.907 19943 Z= 0.320 Chirality : 0.034 0.152 2253 Planarity : 0.004 0.048 1485 Dihedral : 29.836 146.028 4233 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.24 % Allowed : 15.85 % 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: 0.84 (0.30), residues: 831 helix: 1.28 (0.23), residues: 545 sheet: -3.02 (1.06), residues: 17 loop : -0.61 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP K 82 HIS 0.002 0.001 HIS F 75 PHE 0.011 0.001 PHE K 45 TYR 0.008 0.001 TYR B 51 ARG 0.002 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 658) hydrogen bonds : angle 2.59596 ( 1637) covalent geometry : bond 0.00319 (13814) covalent geometry : angle 0.52757 (19943) *********************** 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 164 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.103 Fit side-chains REVERT: A 39 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7263 (t-90) REVERT: A 123 ASP cc_start: 0.8871 (m-30) cc_final: 0.8609 (m-30) REVERT: D 117 LYS cc_start: 0.8815 (tttm) cc_final: 0.8607 (tttp) REVERT: E 56 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8674 (ttmm) REVERT: E 133 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6800 (mt-10) REVERT: F 63 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7811 (mt-10) REVERT: H 105 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8304 (mmtt) REVERT: K 87 ASN cc_start: 0.7459 (t0) cc_final: 0.7099 (p0) outliers start: 16 outliers final: 11 residues processed: 157 average time/residue: 0.3236 time to fit residues: 69.7862 Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.444 ------------------------------------------------------------------------------- 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 E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 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 46 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102030 restraints weight = 20214.082| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 0.98 r_work: 0.3176 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3068 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= 0.227 Angle : 0.586 7.029 19943 Z= 0.346 Chirality : 0.037 0.155 2253 Planarity : 0.004 0.048 1485 Dihedral : 30.111 144.426 4233 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.24 % Allowed : 16.83 % Favored : 80.93 % 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: 0.58 (0.29), residues: 831 helix: 1.11 (0.23), residues: 542 sheet: -2.76 (1.10), residues: 17 loop : -0.78 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP K 82 HIS 0.004 0.001 HIS K 20 PHE 0.011 0.002 PHE C 25 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.05222 ( 658) hydrogen bonds : angle 2.83701 ( 1637) covalent geometry : bond 0.00515 (13814) covalent geometry : angle 0.58600 (19943) *********************** 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 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.964 Fit side-chains REVERT: A 123 ASP cc_start: 0.8874 (m-30) cc_final: 0.8587 (m-30) REVERT: E 56 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8727 (ttmm) REVERT: E 133 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6998 (mt-10) REVERT: F 63 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7886 (mt-10) REVERT: H 44 GLN cc_start: 0.8779 (mt0) cc_final: 0.8565 (mt0) REVERT: H 105 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8342 (mmtt) REVERT: K 87 ASN cc_start: 0.7705 (t0) cc_final: 0.6923 (p0) outliers start: 16 outliers final: 13 residues processed: 153 average time/residue: 0.3467 time to fit residues: 72.9548 Evaluate side-chains 153 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 86 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 110 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.135260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100631 restraints weight = 20381.202| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 0.98 r_work: 0.3153 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13814 Z= 0.270 Angle : 0.627 11.090 19943 Z= 0.365 Chirality : 0.039 0.161 2253 Planarity : 0.005 0.048 1485 Dihedral : 30.431 142.729 4233 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 16.55 % Favored : 80.65 % 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: 0.34 (0.29), residues: 831 helix: 0.89 (0.23), residues: 539 sheet: -3.20 (1.99), residues: 6 loop : -0.88 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP K 82 HIS 0.004 0.001 HIS K 20 PHE 0.014 0.002 PHE C 25 TYR 0.011 0.002 TYR F 51 ARG 0.006 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.05541 ( 658) hydrogen bonds : angle 2.98370 ( 1637) covalent geometry : bond 0.00617 (13814) covalent geometry : angle 0.62739 (19943) *********************** 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 168 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.104 Fit side-chains REVERT: A 76 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: A 123 ASP cc_start: 0.8881 (m-30) cc_final: 0.8586 (m-30) REVERT: B 92 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7654 (ttp80) REVERT: E 56 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8709 (ttmm) REVERT: E 133 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7249 (mt-10) REVERT: F 63 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7857 (mt-10) REVERT: H 44 GLN cc_start: 0.8827 (mt0) cc_final: 0.8580 (mt0) REVERT: H 105 LYS cc_start: 0.8894 (mtpp) cc_final: 0.8356 (mmtt) REVERT: K 87 ASN cc_start: 0.7665 (t0) cc_final: 0.6920 (p0) outliers start: 20 outliers final: 16 residues processed: 157 average time/residue: 0.3842 time to fit residues: 81.0506 Evaluate side-chains 163 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG 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 120 MET Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 86 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102109 restraints weight = 20091.915| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.98 r_work: 0.3176 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13814 Z= 0.173 Angle : 0.581 12.159 19943 Z= 0.346 Chirality : 0.036 0.175 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.401 143.788 4233 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.66 % Allowed : 16.83 % Favored : 80.50 % 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: 0.62 (0.29), residues: 831 helix: 1.11 (0.23), residues: 539 sheet: -2.55 (1.20), residues: 17 loop : -0.67 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP K 82 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.002 PHE K 45 TYR 0.010 0.001 TYR B 51 ARG 0.005 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 658) hydrogen bonds : angle 2.86229 ( 1637) covalent geometry : bond 0.00385 (13814) covalent geometry : angle 0.58114 (19943) *********************** 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 168 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.190 Fit side-chains REVERT: A 76 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7796 (mt0) REVERT: A 123 ASP cc_start: 0.8872 (m-30) cc_final: 0.8582 (m-30) REVERT: E 56 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8702 (ttmm) REVERT: E 133 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7097 (mt-10) REVERT: F 63 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7837 (mt-10) REVERT: H 105 LYS cc_start: 0.8865 (mtpp) cc_final: 0.8344 (mmtt) REVERT: K 87 ASN cc_start: 0.7651 (t0) cc_final: 0.6912 (p0) outliers start: 19 outliers final: 14 residues processed: 157 average time/residue: 0.5102 time to fit residues: 108.2862 Evaluate side-chains 160 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN 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 E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.136129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101476 restraints weight = 20093.194| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.98 r_work: 0.3167 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3195 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= 0.229 Angle : 0.597 12.253 19943 Z= 0.350 Chirality : 0.037 0.163 2253 Planarity : 0.004 0.049 1485 Dihedral : 30.312 142.402 4233 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.24 % Allowed : 17.67 % Favored : 80.08 % 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: 0.59 (0.29), residues: 831 helix: 1.07 (0.23), residues: 540 sheet: -2.44 (1.23), residues: 17 loop : -0.67 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.005 TRP K 82 HIS 0.003 0.001 HIS K 20 PHE 0.011 0.002 PHE C 25 TYR 0.010 0.001 TYR F 51 ARG 0.004 0.001 ARG E 116 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 658) hydrogen bonds : angle 2.88001 ( 1637) covalent geometry : bond 0.00521 (13814) covalent geometry : angle 0.59674 (19943) ********************** 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 162 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.088 Fit side-chains REVERT: A 76 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: A 123 ASP cc_start: 0.8883 (m-30) cc_final: 0.8594 (m-30) REVERT: B 92 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7688 (ttp80) REVERT: E 56 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8706 (ttmm) REVERT: E 133 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7196 (mt-10) REVERT: F 63 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7843 (mt-10) REVERT: H 105 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8359 (mmtt) REVERT: K 87 ASN cc_start: 0.7680 (t0) cc_final: 0.6930 (p0) outliers start: 16 outliers final: 13 residues processed: 154 average time/residue: 0.4312 time to fit residues: 89.2771 Evaluate side-chains 159 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG 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 E residue 73 GLU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 86 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.137461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102950 restraints weight = 20105.844| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 0.98 r_work: 0.3189 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13814 Z= 0.153 Angle : 0.570 12.055 19943 Z= 0.340 Chirality : 0.035 0.181 2253 Planarity : 0.004 0.050 1485 Dihedral : 30.306 143.235 4233 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.96 % Allowed : 18.37 % Favored : 79.66 % 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: 0.82 (0.29), residues: 831 helix: 1.26 (0.23), residues: 545 sheet: -2.52 (1.21), residues: 17 loop : -0.64 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP K 82 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE K 45 TYR 0.010 0.001 TYR B 51 ARG 0.003 0.000 ARG G 77 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 658) hydrogen bonds : angle 2.79603 ( 1637) covalent geometry : bond 0.00336 (13814) covalent geometry : angle 0.56990 (19943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7239.96 seconds wall clock time: 132 minutes 20.60 seconds (7940.60 seconds total)