Starting phenix.real_space_refine on Sun Apr 5 19:37:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zeo_74114/04_2026/9zeo_74114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zeo_74114/04_2026/9zeo_74114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zeo_74114/04_2026/9zeo_74114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zeo_74114/04_2026/9zeo_74114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zeo_74114/04_2026/9zeo_74114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zeo_74114/04_2026/9zeo_74114.map" } resolution = 3.1 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= 0.003 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 18 5.16 5 C 7188 2.51 5 N 2415 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12895 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "A" 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: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 2.51, per 1000 atoms: 0.19 Number of scatterers: 12895 At special positions: 0 Unit cell: (126.27, 107.604, 116.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 288 15.00 O 2986 8.00 N 2415 7.00 C 7188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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: 0.82 Conformation dependent library (CDL) restraints added in 358.5 milliseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 12 sheets defined 60.9% alpha, 6.3% beta 141 base pairs and 262 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.570A pdb=" N ARG A 72 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.539A 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: 4.166A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.699A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.494A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.511A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.639A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.536A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 125 removed outlier: 3.685A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.622A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.530A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.777A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.696A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.554A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.344A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 72 " --> pdb=" O ASN G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.518A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.582A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.547A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.959A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.091A pdb=" N THR K 91 " --> pdb=" O PRO K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.293A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.555A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.173A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.218A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'K' and resid 46 through 50 removed outlier: 3.834A pdb=" N VAL K 48 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 262 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.17 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: 2641 1.33 - 1.45: 4448 1.45 - 1.58: 6018 1.58 - 1.70: 576 1.70 - 1.82: 30 Bond restraints: 13713 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.57e+00 bond pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.31e+00 bond pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" N GLN C 104 " pdb=" CA GLN C 104 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.97e+00 ... (remaining 13708 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19322 2.17 - 4.34: 384 4.34 - 6.51: 46 6.51 - 8.68: 7 8.68 - 10.86: 2 Bond angle restraints: 19761 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 131.53 -9.99 1.91e+00 2.74e-01 2.74e+01 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 112.50 118.16 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.11 4.85 1.00e+00 1.00e+00 2.35e+01 angle pdb=" N VAL K 29 " pdb=" CA VAL K 29 " pdb=" C VAL K 29 " ideal model delta sigma weight residual 112.29 108.30 3.99 9.40e-01 1.13e+00 1.81e+01 angle pdb=" CA LYS H 34 " pdb=" CB LYS H 34 " pdb=" CG LYS H 34 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 ... (remaining 19756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 6094 35.25 - 70.49: 1366 70.49 - 105.74: 27 105.74 - 140.98: 3 140.98 - 176.23: 2 Dihedral angle restraints: 7492 sinusoidal: 4946 harmonic: 2546 Sorted by residual: dihedral pdb=" CA GLN K 107 " pdb=" C GLN K 107 " pdb=" N ILE K 108 " pdb=" CA ILE K 108 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.23 -176.23 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.69 145.31 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1702 0.046 - 0.091: 432 0.091 - 0.136: 90 0.136 - 0.182: 11 0.182 - 0.227: 2 Chirality restraints: 2237 Sorted by residual: chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL K 29 " pdb=" CA VAL K 29 " pdb=" CG1 VAL K 29 " pdb=" CG2 VAL K 29 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.53 -0.18 2.00e-01 2.50e+01 8.23e-01 ... (remaining 2234 not shown) Planarity restraints: 1504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 80 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.41e+00 pdb=" N PRO G 80 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 121 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.030 5.00e-02 4.00e+02 ... (remaining 1501 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 3891 2.88 - 3.38: 10385 3.38 - 3.89: 24330 3.89 - 4.39: 28365 4.39 - 4.90: 40350 Nonbonded interactions: 107321 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.369 3.040 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE2 GLU D 35 " model vdw 2.390 3.120 nonbonded pdb=" O ILE B 50 " pdb=" OG1 THR B 54 " model vdw 2.394 3.040 nonbonded pdb=" O LEU A 61 " pdb=" NH1 ARG B 36 " model vdw 2.400 3.120 nonbonded pdb=" O THR H 115 " pdb=" OG1 THR H 119 " model vdw 2.404 3.040 ... (remaining 107316 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 32 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = (chain 'H' and ((resid 32 and (name N or name CA or name C or name O or name CB \ )) or resid 33 through 125)) } 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=1.00 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.004 0.063 13714 Z= 0.208 Angle : 0.745 10.855 19763 Z= 0.436 Chirality : 0.043 0.227 2237 Planarity : 0.006 0.064 1504 Dihedral : 27.019 176.225 5857 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -1.45 (0.25), residues: 866 helix: -0.65 (0.19), residues: 524 sheet: -1.49 (0.77), residues: 44 loop : -1.18 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 79 TYR 0.022 0.001 TYR D 37 PHE 0.012 0.002 PHE D 65 TRP 0.003 0.001 TRP K 114 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00441 (13713) covalent geometry : angle 0.74523 (19761) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.18694 ( 2) hydrogen bonds : bond 0.11795 ( 747) hydrogen bonds : angle 4.27270 ( 1853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8699 (ttmm) cc_final: 0.8480 (ttmm) REVERT: A 79 LYS cc_start: 0.8763 (tttm) cc_final: 0.8558 (ttpp) REVERT: A 90 MET cc_start: 0.8214 (mmm) cc_final: 0.7980 (mmp) REVERT: H 35 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7871 (mm-30) REVERT: H 42 TYR cc_start: 0.8432 (t80) cc_final: 0.8213 (t80) REVERT: K 81 LEU cc_start: 0.8363 (tp) cc_final: 0.7942 (tt) REVERT: K 84 ASN cc_start: 0.7976 (m-40) cc_final: 0.7617 (m-40) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1611 time to fit residues: 42.8764 Evaluate side-chains 179 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 84 GLN C 112 GLN D 84 ASN H 47 GLN H 109 HIS K 13 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.076937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.063798 restraints weight = 34283.438| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.48 r_work: 0.3107 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 13714 Z= 0.371 Angle : 0.674 6.032 19763 Z= 0.395 Chirality : 0.043 0.161 2237 Planarity : 0.005 0.050 1504 Dihedral : 30.460 179.522 4160 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.93 % Allowed : 9.78 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: -0.03 (0.28), residues: 866 helix: 0.79 (0.22), residues: 533 sheet: -1.23 (0.70), residues: 55 loop : -1.24 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 40 TYR 0.013 0.002 TYR K 59 PHE 0.014 0.002 PHE D 65 TRP 0.004 0.001 TRP K 114 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00835 (13713) covalent geometry : angle 0.67408 (19761) SS BOND : bond 0.00204 ( 1) SS BOND : angle 2.03555 ( 2) hydrogen bonds : bond 0.06893 ( 747) hydrogen bonds : angle 3.19266 ( 1853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8504 (tttm) cc_final: 0.8258 (ttpp) REVERT: C 95 LYS cc_start: 0.9041 (ptmt) cc_final: 0.8720 (ttpp) REVERT: E 73 GLU cc_start: 0.8381 (pt0) cc_final: 0.8155 (pt0) REVERT: H 35 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7258 (mm-30) REVERT: K 36 TRP cc_start: 0.8029 (m100) cc_final: 0.7611 (m-10) REVERT: K 59 TYR cc_start: 0.7544 (m-80) cc_final: 0.7259 (m-10) REVERT: K 81 LEU cc_start: 0.8576 (tp) cc_final: 0.7491 (tp) REVERT: K 83 MET cc_start: 0.8197 (mpp) cc_final: 0.7825 (mpp) REVERT: K 94 TYR cc_start: 0.8304 (m-80) cc_final: 0.8049 (m-10) REVERT: K 95 TYR cc_start: 0.8038 (m-10) cc_final: 0.7787 (m-10) outliers start: 14 outliers final: 9 residues processed: 187 average time/residue: 0.1640 time to fit residues: 39.9432 Evaluate side-chains 181 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS K 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.078564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.065619 restraints weight = 34371.024| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.45 r_work: 0.3160 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13714 Z= 0.183 Angle : 0.590 5.942 19763 Z= 0.354 Chirality : 0.037 0.150 2237 Planarity : 0.004 0.051 1504 Dihedral : 30.445 178.584 4160 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.52 % Allowed : 12.40 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.67 (0.28), residues: 866 helix: 1.47 (0.23), residues: 532 sheet: -1.28 (0.70), residues: 47 loop : -1.18 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 53 TYR 0.028 0.001 TYR K 105 PHE 0.010 0.001 PHE K 68 TRP 0.002 0.001 TRP K 114 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00396 (13713) covalent geometry : angle 0.58932 (19761) SS BOND : bond 0.01020 ( 1) SS BOND : angle 1.86224 ( 2) hydrogen bonds : bond 0.05153 ( 747) hydrogen bonds : angle 3.03514 ( 1853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7231 (mm-30) REVERT: K 36 TRP cc_start: 0.7988 (m100) cc_final: 0.7557 (m-10) REVERT: K 38 ARG cc_start: 0.7735 (ptm160) cc_final: 0.7311 (ptm160) REVERT: K 81 LEU cc_start: 0.8629 (tp) cc_final: 0.7638 (tp) REVERT: K 83 MET cc_start: 0.7984 (mpp) cc_final: 0.7713 (mpp) REVERT: K 104 ASP cc_start: 0.8309 (m-30) cc_final: 0.8099 (m-30) outliers start: 11 outliers final: 11 residues processed: 188 average time/residue: 0.1573 time to fit residues: 38.7293 Evaluate side-chains 186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 73 ASN D 47 GLN D 84 ASN H 63 ASN K 82 GLN K 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.078304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.065395 restraints weight = 34455.501| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.50 r_work: 0.3153 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13714 Z= 0.231 Angle : 0.583 5.797 19763 Z= 0.348 Chirality : 0.037 0.152 2237 Planarity : 0.004 0.040 1504 Dihedral : 30.309 177.795 4160 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.34 % Allowed : 13.91 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 0.96 (0.29), residues: 866 helix: 1.70 (0.23), residues: 532 sheet: -0.93 (0.71), residues: 47 loop : -1.12 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 79 TYR 0.011 0.001 TYR K 105 PHE 0.014 0.001 PHE K 68 TRP 0.001 0.000 TRP K 36 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00516 (13713) covalent geometry : angle 0.58287 (19761) SS BOND : bond 0.00195 ( 1) SS BOND : angle 1.95969 ( 2) hydrogen bonds : bond 0.04989 ( 747) hydrogen bonds : angle 2.87745 ( 1853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7938 (mt-10) REVERT: H 63 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8489 (m-40) REVERT: K 34 MET cc_start: 0.7557 (mpp) cc_final: 0.6634 (mpp) REVERT: K 36 TRP cc_start: 0.7965 (m100) cc_final: 0.7558 (m-10) REVERT: K 81 LEU cc_start: 0.8822 (tp) cc_final: 0.7718 (tp) REVERT: K 83 MET cc_start: 0.8192 (mpp) cc_final: 0.7804 (mpp) REVERT: K 114 TRP cc_start: 0.8789 (m100) cc_final: 0.8269 (m100) outliers start: 17 outliers final: 11 residues processed: 183 average time/residue: 0.1593 time to fit residues: 38.2900 Evaluate side-chains 182 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 84 ASN H 63 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.078745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065881 restraints weight = 34394.066| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.47 r_work: 0.3166 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13714 Z= 0.203 Angle : 0.570 5.965 19763 Z= 0.340 Chirality : 0.036 0.145 2237 Planarity : 0.004 0.039 1504 Dihedral : 30.233 177.523 4160 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 15.01 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.29), residues: 866 helix: 1.85 (0.23), residues: 531 sheet: -0.64 (0.74), residues: 47 loop : -1.01 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.011 0.001 TYR C 57 PHE 0.015 0.001 PHE K 68 TRP 0.004 0.001 TRP K 114 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00449 (13713) covalent geometry : angle 0.56962 (19761) SS BOND : bond 0.00513 ( 1) SS BOND : angle 1.92674 ( 2) hydrogen bonds : bond 0.04561 ( 747) hydrogen bonds : angle 2.74636 ( 1853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: H 63 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8475 (m-40) REVERT: K 36 TRP cc_start: 0.7886 (m100) cc_final: 0.7554 (m-10) REVERT: K 81 LEU cc_start: 0.8852 (tp) cc_final: 0.7845 (tp) REVERT: K 83 MET cc_start: 0.8002 (mpp) cc_final: 0.7635 (mpp) REVERT: K 114 TRP cc_start: 0.8925 (m100) cc_final: 0.8402 (m100) outliers start: 14 outliers final: 11 residues processed: 186 average time/residue: 0.1571 time to fit residues: 38.1689 Evaluate side-chains 182 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 76 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 47 GLN H 63 ASN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065627 restraints weight = 34334.098| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.49 r_work: 0.3160 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13714 Z= 0.212 Angle : 0.576 5.840 19763 Z= 0.343 Chirality : 0.036 0.147 2237 Planarity : 0.004 0.039 1504 Dihedral : 30.240 177.641 4160 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.34 % Allowed : 15.29 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.27 (0.29), residues: 866 helix: 1.90 (0.23), residues: 531 sheet: -0.29 (0.74), residues: 54 loop : -1.00 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.011 0.001 TYR C 57 PHE 0.015 0.001 PHE K 68 TRP 0.005 0.001 TRP K 114 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00470 (13713) covalent geometry : angle 0.57593 (19761) SS BOND : bond 0.00410 ( 1) SS BOND : angle 1.88707 ( 2) hydrogen bonds : bond 0.04711 ( 747) hydrogen bonds : angle 2.77024 ( 1853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: E 100 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8977 (mt) REVERT: F 92 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7504 (ttm-80) REVERT: H 63 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8473 (m-40) REVERT: K 36 TRP cc_start: 0.7874 (m100) cc_final: 0.7488 (m-10) REVERT: K 38 ARG cc_start: 0.7741 (ptm160) cc_final: 0.7202 (ptm160) REVERT: K 81 LEU cc_start: 0.8823 (tp) cc_final: 0.7897 (tp) REVERT: K 83 MET cc_start: 0.7939 (mpp) cc_final: 0.7598 (mpp) REVERT: K 84 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (p0) REVERT: K 114 TRP cc_start: 0.8929 (m100) cc_final: 0.8454 (m100) outliers start: 17 outliers final: 12 residues processed: 184 average time/residue: 0.1530 time to fit residues: 37.0308 Evaluate side-chains 187 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain K residue 84 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 35 optimal weight: 0.1980 chunk 30 optimal weight: 0.0040 chunk 15 optimal weight: 4.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 47 GLN F 75 HIS H 63 ASN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.079834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.067203 restraints weight = 34287.103| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.43 r_work: 0.3200 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13714 Z= 0.146 Angle : 0.562 6.576 19763 Z= 0.336 Chirality : 0.034 0.141 2237 Planarity : 0.003 0.037 1504 Dihedral : 30.220 177.057 4160 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.48 % Allowed : 15.29 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.48 (0.29), residues: 866 helix: 2.06 (0.23), residues: 531 sheet: -0.15 (0.74), residues: 54 loop : -0.90 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 38 TYR 0.011 0.001 TYR C 57 PHE 0.015 0.001 PHE K 68 TRP 0.004 0.001 TRP K 114 HIS 0.004 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00308 (13713) covalent geometry : angle 0.56193 (19761) SS BOND : bond 0.00255 ( 1) SS BOND : angle 1.77454 ( 2) hydrogen bonds : bond 0.03940 ( 747) hydrogen bonds : angle 2.72289 ( 1853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: E 100 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8938 (mt) REVERT: F 92 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7495 (ttm-80) REVERT: G 64 GLU cc_start: 0.8517 (tt0) cc_final: 0.8287 (tt0) REVERT: K 36 TRP cc_start: 0.7856 (m100) cc_final: 0.7474 (m-10) REVERT: K 38 ARG cc_start: 0.7689 (ptm160) cc_final: 0.7091 (ptm160) REVERT: K 39 GLN cc_start: 0.8167 (tp40) cc_final: 0.7917 (tp40) REVERT: K 81 LEU cc_start: 0.8824 (tp) cc_final: 0.7858 (tp) REVERT: K 83 MET cc_start: 0.7841 (mpp) cc_final: 0.7491 (mpp) REVERT: K 84 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8309 (p0) REVERT: K 114 TRP cc_start: 0.8894 (m100) cc_final: 0.8449 (m100) outliers start: 18 outliers final: 13 residues processed: 189 average time/residue: 0.1598 time to fit residues: 39.7067 Evaluate side-chains 190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 84 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.078821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.066039 restraints weight = 34193.310| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.50 r_work: 0.3168 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13714 Z= 0.203 Angle : 0.576 6.480 19763 Z= 0.342 Chirality : 0.036 0.146 2237 Planarity : 0.004 0.038 1504 Dihedral : 30.164 177.466 4160 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 15.01 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.29), residues: 866 helix: 2.03 (0.23), residues: 532 sheet: -0.01 (0.76), residues: 54 loop : -0.92 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 79 TYR 0.014 0.001 TYR C 57 PHE 0.017 0.001 PHE K 68 TRP 0.005 0.001 TRP K 36 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd covalent geometry : bond 0.00450 (13713) covalent geometry : angle 0.57578 (19761) SS BOND : bond 0.00422 ( 1) SS BOND : angle 1.97890 ( 2) hydrogen bonds : bond 0.04573 ( 747) hydrogen bonds : angle 2.74016 ( 1853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: E 100 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8936 (mt) REVERT: F 92 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7521 (ttm-80) REVERT: G 90 ASP cc_start: 0.8236 (t0) cc_final: 0.8035 (t0) REVERT: K 36 TRP cc_start: 0.7883 (m100) cc_final: 0.7493 (m-10) REVERT: K 38 ARG cc_start: 0.7734 (ptm160) cc_final: 0.7148 (ptm160) REVERT: K 39 GLN cc_start: 0.8211 (tp40) cc_final: 0.7946 (mm110) REVERT: K 68 PHE cc_start: 0.8008 (m-10) cc_final: 0.7765 (m-80) REVERT: K 81 LEU cc_start: 0.8800 (tp) cc_final: 0.7888 (tp) REVERT: K 114 TRP cc_start: 0.8901 (m100) cc_final: 0.8475 (m100) outliers start: 16 outliers final: 12 residues processed: 183 average time/residue: 0.1609 time to fit residues: 38.5993 Evaluate side-chains 186 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 73 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 26 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN H 84 ASN ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.079326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.066617 restraints weight = 34252.351| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.42 r_work: 0.3184 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13714 Z= 0.164 Angle : 0.583 8.008 19763 Z= 0.346 Chirality : 0.035 0.147 2237 Planarity : 0.004 0.038 1504 Dihedral : 30.177 177.320 4160 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.07 % Allowed : 15.84 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.48 (0.29), residues: 866 helix: 2.04 (0.23), residues: 532 sheet: -0.10 (0.74), residues: 54 loop : -0.88 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 72 TYR 0.018 0.001 TYR C 57 PHE 0.020 0.001 PHE K 68 TRP 0.004 0.001 TRP K 36 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (13713) covalent geometry : angle 0.58320 (19761) SS BOND : bond 0.00433 ( 1) SS BOND : angle 1.91302 ( 2) hydrogen bonds : bond 0.04291 ( 747) hydrogen bonds : angle 2.72821 ( 1853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8274 (pm20) cc_final: 0.8056 (pm20) REVERT: E 100 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8940 (mt) REVERT: F 92 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7491 (ttm-80) REVERT: K 36 TRP cc_start: 0.7864 (m100) cc_final: 0.7470 (m-10) REVERT: K 39 GLN cc_start: 0.8226 (tp40) cc_final: 0.7928 (tp40) REVERT: K 81 LEU cc_start: 0.8843 (tp) cc_final: 0.8192 (tp) REVERT: K 90 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: K 114 TRP cc_start: 0.8916 (m100) cc_final: 0.8470 (m100) outliers start: 15 outliers final: 12 residues processed: 183 average time/residue: 0.1531 time to fit residues: 36.6732 Evaluate side-chains 184 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.079605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066898 restraints weight = 34374.306| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.51 r_work: 0.3191 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13714 Z= 0.161 Angle : 0.585 8.652 19763 Z= 0.344 Chirality : 0.035 0.146 2237 Planarity : 0.003 0.038 1504 Dihedral : 30.158 176.890 4160 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 16.12 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.51 (0.29), residues: 866 helix: 2.07 (0.23), residues: 532 sheet: -0.07 (0.75), residues: 54 loop : -0.91 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 72 TYR 0.019 0.001 TYR C 57 PHE 0.007 0.001 PHE K 68 TRP 0.004 0.001 TRP K 114 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00351 (13713) covalent geometry : angle 0.58506 (19761) SS BOND : bond 0.00545 ( 1) SS BOND : angle 1.99631 ( 2) hydrogen bonds : bond 0.04076 ( 747) hydrogen bonds : angle 2.71230 ( 1853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8378 (pm20) cc_final: 0.8162 (pm20) REVERT: E 100 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8934 (mt) REVERT: F 92 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7509 (ttm-80) REVERT: K 36 TRP cc_start: 0.7858 (m100) cc_final: 0.7456 (m-10) REVERT: K 39 GLN cc_start: 0.8263 (tp40) cc_final: 0.7966 (tp40) REVERT: K 68 PHE cc_start: 0.7801 (m-80) cc_final: 0.7392 (m-80) REVERT: K 81 LEU cc_start: 0.8828 (tp) cc_final: 0.8117 (tp) REVERT: K 90 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8574 (m-30) REVERT: K 114 TRP cc_start: 0.8908 (m100) cc_final: 0.8468 (m100) outliers start: 16 outliers final: 12 residues processed: 182 average time/residue: 0.1568 time to fit residues: 37.4187 Evaluate side-chains 187 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 104 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.079922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067284 restraints weight = 34367.232| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.50 r_work: 0.3202 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13714 Z= 0.150 Angle : 0.588 8.981 19763 Z= 0.345 Chirality : 0.034 0.148 2237 Planarity : 0.004 0.038 1504 Dihedral : 30.145 176.788 4160 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.93 % Allowed : 16.39 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.54 (0.29), residues: 866 helix: 2.08 (0.23), residues: 532 sheet: -0.09 (0.75), residues: 54 loop : -0.84 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 72 TYR 0.010 0.001 TYR C 57 PHE 0.008 0.001 PHE H 70 TRP 0.003 0.001 TRP K 114 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00324 (13713) covalent geometry : angle 0.58781 (19761) SS BOND : bond 0.00491 ( 1) SS BOND : angle 1.88233 ( 2) hydrogen bonds : bond 0.03947 ( 747) hydrogen bonds : angle 2.69535 ( 1853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3352.20 seconds wall clock time: 57 minutes 45.13 seconds (3465.13 seconds total)