Starting phenix.real_space_refine on Sat Aug 23 21:49:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7i_38099/08_2025/8x7i_38099.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7i_38099/08_2025/8x7i_38099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2025/8x7i_38099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2025/8x7i_38099.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2025/8x7i_38099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7i_38099/08_2025/8x7i_38099.map" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1119 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 28 5.16 5 C 8076 2.51 5 N 2655 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14300 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 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: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1125 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 641 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 73} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 413 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 56} Chain breaks: 3 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13447 SG CYS L 31 56.643 71.877 28.876 1.00218.04 S ATOM 13589 SG CYS L 51 58.205 75.289 28.905 1.00210.14 S ATOM 13613 SG CYS L 54 54.564 75.086 28.068 1.00213.50 S ATOM 13338 SG CYS L 16 67.989 71.834 23.293 1.00283.03 S ATOM 13356 SG CYS L 19 71.632 71.909 22.328 1.00282.47 S ATOM 13486 SG CYS L 36 70.625 69.933 25.344 1.00253.66 S ATOM 13504 SG CYS L 39 70.429 73.629 25.607 1.00248.31 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 75 " occ=0.45 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.45 Time building chain proxies: 2.45, per 1000 atoms: 0.17 Number of scatterers: 14300 At special positions: 0 Unit cell: (118.14, 128.88, 112.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 294 15.00 O 3245 8.00 N 2655 7.00 C 8076 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: 1.09 Conformation dependent library (CDL) restraints added in 383.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 33 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 54 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 16 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 202 " - pdb=" SG CYS L 19 " Number of angles added : 9 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 13 sheets defined 62.3% alpha, 4.2% beta 143 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.594A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.816A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.627A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 3.667A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.548A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.523A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.514A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.587A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.512A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.548A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 2 through 16 Processing helix chain 'K' and resid 86 through 91 Processing helix chain 'K' and resid 98 through 112 Processing helix chain 'K' and resid 120 through 130 Processing helix chain 'K' and resid 130 through 145 Processing helix chain 'L' and resid 10 through 15 Processing helix chain 'L' and resid 36 through 47 removed outlier: 4.833A pdb=" N GLU L 45 " --> pdb=" O GLN L 41 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA L 47 " --> pdb=" O THR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 69 removed outlier: 3.757A pdb=" N ARG L 67 " --> pdb=" O ARG L 63 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG L 68 " --> pdb=" O TYR L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 84 Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.469A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 removed outlier: 6.817A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.062A 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: 7.292A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (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 32 through 38 Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 28 removed outlier: 3.552A pdb=" N LEU L 35 " --> pdb=" O VAL L 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 6 484 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 343 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.34 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: 3279 1.33 - 1.45: 4408 1.45 - 1.57: 6848 1.57 - 1.69: 586 1.69 - 1.81: 44 Bond restraints: 15165 Sorted by residual: bond pdb=" CA ILE C 79 " pdb=" CB ILE C 79 " ideal model delta sigma weight residual 1.546 1.534 0.012 8.80e-03 1.29e+04 2.01e+00 bond pdb=" CA ILE G 79 " pdb=" CB ILE G 79 " ideal model delta sigma weight residual 1.546 1.534 0.012 8.80e-03 1.29e+04 1.97e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.29e+00 bond pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " ideal model delta sigma weight residual 1.523 1.502 0.021 2.00e-02 2.50e+03 1.14e+00 ... (remaining 15160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 20960 1.44 - 2.88: 761 2.88 - 4.32: 45 4.32 - 5.76: 14 5.76 - 7.20: 1 Bond angle restraints: 21781 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.47 109.08 4.39 1.01e+00 9.80e-01 1.89e+01 angle pdb=" C PRO L 4 " pdb=" N LYS L 5 " pdb=" CA LYS L 5 " ideal model delta sigma weight residual 121.70 128.90 -7.20 1.80e+00 3.09e-01 1.60e+01 angle pdb=" N VAL L 58 " pdb=" CA VAL L 58 " pdb=" C VAL L 58 " ideal model delta sigma weight residual 113.20 109.66 3.54 9.60e-01 1.09e+00 1.36e+01 angle pdb=" N GLN C 24 " pdb=" CA GLN C 24 " pdb=" C GLN C 24 " ideal model delta sigma weight residual 114.04 109.54 4.50 1.24e+00 6.50e-01 1.32e+01 angle pdb=" C ASP K 59 " pdb=" N TYR K 60 " pdb=" CA TYR K 60 " ideal model delta sigma weight residual 120.39 124.50 -4.11 1.39e+00 5.18e-01 8.73e+00 ... (remaining 21776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 7056 35.16 - 70.32: 1302 70.32 - 105.48: 11 105.48 - 140.64: 1 140.64 - 175.80: 2 Dihedral angle restraints: 8372 sinusoidal: 5285 harmonic: 3087 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 44.20 175.80 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 58.69 161.31 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 84.74 135.26 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 8369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1584 0.032 - 0.064: 688 0.064 - 0.095: 164 0.095 - 0.127: 49 0.127 - 0.159: 4 Chirality restraints: 2489 Sorted by residual: chirality pdb=" CA PRO L 4 " pdb=" N PRO L 4 " pdb=" C PRO L 4 " pdb=" CB PRO L 4 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CA ILE M 36 " pdb=" N ILE M 36 " pdb=" C ILE M 36 " pdb=" CB ILE M 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" C3' DT I -59 " pdb=" C4' DT I -59 " pdb=" O3' DT I -59 " pdb=" C2' DT I -59 " both_signs ideal model delta sigma weight residual False -2.66 -2.53 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 2486 not shown) Planarity restraints: 1746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 3 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO L 4 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO L 4 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 4 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " 0.024 2.00e-02 2.50e+03 9.90e-03 2.69e+00 pdb=" N9 DA I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.024 2.00e-02 2.50e+03 9.41e-03 2.66e+00 pdb=" N9 DG I -35 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.003 2.00e-02 2.50e+03 ... (remaining 1743 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 425 2.65 - 3.22: 12761 3.22 - 3.78: 27171 3.78 - 4.34: 34185 4.34 - 4.90: 49782 Nonbonded interactions: 124324 Sorted by model distance: nonbonded pdb=" N2 DG I 51 " pdb=" O2 DC J -51 " model vdw 2.093 2.496 nonbonded pdb=" N2 DG I 46 " pdb=" O2 DC J -46 " model vdw 2.094 2.496 nonbonded pdb=" O2 DC I 52 " pdb=" N2 DG J -52 " model vdw 2.109 2.496 nonbonded pdb=" O2 DC I 40 " pdb=" N2 DG J -40 " model vdw 2.115 2.496 nonbonded pdb=" O2 DC I -52 " pdb=" N2 DG J 52 " model vdw 2.122 2.496 ... (remaining 124319 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' and (resid 19 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 14 or resid 16 through 118)) selection = (chain 'G' and (resid 10 through 14 or resid 16 through 118)) } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.690 Find NCS groups from input model: 0.120 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 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 : 0.006 0.046 15173 Z= 0.260 Angle : 0.606 7.198 21790 Z= 0.372 Chirality : 0.037 0.159 2489 Planarity : 0.004 0.053 1746 Dihedral : 25.488 175.796 6370 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 4.61 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.27), residues: 1033 helix: 1.99 (0.21), residues: 656 sheet: -0.84 (1.01), residues: 24 loop : -0.72 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 88 TYR 0.008 0.001 TYR B 51 PHE 0.011 0.001 PHE E 67 TRP 0.010 0.002 TRP K 93 HIS 0.003 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00563 (15165) covalent geometry : angle 0.60310 (21781) hydrogen bonds : bond 0.13883 ( 827) hydrogen bonds : angle 4.47578 ( 2029) metal coordination : bond 0.00525 ( 8) metal coordination : angle 2.98548 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 273 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 38 ASN cc_start: 0.8754 (m-40) cc_final: 0.7563 (m-40) REVERT: C 68 ASN cc_start: 0.8990 (m-40) cc_final: 0.8672 (m-40) REVERT: E 73 GLU cc_start: 0.8063 (tt0) cc_final: 0.7672 (tt0) REVERT: E 94 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 115 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8944 (mppt) REVERT: F 88 TYR cc_start: 0.8862 (m-10) cc_final: 0.6969 (m-10) REVERT: F 91 LYS cc_start: 0.9298 (ttmt) cc_final: 0.8971 (ttpt) REVERT: G 61 GLU cc_start: 0.8624 (tp30) cc_final: 0.8342 (mm-30) REVERT: D 93 GLU cc_start: 0.8250 (mp0) cc_final: 0.7960 (mp0) REVERT: D 116 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8617 (mtpt) REVERT: H 68 ASP cc_start: 0.8790 (t70) cc_final: 0.8487 (t0) REVERT: H 72 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8848 (mtt180) REVERT: K 38 MET cc_start: 0.8957 (mtt) cc_final: 0.8534 (tpt) REVERT: K 62 PHE cc_start: 0.9102 (m-80) cc_final: 0.8871 (m-80) REVERT: K 87 ASP cc_start: 0.8780 (p0) cc_final: 0.8481 (p0) REVERT: K 92 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8579 (tp-100) REVERT: K 120 VAL cc_start: 0.7361 (t) cc_final: 0.7125 (t) REVERT: L 20 MET cc_start: 0.7447 (mmt) cc_final: 0.7150 (mmt) REVERT: L 45 GLU cc_start: 0.8965 (pm20) cc_final: 0.8601 (pm20) REVERT: L 60 SER cc_start: 0.8715 (m) cc_final: 0.8424 (m) REVERT: L 73 ASN cc_start: 0.7355 (OUTLIER) cc_final: 0.7141 (t0) outliers start: 16 outliers final: 5 residues processed: 285 average time/residue: 0.1252 time to fit residues: 47.9121 Evaluate side-chains 207 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain L residue 14 CYS Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN E 68 GLN F 27 GLN G 84 GLN D 47 GLN D 95 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS L 41 GLN L 73 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.049210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.032911 restraints weight = 81735.976| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.00 r_work: 0.2546 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15173 Z= 0.226 Angle : 0.627 10.454 21790 Z= 0.363 Chirality : 0.038 0.148 2489 Planarity : 0.004 0.055 1746 Dihedral : 29.380 174.916 4396 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 2.54 % Allowed : 13.49 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.27), residues: 1033 helix: 2.20 (0.21), residues: 656 sheet: -0.69 (0.98), residues: 24 loop : -0.72 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 136 TYR 0.013 0.001 TYR D 83 PHE 0.014 0.002 PHE K 51 TRP 0.026 0.003 TRP K 141 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00502 (15165) covalent geometry : angle 0.62535 (21781) hydrogen bonds : bond 0.08809 ( 827) hydrogen bonds : angle 3.60913 ( 2029) metal coordination : bond 0.00531 ( 8) metal coordination : angle 2.19378 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9169 (pm20) cc_final: 0.8883 (pm20) REVERT: A 73 GLU cc_start: 0.9452 (tm-30) cc_final: 0.9195 (tm-30) REVERT: A 94 GLU cc_start: 0.8927 (tp30) cc_final: 0.8606 (tt0) REVERT: A 125 GLN cc_start: 0.9249 (mt0) cc_final: 0.8095 (mt0) REVERT: C 24 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8872 (mp10) REVERT: C 68 ASN cc_start: 0.9110 (m-40) cc_final: 0.8716 (m-40) REVERT: E 94 GLU cc_start: 0.9229 (mm-30) cc_final: 0.9014 (mm-30) REVERT: E 115 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9236 (mppt) REVERT: F 91 LYS cc_start: 0.9431 (ttmt) cc_final: 0.9100 (ttpt) REVERT: G 61 GLU cc_start: 0.9094 (tp30) cc_final: 0.8761 (tp30) REVERT: D 93 GLU cc_start: 0.8921 (mp0) cc_final: 0.8584 (mp0) REVERT: D 116 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9123 (mtpt) REVERT: H 33 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7683 (ttt180) REVERT: H 68 ASP cc_start: 0.9264 (t70) cc_final: 0.9059 (t0) REVERT: H 105 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7804 (tm-30) REVERT: H 106 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9125 (mt) REVERT: K 1 MET cc_start: 0.7493 (tmm) cc_final: 0.7178 (tmm) REVERT: K 16 ASP cc_start: 0.9272 (m-30) cc_final: 0.9013 (p0) REVERT: K 38 MET cc_start: 0.9060 (mtt) cc_final: 0.8691 (tpt) REVERT: K 87 ASP cc_start: 0.9020 (p0) cc_final: 0.8788 (p0) REVERT: K 92 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8681 (tp-100) REVERT: K 120 VAL cc_start: 0.7612 (t) cc_final: 0.7253 (t) REVERT: L 20 MET cc_start: 0.7503 (mmt) cc_final: 0.7123 (mmt) REVERT: L 73 ASN cc_start: 0.7222 (t0) cc_final: 0.7000 (t0) outliers start: 22 outliers final: 14 residues processed: 241 average time/residue: 0.1211 time to fit residues: 40.0975 Evaluate side-chains 219 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.048804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032360 restraints weight = 82568.754| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 3.02 r_work: 0.2523 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15173 Z= 0.274 Angle : 0.630 10.499 21790 Z= 0.365 Chirality : 0.039 0.157 2489 Planarity : 0.004 0.053 1746 Dihedral : 29.452 174.680 4393 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 3.00 % Allowed : 15.92 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.27), residues: 1033 helix: 2.19 (0.20), residues: 655 sheet: -0.75 (0.97), residues: 24 loop : -0.75 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 92 TYR 0.033 0.002 TYR D 83 PHE 0.012 0.002 PHE A 67 TRP 0.012 0.002 TRP K 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00614 (15165) covalent geometry : angle 0.62670 (21781) hydrogen bonds : bond 0.08312 ( 827) hydrogen bonds : angle 3.58049 ( 2029) metal coordination : bond 0.00806 ( 8) metal coordination : angle 3.34187 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9142 (pm20) cc_final: 0.8811 (pm20) REVERT: A 73 GLU cc_start: 0.9479 (tm-30) cc_final: 0.9240 (tm-30) REVERT: A 94 GLU cc_start: 0.8902 (tp30) cc_final: 0.8589 (tt0) REVERT: C 24 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8829 (mp10) REVERT: C 56 GLU cc_start: 0.9337 (tt0) cc_final: 0.8955 (tt0) REVERT: E 73 GLU cc_start: 0.8592 (tt0) cc_final: 0.8358 (tt0) REVERT: E 94 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8987 (mm-30) REVERT: E 115 LYS cc_start: 0.9472 (OUTLIER) cc_final: 0.9247 (mppt) REVERT: F 91 LYS cc_start: 0.9442 (ttmt) cc_final: 0.9130 (ttpt) REVERT: G 61 GLU cc_start: 0.9121 (tp30) cc_final: 0.8784 (tp30) REVERT: D 93 GLU cc_start: 0.8943 (mp0) cc_final: 0.8654 (mp0) REVERT: H 33 ARG cc_start: 0.8456 (mtp85) cc_final: 0.7567 (ttt90) REVERT: H 83 TYR cc_start: 0.8587 (m-10) cc_final: 0.8190 (m-10) REVERT: H 113 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8985 (mm-30) REVERT: K 1 MET cc_start: 0.7476 (tmm) cc_final: 0.7191 (tmm) REVERT: K 38 MET cc_start: 0.9087 (mtt) cc_final: 0.8690 (tpt) REVERT: K 87 ASP cc_start: 0.9036 (p0) cc_final: 0.8816 (p0) REVERT: K 92 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8711 (tp-100) REVERT: K 120 VAL cc_start: 0.7406 (t) cc_final: 0.7027 (t) REVERT: K 147 MET cc_start: 0.8706 (mtt) cc_final: 0.8199 (mpp) outliers start: 26 outliers final: 19 residues processed: 226 average time/residue: 0.1103 time to fit residues: 34.9077 Evaluate side-chains 218 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 69 PHE Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 8.9990 chunk 117 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.048665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.032222 restraints weight = 82324.800| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 3.02 r_work: 0.2520 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2516 r_free = 0.2516 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15173 Z= 0.264 Angle : 0.626 8.690 21790 Z= 0.363 Chirality : 0.038 0.153 2489 Planarity : 0.004 0.056 1746 Dihedral : 29.542 174.550 4385 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.03 % Rotamer: Outliers : 3.11 % Allowed : 16.03 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.27), residues: 1033 helix: 2.26 (0.20), residues: 649 sheet: -0.73 (0.96), residues: 24 loop : -0.81 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 128 TYR 0.047 0.002 TYR D 83 PHE 0.012 0.002 PHE E 67 TRP 0.020 0.002 TRP K 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00592 (15165) covalent geometry : angle 0.62281 (21781) hydrogen bonds : bond 0.08218 ( 827) hydrogen bonds : angle 3.55749 ( 2029) metal coordination : bond 0.00734 ( 8) metal coordination : angle 3.06195 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9110 (pm20) cc_final: 0.8767 (pm20) REVERT: A 73 GLU cc_start: 0.9485 (tm-30) cc_final: 0.9240 (tm-30) REVERT: A 94 GLU cc_start: 0.8892 (tp30) cc_final: 0.8588 (tt0) REVERT: C 24 GLN cc_start: 0.9384 (mm-40) cc_final: 0.9028 (mm-40) REVERT: C 56 GLU cc_start: 0.9351 (tt0) cc_final: 0.9105 (tt0) REVERT: E 73 GLU cc_start: 0.8612 (tt0) cc_final: 0.8406 (tt0) REVERT: E 94 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9003 (mm-30) REVERT: F 91 LYS cc_start: 0.9444 (ttmt) cc_final: 0.9124 (ttpt) REVERT: G 61 GLU cc_start: 0.9102 (tp30) cc_final: 0.8765 (tp30) REVERT: G 64 GLU cc_start: 0.9310 (OUTLIER) cc_final: 0.9060 (pp20) REVERT: D 93 GLU cc_start: 0.8932 (mp0) cc_final: 0.8679 (mp0) REVERT: H 33 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7727 (ttt90) REVERT: H 83 TYR cc_start: 0.8634 (m-10) cc_final: 0.8299 (m-10) REVERT: H 106 LEU cc_start: 0.9425 (mt) cc_final: 0.9110 (mt) REVERT: H 113 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8993 (mm-30) REVERT: K 1 MET cc_start: 0.7487 (tmm) cc_final: 0.7149 (tmm) REVERT: K 38 MET cc_start: 0.9131 (mtt) cc_final: 0.8699 (tpt) REVERT: K 92 GLN cc_start: 0.9113 (tp-100) cc_final: 0.8772 (tp-100) REVERT: K 120 VAL cc_start: 0.7445 (t) cc_final: 0.6931 (m) REVERT: K 125 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8572 (ptp-170) REVERT: K 147 MET cc_start: 0.8683 (mtt) cc_final: 0.8110 (mpp) REVERT: L 20 MET cc_start: 0.7169 (mmm) cc_final: 0.6931 (mmt) outliers start: 27 outliers final: 21 residues processed: 221 average time/residue: 0.1028 time to fit residues: 32.5430 Evaluate side-chains 224 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 40 PHE Chi-restraints excluded: chain L residue 44 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 125 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.049446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.033036 restraints weight = 81457.875| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.02 r_work: 0.2555 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15173 Z= 0.171 Angle : 0.601 11.261 21790 Z= 0.347 Chirality : 0.036 0.146 2489 Planarity : 0.004 0.058 1746 Dihedral : 29.483 173.766 4381 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.54 % Allowed : 17.42 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.27), residues: 1033 helix: 2.35 (0.21), residues: 654 sheet: -0.51 (0.98), residues: 24 loop : -0.70 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 125 TYR 0.030 0.002 TYR D 83 PHE 0.012 0.001 PHE A 67 TRP 0.011 0.002 TRP K 141 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00376 (15165) covalent geometry : angle 0.59819 (21781) hydrogen bonds : bond 0.08191 ( 827) hydrogen bonds : angle 3.35121 ( 2029) metal coordination : bond 0.00485 ( 8) metal coordination : angle 3.06544 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9146 (pm20) cc_final: 0.8789 (pm20) REVERT: A 62 ILE cc_start: 0.9491 (mt) cc_final: 0.9148 (mt) REVERT: A 73 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9217 (tm-30) REVERT: A 94 GLU cc_start: 0.8875 (tp30) cc_final: 0.8575 (tt0) REVERT: A 97 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8590 (mm-30) REVERT: C 24 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8769 (mp10) REVERT: C 56 GLU cc_start: 0.9342 (tt0) cc_final: 0.8869 (tt0) REVERT: F 91 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9094 (ttpt) REVERT: G 61 GLU cc_start: 0.9031 (tp30) cc_final: 0.8716 (tp30) REVERT: G 64 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8953 (pp20) REVERT: D 93 GLU cc_start: 0.8899 (mp0) cc_final: 0.8674 (mp0) REVERT: H 33 ARG cc_start: 0.8400 (mtp85) cc_final: 0.7740 (ttt90) REVERT: H 51 ASP cc_start: 0.8681 (p0) cc_final: 0.8465 (p0) REVERT: H 83 TYR cc_start: 0.8609 (m-10) cc_final: 0.8313 (m-10) REVERT: H 106 LEU cc_start: 0.9391 (mt) cc_final: 0.9069 (mt) REVERT: H 113 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8986 (mm-30) REVERT: K 1 MET cc_start: 0.7498 (tmm) cc_final: 0.7168 (tmm) REVERT: K 38 MET cc_start: 0.9093 (mtt) cc_final: 0.8685 (tpt) REVERT: K 87 ASP cc_start: 0.8733 (p0) cc_final: 0.8507 (t0) REVERT: K 136 ARG cc_start: 0.9347 (ptt90) cc_final: 0.9086 (ttp-110) REVERT: L 50 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7474 (t) outliers start: 22 outliers final: 14 residues processed: 225 average time/residue: 0.1463 time to fit residues: 46.1033 Evaluate side-chains 214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 113 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.033353 restraints weight = 81509.850| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.97 r_work: 0.2574 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15173 Z= 0.161 Angle : 0.597 9.159 21790 Z= 0.344 Chirality : 0.036 0.156 2489 Planarity : 0.004 0.058 1746 Dihedral : 29.376 173.201 4381 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.31 % Allowed : 17.07 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.27), residues: 1033 helix: 2.41 (0.20), residues: 654 sheet: -0.69 (0.92), residues: 24 loop : -0.69 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 55 TYR 0.022 0.001 TYR B 88 PHE 0.016 0.001 PHE K 62 TRP 0.008 0.001 TRP K 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (15165) covalent geometry : angle 0.59332 (21781) hydrogen bonds : bond 0.08158 ( 827) hydrogen bonds : angle 3.26377 ( 2029) metal coordination : bond 0.01025 ( 8) metal coordination : angle 3.39505 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9120 (pm20) cc_final: 0.8785 (pm20) REVERT: A 62 ILE cc_start: 0.9434 (mt) cc_final: 0.9144 (mt) REVERT: A 73 GLU cc_start: 0.9472 (tm-30) cc_final: 0.9167 (tm-30) REVERT: A 94 GLU cc_start: 0.8893 (tp30) cc_final: 0.8566 (tt0) REVERT: A 97 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8588 (mm-30) REVERT: C 24 GLN cc_start: 0.9290 (mm-40) cc_final: 0.8770 (mp10) REVERT: C 56 GLU cc_start: 0.9298 (tt0) cc_final: 0.8721 (tt0) REVERT: E 73 GLU cc_start: 0.8711 (tt0) cc_final: 0.8510 (tt0) REVERT: F 88 TYR cc_start: 0.8998 (m-10) cc_final: 0.8577 (m-10) REVERT: F 91 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9082 (ttpt) REVERT: G 61 GLU cc_start: 0.8972 (tp30) cc_final: 0.8699 (tp30) REVERT: G 64 GLU cc_start: 0.9327 (OUTLIER) cc_final: 0.8967 (pp20) REVERT: D 93 GLU cc_start: 0.8894 (mp0) cc_final: 0.8673 (mp0) REVERT: H 33 ARG cc_start: 0.8342 (mtp85) cc_final: 0.7671 (ttt90) REVERT: H 83 TYR cc_start: 0.8548 (m-10) cc_final: 0.8187 (m-10) REVERT: H 106 LEU cc_start: 0.9377 (mt) cc_final: 0.9088 (mt) REVERT: H 113 GLU cc_start: 0.9313 (mm-30) cc_final: 0.8894 (mt-10) REVERT: K 1 MET cc_start: 0.7552 (tmm) cc_final: 0.7229 (tmm) REVERT: K 38 MET cc_start: 0.9141 (mtt) cc_final: 0.8798 (tpt) REVERT: K 41 ASN cc_start: 0.8599 (m-40) cc_final: 0.8388 (p0) REVERT: K 87 ASP cc_start: 0.8831 (p0) cc_final: 0.8623 (t0) REVERT: K 125 ARG cc_start: 0.8855 (mtm110) cc_final: 0.8647 (ptp-170) REVERT: K 136 ARG cc_start: 0.9377 (ptt90) cc_final: 0.9052 (ttp-110) REVERT: L 50 CYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7767 (t) outliers start: 20 outliers final: 13 residues processed: 224 average time/residue: 0.1455 time to fit residues: 45.6935 Evaluate side-chains 214 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 45 TYR Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 50 CYS Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 8.9990 chunk 26 optimal weight: 0.0010 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.049534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.033220 restraints weight = 81058.485| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.98 r_work: 0.2562 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2557 r_free = 0.2557 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15173 Z= 0.193 Angle : 0.603 8.637 21790 Z= 0.348 Chirality : 0.036 0.149 2489 Planarity : 0.004 0.058 1746 Dihedral : 29.406 173.452 4381 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.19 % Allowed : 18.11 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.27), residues: 1033 helix: 2.43 (0.20), residues: 654 sheet: -0.87 (0.90), residues: 24 loop : -0.67 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 131 TYR 0.052 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.009 0.001 TRP K 141 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00431 (15165) covalent geometry : angle 0.60078 (21781) hydrogen bonds : bond 0.08024 ( 827) hydrogen bonds : angle 3.26216 ( 2029) metal coordination : bond 0.00604 ( 8) metal coordination : angle 2.77825 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9080 (pm20) cc_final: 0.8761 (pm20) REVERT: A 62 ILE cc_start: 0.9438 (mt) cc_final: 0.9146 (mt) REVERT: A 73 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9173 (tm-30) REVERT: A 94 GLU cc_start: 0.8911 (tp30) cc_final: 0.8599 (tt0) REVERT: B 88 TYR cc_start: 0.8811 (m-80) cc_final: 0.8365 (m-80) REVERT: C 24 GLN cc_start: 0.9354 (mm-40) cc_final: 0.8785 (mp10) REVERT: C 56 GLU cc_start: 0.9317 (tt0) cc_final: 0.8813 (tt0) REVERT: C 95 LYS cc_start: 0.9648 (tptt) cc_final: 0.9426 (tptp) REVERT: E 73 GLU cc_start: 0.8592 (tt0) cc_final: 0.8299 (tt0) REVERT: F 88 TYR cc_start: 0.9028 (m-10) cc_final: 0.8592 (m-10) REVERT: F 91 LYS cc_start: 0.9443 (ttmt) cc_final: 0.9094 (ttpt) REVERT: G 61 GLU cc_start: 0.9024 (tp30) cc_final: 0.8778 (tp30) REVERT: G 64 GLU cc_start: 0.9351 (OUTLIER) cc_final: 0.8999 (pp20) REVERT: H 33 ARG cc_start: 0.8316 (mtp85) cc_final: 0.7651 (ttt90) REVERT: H 83 TYR cc_start: 0.8542 (m-10) cc_final: 0.8268 (m-10) REVERT: H 106 LEU cc_start: 0.9397 (mt) cc_final: 0.9093 (mt) REVERT: H 113 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8896 (mt-10) REVERT: K 1 MET cc_start: 0.7492 (tmm) cc_final: 0.7180 (tmm) REVERT: K 38 MET cc_start: 0.9150 (mtt) cc_final: 0.8793 (tpt) REVERT: K 87 ASP cc_start: 0.8860 (p0) cc_final: 0.8622 (t0) REVERT: K 125 ARG cc_start: 0.8806 (mtm110) cc_final: 0.8570 (ptp-170) REVERT: K 136 ARG cc_start: 0.9365 (ptt90) cc_final: 0.9044 (ttp-110) outliers start: 19 outliers final: 17 residues processed: 217 average time/residue: 0.1399 time to fit residues: 43.0985 Evaluate side-chains 215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 27 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.049816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.033827 restraints weight = 81773.042| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.95 r_work: 0.2594 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15173 Z= 0.157 Angle : 0.603 11.806 21790 Z= 0.347 Chirality : 0.035 0.150 2489 Planarity : 0.004 0.060 1746 Dihedral : 29.353 172.899 4381 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.73 % Allowed : 19.26 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.27), residues: 1033 helix: 2.46 (0.20), residues: 649 sheet: -0.84 (0.90), residues: 24 loop : -0.60 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 55 TYR 0.056 0.002 TYR D 83 PHE 0.018 0.001 PHE K 62 TRP 0.008 0.001 TRP K 141 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00344 (15165) covalent geometry : angle 0.60157 (21781) hydrogen bonds : bond 0.08145 ( 827) hydrogen bonds : angle 3.18020 ( 2029) metal coordination : bond 0.00497 ( 8) metal coordination : angle 2.38861 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9106 (pm20) cc_final: 0.8766 (pm20) REVERT: A 62 ILE cc_start: 0.9459 (mt) cc_final: 0.9132 (mt) REVERT: A 73 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9152 (tm-30) REVERT: A 97 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8544 (mm-30) REVERT: C 24 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8765 (mp10) REVERT: C 56 GLU cc_start: 0.9285 (tt0) cc_final: 0.8708 (tt0) REVERT: C 95 LYS cc_start: 0.9604 (tptt) cc_final: 0.9399 (tptp) REVERT: E 73 GLU cc_start: 0.8683 (tt0) cc_final: 0.8393 (tt0) REVERT: F 88 TYR cc_start: 0.9003 (m-10) cc_final: 0.8574 (m-10) REVERT: F 91 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9090 (ttpt) REVERT: G 61 GLU cc_start: 0.8907 (tp30) cc_final: 0.8677 (tp30) REVERT: G 64 GLU cc_start: 0.9338 (tm-30) cc_final: 0.8975 (pp20) REVERT: D 83 TYR cc_start: 0.8136 (m-80) cc_final: 0.7762 (m-80) REVERT: D 93 GLU cc_start: 0.8827 (mp0) cc_final: 0.8463 (mp0) REVERT: D 99 ARG cc_start: 0.9368 (mtt90) cc_final: 0.9083 (mtt90) REVERT: H 33 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7668 (ttt90) REVERT: H 51 ASP cc_start: 0.8616 (p0) cc_final: 0.8362 (p0) REVERT: H 83 TYR cc_start: 0.8506 (m-10) cc_final: 0.8247 (m-10) REVERT: H 101 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8919 (mm) REVERT: H 106 LEU cc_start: 0.9372 (mt) cc_final: 0.9077 (mt) REVERT: H 113 GLU cc_start: 0.9302 (mm-30) cc_final: 0.8894 (mt-10) REVERT: K 1 MET cc_start: 0.7508 (tmm) cc_final: 0.7158 (tmm) REVERT: K 38 MET cc_start: 0.9097 (mtt) cc_final: 0.8766 (tpt) REVERT: K 87 ASP cc_start: 0.8861 (p0) cc_final: 0.8655 (t0) REVERT: K 125 ARG cc_start: 0.8839 (mtm110) cc_final: 0.8606 (ptp-170) REVERT: K 136 ARG cc_start: 0.9383 (ptt90) cc_final: 0.9047 (ttp-110) outliers start: 15 outliers final: 11 residues processed: 221 average time/residue: 0.1374 time to fit residues: 43.4528 Evaluate side-chains 211 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 107 optimal weight: 0.0370 chunk 106 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.049160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.032772 restraints weight = 81657.181| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.99 r_work: 0.2548 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15173 Z= 0.236 Angle : 0.634 11.587 21790 Z= 0.362 Chirality : 0.038 0.189 2489 Planarity : 0.004 0.057 1746 Dihedral : 29.479 173.799 4379 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.19 % Allowed : 19.61 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.27), residues: 1033 helix: 2.43 (0.20), residues: 649 sheet: -0.86 (0.90), residues: 24 loop : -0.55 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 125 TYR 0.066 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.037 0.003 TRP K 93 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00529 (15165) covalent geometry : angle 0.63114 (21781) hydrogen bonds : bond 0.08017 ( 827) hydrogen bonds : angle 3.34413 ( 2029) metal coordination : bond 0.00812 ( 8) metal coordination : angle 2.86382 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9119 (pm20) cc_final: 0.8795 (pm20) REVERT: A 62 ILE cc_start: 0.9426 (mt) cc_final: 0.9130 (mt) REVERT: A 73 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9159 (tm-30) REVERT: A 97 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8551 (mm-30) REVERT: C 24 GLN cc_start: 0.9369 (mm-40) cc_final: 0.8836 (mp10) REVERT: C 95 LYS cc_start: 0.9619 (tptt) cc_final: 0.9418 (tptp) REVERT: E 73 GLU cc_start: 0.8637 (tt0) cc_final: 0.8356 (tt0) REVERT: F 88 TYR cc_start: 0.9076 (m-10) cc_final: 0.8618 (m-10) REVERT: F 91 LYS cc_start: 0.9462 (ttmt) cc_final: 0.9122 (ttpt) REVERT: G 61 GLU cc_start: 0.9065 (tp30) cc_final: 0.8809 (tp30) REVERT: G 64 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.9024 (pp20) REVERT: D 93 GLU cc_start: 0.8869 (mp0) cc_final: 0.8659 (mp0) REVERT: H 33 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7512 (ttt90) REVERT: H 83 TYR cc_start: 0.8550 (m-10) cc_final: 0.8273 (m-10) REVERT: H 101 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.8933 (mm) REVERT: H 106 LEU cc_start: 0.9397 (mt) cc_final: 0.9097 (mt) REVERT: H 113 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9053 (mm-30) REVERT: K 1 MET cc_start: 0.7497 (tmm) cc_final: 0.7170 (tmm) REVERT: K 38 MET cc_start: 0.9108 (mtt) cc_final: 0.8669 (tpt) REVERT: K 87 ASP cc_start: 0.8848 (p0) cc_final: 0.8610 (t0) REVERT: K 136 ARG cc_start: 0.9407 (ptt90) cc_final: 0.9059 (ttp-110) outliers start: 19 outliers final: 16 residues processed: 208 average time/residue: 0.1398 time to fit residues: 41.6827 Evaluate side-chains 209 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 102 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 9 optimal weight: 0.0020 chunk 120 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.050134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034019 restraints weight = 81314.560| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.95 r_work: 0.2601 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15173 Z= 0.153 Angle : 0.620 11.416 21790 Z= 0.354 Chirality : 0.036 0.188 2489 Planarity : 0.004 0.060 1746 Dihedral : 29.366 172.375 4379 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.50 % Allowed : 21.11 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.27), residues: 1033 helix: 2.38 (0.20), residues: 650 sheet: -0.72 (0.92), residues: 24 loop : -0.61 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 125 TYR 0.057 0.002 TYR D 83 PHE 0.019 0.001 PHE K 62 TRP 0.025 0.002 TRP K 93 HIS 0.003 0.001 HIS K 75 Details of bonding type rmsd covalent geometry : bond 0.00334 (15165) covalent geometry : angle 0.61849 (21781) hydrogen bonds : bond 0.08266 ( 827) hydrogen bonds : angle 3.19919 ( 2029) metal coordination : bond 0.00616 ( 8) metal coordination : angle 2.14860 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9116 (pm20) cc_final: 0.8813 (pm20) REVERT: A 62 ILE cc_start: 0.9443 (mt) cc_final: 0.9137 (mt) REVERT: A 73 GLU cc_start: 0.9460 (tm-30) cc_final: 0.9168 (tm-30) REVERT: A 97 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8588 (mm-30) REVERT: B 62 LEU cc_start: 0.9796 (mt) cc_final: 0.9569 (mt) REVERT: C 24 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8767 (mp10) REVERT: C 56 GLU cc_start: 0.9267 (tt0) cc_final: 0.8977 (tt0) REVERT: E 73 GLU cc_start: 0.8728 (tt0) cc_final: 0.8518 (tt0) REVERT: F 88 TYR cc_start: 0.9029 (m-10) cc_final: 0.8587 (m-10) REVERT: F 91 LYS cc_start: 0.9433 (ttmt) cc_final: 0.9082 (ttpt) REVERT: G 61 GLU cc_start: 0.8953 (tp30) cc_final: 0.8733 (tp30) REVERT: G 64 GLU cc_start: 0.9364 (tm-30) cc_final: 0.8994 (pp20) REVERT: D 93 GLU cc_start: 0.8860 (mp0) cc_final: 0.8486 (mp0) REVERT: H 33 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7647 (ttt90) REVERT: H 51 ASP cc_start: 0.8684 (p0) cc_final: 0.8468 (p0) REVERT: H 83 TYR cc_start: 0.8472 (m-10) cc_final: 0.8233 (m-10) REVERT: H 88 THR cc_start: 0.9340 (m) cc_final: 0.9116 (p) REVERT: H 101 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8922 (mm) REVERT: H 106 LEU cc_start: 0.9363 (mt) cc_final: 0.9090 (mt) REVERT: H 113 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8890 (mt-10) REVERT: K 1 MET cc_start: 0.7421 (tmm) cc_final: 0.7078 (tmm) REVERT: K 38 MET cc_start: 0.9032 (mtt) cc_final: 0.8639 (tpt) REVERT: K 136 ARG cc_start: 0.9408 (ptt90) cc_final: 0.9052 (ttp-110) outliers start: 13 outliers final: 10 residues processed: 210 average time/residue: 0.1360 time to fit residues: 41.0709 Evaluate side-chains 209 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 127 optimal weight: 40.0000 chunk 72 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 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 = 0.3394 r_free = 0.3394 target = 0.049639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.033366 restraints weight = 81459.537| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.98 r_work: 0.2572 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15173 Z= 0.207 Angle : 0.626 9.154 21790 Z= 0.359 Chirality : 0.037 0.171 2489 Planarity : 0.004 0.058 1746 Dihedral : 29.449 173.397 4379 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.61 % Allowed : 20.99 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.27), residues: 1033 helix: 2.35 (0.21), residues: 650 sheet: -0.82 (0.90), residues: 24 loop : -0.53 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 125 TYR 0.066 0.002 TYR D 83 PHE 0.012 0.001 PHE E 67 TRP 0.024 0.002 TRP K 93 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (15165) covalent geometry : angle 0.62399 (21781) hydrogen bonds : bond 0.07956 ( 827) hydrogen bonds : angle 3.28335 ( 2029) metal coordination : bond 0.00489 ( 8) metal coordination : angle 2.40521 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3563.71 seconds wall clock time: 61 minutes 51.63 seconds (3711.63 seconds total)