Starting phenix.real_space_refine on Fri Sep 11 16:56:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lv8_23529/09_2026/7lv8_23529.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lv8_23529/09_2026/7lv8_23529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lv8_23529/09_2026/7lv8_23529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lv8_23529/09_2026/7lv8_23529.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lv8_23529/09_2026/7lv8_23529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lv8_23529/09_2026/7lv8_23529.map" } resolution = 3.4 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= 1.001 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 242 5.49 5 S 30 5.16 5 C 5913 2.51 5 N 1961 2.21 5 O 2505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10651 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 770 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 659 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 688 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 731 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 772 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 659 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 680 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2495 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Chain: "J" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2466 Classifications: {'DNA': 121} Link IDs: {'rna3p': 120} Time building chain proxies: 1.85, per 1000 atoms: 0.17 Number of scatterers: 10651 At special positions: 0 Unit cell: (82.84, 115.54, 118.81, 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 30 16.00 P 242 15.00 O 2505 8.00 N 1961 7.00 C 5913 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 Links applied TRANS " CYS A 113 " - " SER B 112 " " GLU C 105 " - " LYS D 104 " " CYS E 113 " - " SER F 112 " " GLU G 105 " - " LYS H 104 " Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 186.4 milliseconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 7 sheets defined 67.8% alpha, 1.8% beta 112 base pairs and 205 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'B' and resid 28 through 39 removed outlier: 3.660A pdb=" N LEU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 74 removed outlier: 3.675A pdb=" N LEU B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.554A pdb=" N VAL B 84 " --> pdb=" O MET B 80 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 136 removed outlier: 3.511A pdb=" N VAL A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.739A pdb=" N LYS A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 195 removed outlier: 3.503A pdb=" N ILE A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.603A pdb=" N ILE A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 35 through 61 Processing helix chain 'D' and resid 69 through 81 removed outlier: 3.753A pdb=" N VAL D 73 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 103 removed outlier: 3.745A pdb=" N GLY D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 92 " --> pdb=" O HIS D 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 120 through 130 Processing helix chain 'C' and resid 138 through 167 removed outlier: 3.561A pdb=" N ALA C 142 " --> pdb=" O SER C 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 184 removed outlier: 3.592A pdb=" N ASP C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.538A pdb=" N ALA C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 removed outlier: 3.570A pdb=" N GLN F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 39 " --> pdb=" O LEU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 74 removed outlier: 3.595A pdb=" N LEU F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.545A pdb=" N VAL F 84 " --> pdb=" O MET F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.525A pdb=" N VAL E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 136 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 3.848A pdb=" N GLU E 159 " --> pdb=" O ILE E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 195 removed outlier: 3.586A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 211 removed outlier: 3.717A pdb=" N ILE E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 29 Processing helix chain 'H' and resid 35 through 61 Processing helix chain 'H' and resid 69 through 81 removed outlier: 3.698A pdb=" N VAL H 73 " --> pdb=" O LYS H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 103 removed outlier: 3.547A pdb=" N GLY H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 138 through 167 removed outlier: 3.771A pdb=" N ALA G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE G 152 " --> pdb=" O ALA G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 183 removed outlier: 3.545A pdb=" N ILE G 181 " --> pdb=" O ILE G 177 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN G 182 " --> pdb=" O THR G 178 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN G 183 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.735A pdb=" N ALA G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 78 through 79 Processing sheet with id=AA2, first strand: chain 'D' and resid 33 through 34 removed outlier: 7.315A pdb=" N SER D 33 " --> pdb=" O ILE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AA4, first strand: chain 'F' and resid 43 through 44 removed outlier: 6.959A pdb=" N SER F 43 " --> pdb=" O VAL E 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 34 removed outlier: 7.202A pdb=" N SER H 33 " --> pdb=" O ILE G 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 67 through 68 350 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 291 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 112 basepair parallelities 205 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2538 1.34 - 1.46: 3383 1.46 - 1.58: 4857 1.58 - 1.70: 482 1.70 - 1.82: 52 Bond restraints: 11312 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.45e+01 bond pdb=" C3' DG I -37 " pdb=" C2' DG I -37 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.38e+01 bond pdb=" C5' DA J 57 " pdb=" C4' DA J 57 " ideal model delta sigma weight residual 1.512 1.537 -0.025 7.00e-03 2.04e+04 1.30e+01 bond pdb=" C3' DC J -18 " pdb=" C2' DC J -18 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 ... (remaining 11307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 15897 2.33 - 4.66: 374 4.66 - 6.99: 16 6.99 - 9.32: 1 9.32 - 11.65: 1 Bond angle restraints: 16289 Sorted by residual: angle pdb=" O4' DG J 47 " pdb=" C4' DG J 47 " pdb=" C3' DG J 47 " ideal model delta sigma weight residual 106.00 102.74 3.26 6.00e-01 2.78e+00 2.95e+01 angle pdb=" O5' DA J 57 " pdb=" C5' DA J 57 " pdb=" C4' DA J 57 " ideal model delta sigma weight residual 109.40 113.11 -3.71 8.00e-01 1.56e+00 2.15e+01 angle pdb=" N3 DT J -17 " pdb=" C4 DT J -17 " pdb=" O4 DT J -17 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J -39 " pdb=" C4 DT J -39 " pdb=" O4 DT J -39 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J -28 " pdb=" C4 DT J -28 " pdb=" O4 DT J -28 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 ... (remaining 16284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5040 34.62 - 69.24: 1127 69.24 - 103.86: 18 103.86 - 138.48: 0 138.48 - 173.11: 3 Dihedral angle restraints: 6188 sinusoidal: 4016 harmonic: 2172 Sorted by residual: 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 46.89 173.11 1 3.50e+01 8.16e-04 1.56e+01 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 76.29 143.71 1 3.50e+01 8.16e-04 1.42e+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 80.70 139.30 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1214 0.039 - 0.078: 509 0.078 - 0.118: 153 0.118 - 0.157: 11 0.157 - 0.196: 4 Chirality restraints: 1891 Sorted by residual: chirality pdb=" C3' DC I 52 " pdb=" C4' DC I 52 " pdb=" O3' DC I 52 " pdb=" C2' DC I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.60e-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 -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.64e-01 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 1888 not shown) Planarity restraints: 1215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 47 " -0.016 2.00e-02 2.50e+03 3.17e-02 1.00e+01 pdb=" C ASP F 47 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP F 47 " -0.021 2.00e-02 2.50e+03 pdb=" N THR F 48 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 178 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU A 178 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 178 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 178 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 36 " 0.023 2.00e-02 2.50e+03 1.13e-02 2.88e+00 pdb=" N1 DC J 36 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DC J 36 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC J 36 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 36 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 36 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 36 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DC J 36 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DC J 36 " -0.005 2.00e-02 2.50e+03 ... (remaining 1212 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 941 2.74 - 3.28: 9222 3.28 - 3.82: 20333 3.82 - 4.36: 23381 4.36 - 4.90: 33904 Nonbonded interactions: 87781 Sorted by model distance: nonbonded pdb=" O LYS B 29 " pdb=" OG1 THR B 32 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR E 123 " pdb=" OP2 DA I -14 " model vdw 2.333 3.040 nonbonded pdb=" O LEU B 42 " pdb=" ND2 ASN A 128 " model vdw 2.336 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OE2 GLU H 37 " model vdw 2.350 3.040 nonbonded pdb=" NH1 ARG C 111 " pdb=" OE1 GLU C 125 " model vdw 2.360 3.120 ... (remaining 87776 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' selection = (chain 'E' and (resid 113 through 122 or (resid 123 and (name N or name CA or na \ me C or name O or name CB )) or resid 124 through 214)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 105 through 106 or (resid 107 through 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 157 or (resid 158 \ and (name N or name CA or name C or name O or name CB )) or resid 159 through 19 \ 8)) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 0.049 11316 Z= 0.532 Angle : 0.803 11.653 16301 Z= 0.693 Chirality : 0.045 0.196 1891 Planarity : 0.004 0.046 1211 Dihedral : 27.117 173.105 4772 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.17 % Allowed : 0.00 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.26 (0.22), residues: 748 helix: -2.34 (0.15), residues: 488 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 129 TYR 0.024 0.003 TYR H 100 PHE 0.024 0.002 PHE G 152 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.53 (11312) covalent geometry : angle 0.80311 / 0.69 (16289) hydrogen bonds : bond 0.20718 / 14.02 ( 641) hydrogen bonds : angle 5.81533 / 4.11 ( 1628) link_TRANS : bond 0.00665 / 0.33 ( 4) link_TRANS : angle 0.95169 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.217 Fit side-chains REVERT: B 41 SER cc_start: 0.9244 (t) cc_final: 0.8839 (p) REVERT: F 41 SER cc_start: 0.9270 (m) cc_final: 0.8805 (p) REVERT: F 80 MET cc_start: 0.7904 (mtp) cc_final: 0.7522 (mtt) REVERT: E 131 GLU cc_start: 0.8253 (tp30) cc_final: 0.7496 (tt0) REVERT: G 169 LYS cc_start: 0.7190 (mmtp) cc_final: 0.6789 (mtpt) REVERT: G 184 ASP cc_start: 0.7671 (t70) cc_final: 0.7159 (t0) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.1017 time to fit residues: 15.6531 Evaluate side-chains 70 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN G 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.133239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.098516 restraints weight = 18417.856| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.41 r_work: 0.3200 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11316 Z= 0.169 Angle : 0.647 7.905 16301 Z= 0.389 Chirality : 0.043 0.245 1891 Planarity : 0.005 0.049 1211 Dihedral : 30.140 172.821 3432 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.34 % Allowed : 8.35 % Favored : 90.32 % 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: 0.04 (0.28), residues: 748 helix: 0.77 (0.22), residues: 492 sheet: None (None), residues: 0 loop : -1.37 (0.32), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.018 0.002 TYR H 81 PHE 0.033 0.002 PHE G 152 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (11312) covalent geometry : angle 0.64679 / 0.39 (16289) hydrogen bonds : bond 0.06263 / 4.24 ( 641) hydrogen bonds : angle 3.21036 / 2.27 ( 1628) link_TRANS : bond 0.00147 / 0.07 ( 4) link_TRANS : angle 0.34019 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.248 Fit side-chains REVERT: B 41 SER cc_start: 0.9313 (t) cc_final: 0.8893 (p) REVERT: A 128 ASN cc_start: 0.7695 (t0) cc_final: 0.7390 (t0) REVERT: A 155 ILE cc_start: 0.8110 (mm) cc_final: 0.7905 (mm) REVERT: C 125 GLU cc_start: 0.8029 (tt0) cc_final: 0.7817 (tt0) REVERT: G 169 LYS cc_start: 0.6659 (mmtp) cc_final: 0.6252 (mtpt) outliers start: 8 outliers final: 5 residues processed: 82 average time/residue: 0.1033 time to fit residues: 12.0579 Evaluate side-chains 75 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain G residue 182 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.3980 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 GLN D 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094570 restraints weight = 18347.753| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.42 r_work: 0.3136 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11316 Z= 0.196 Angle : 0.653 7.181 16301 Z= 0.383 Chirality : 0.044 0.280 1891 Planarity : 0.004 0.045 1211 Dihedral : 30.172 171.584 3430 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.50 % Allowed : 11.02 % Favored : 86.48 % 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: 1.04 (0.29), residues: 748 helix: 1.61 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -1.18 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 37 TYR 0.021 0.002 TYR H 81 PHE 0.036 0.003 PHE C 152 HIS 0.004 0.001 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (11312) covalent geometry : angle 0.65270 / 0.38 (16289) hydrogen bonds : bond 0.05580 / 3.78 ( 641) hydrogen bonds : angle 3.00895 / 2.13 ( 1628) link_TRANS : bond 0.00168 / 0.08 ( 4) link_TRANS : angle 0.41414 / 0.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.260 Fit side-chains REVERT: B 41 SER cc_start: 0.9331 (t) cc_final: 0.9002 (p) REVERT: A 186 GLU cc_start: 0.7803 (tt0) cc_final: 0.7566 (mt-10) REVERT: C 125 GLU cc_start: 0.8284 (tt0) cc_final: 0.8001 (tt0) REVERT: G 169 LYS cc_start: 0.6806 (mmtp) cc_final: 0.6410 (mtpt) REVERT: G 184 ASP cc_start: 0.7752 (t70) cc_final: 0.6920 (t0) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1042 time to fit residues: 12.5914 Evaluate side-chains 82 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 16 ASN Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain H residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 72 GLN G 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.097164 restraints weight = 18148.555| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.39 r_work: 0.3179 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11316 Z= 0.134 Angle : 0.567 5.661 16301 Z= 0.347 Chirality : 0.041 0.284 1891 Planarity : 0.003 0.045 1211 Dihedral : 30.083 169.488 3430 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 13.02 % Favored : 85.64 % 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: 1.68 (0.30), residues: 748 helix: 2.17 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -1.07 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.018 0.001 TYR H 81 PHE 0.026 0.002 PHE G 152 HIS 0.002 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (11312) covalent geometry : angle 0.56695 / 0.35 (16289) hydrogen bonds : bond 0.04652 / 3.17 ( 641) hydrogen bonds : angle 2.77143 / 1.96 ( 1628) link_TRANS : bond 0.00127 / 0.06 ( 4) link_TRANS : angle 0.28198 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.185 Fit side-chains REVERT: B 41 SER cc_start: 0.9324 (t) cc_final: 0.8988 (p) REVERT: B 71 MET cc_start: 0.8817 (ttp) cc_final: 0.8571 (tmm) REVERT: A 186 GLU cc_start: 0.7796 (tt0) cc_final: 0.7575 (mt-10) REVERT: H 31 ASP cc_start: 0.8513 (p0) cc_final: 0.8260 (p0) REVERT: H 63 GLU cc_start: 0.7346 (pm20) cc_final: 0.6854 (mm-30) REVERT: G 169 LYS cc_start: 0.6674 (mmtp) cc_final: 0.6263 (mtpt) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.0916 time to fit residues: 11.1527 Evaluate side-chains 80 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain G residue 196 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 HIS D 16 ASN D 35 GLN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.121567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085868 restraints weight = 18050.805| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.26 r_work: 0.3005 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 11316 Z= 0.354 Angle : 0.900 9.859 16301 Z= 0.483 Chirality : 0.055 0.275 1891 Planarity : 0.006 0.048 1211 Dihedral : 30.465 173.012 3430 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.67 % Allowed : 14.36 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.29), residues: 748 helix: 1.33 (0.22), residues: 494 sheet: None (None), residues: 0 loop : -1.33 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 129 TYR 0.050 0.003 TYR H 81 PHE 0.056 0.005 PHE G 152 HIS 0.008 0.002 HIS B 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.35 (11312) covalent geometry : angle 0.90054 / 0.48 (16289) hydrogen bonds : bond 0.06842 / 4.64 ( 641) hydrogen bonds : angle 3.64179 / 2.54 ( 1628) link_TRANS : bond 0.00186 / 0.09 ( 4) link_TRANS : angle 0.73590 / 0.32 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.279 Fit side-chains REVERT: B 41 SER cc_start: 0.9371 (t) cc_final: 0.9008 (p) REVERT: A 187 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8303 (mttm) REVERT: D 16 ASN cc_start: 0.6613 (OUTLIER) cc_final: 0.6406 (p0) REVERT: H 31 ASP cc_start: 0.8597 (p0) cc_final: 0.8343 (p0) REVERT: G 169 LYS cc_start: 0.7262 (mmtp) cc_final: 0.7019 (mtpt) outliers start: 28 outliers final: 17 residues processed: 95 average time/residue: 0.0939 time to fit residues: 13.0730 Evaluate side-chains 89 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 16 ASN Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain G residue 134 CYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 182 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.126785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.091592 restraints weight = 18075.818| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.34 r_work: 0.3087 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11316 Z= 0.147 Angle : 0.615 6.078 16301 Z= 0.365 Chirality : 0.043 0.299 1891 Planarity : 0.003 0.040 1211 Dihedral : 30.279 170.731 3430 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.84 % Allowed : 17.53 % Favored : 80.63 % 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: 1.62 (0.31), residues: 748 helix: 2.09 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -0.98 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.026 0.002 TYR H 81 PHE 0.030 0.002 PHE G 152 HIS 0.003 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.15 (11312) covalent geometry : angle 0.61512 / 0.37 (16289) hydrogen bonds : bond 0.04957 / 3.41 ( 641) hydrogen bonds : angle 2.89914 / 2.04 ( 1628) link_TRANS : bond 0.00083 / 0.04 ( 4) link_TRANS : angle 0.34887 / 0.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.273 Fit side-chains REVERT: B 41 SER cc_start: 0.9395 (t) cc_final: 0.9048 (p) REVERT: E 172 MET cc_start: 0.8306 (ttm) cc_final: 0.8095 (ttp) REVERT: H 31 ASP cc_start: 0.8559 (p0) cc_final: 0.8312 (p0) REVERT: H 100 TYR cc_start: 0.8768 (t80) cc_final: 0.8471 (t80) REVERT: G 169 LYS cc_start: 0.7013 (mmtp) cc_final: 0.6588 (mtpt) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.0962 time to fit residues: 11.0563 Evaluate side-chains 79 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain G residue 182 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN G 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092982 restraints weight = 17956.072| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.28 r_work: 0.3113 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 11316 Z= 0.138 Angle : 0.593 6.524 16301 Z= 0.353 Chirality : 0.042 0.289 1891 Planarity : 0.003 0.040 1211 Dihedral : 30.213 170.875 3430 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.84 % Allowed : 16.69 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.99 (0.31), residues: 748 helix: 2.39 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -0.88 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 129 TYR 0.021 0.001 TYR H 81 PHE 0.030 0.002 PHE G 152 HIS 0.003 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (11312) covalent geometry : angle 0.59270 / 0.35 (16289) hydrogen bonds : bond 0.04585 / 3.14 ( 641) hydrogen bonds : angle 2.74866 / 1.93 ( 1628) link_TRANS : bond 0.00076 / 0.04 ( 4) link_TRANS : angle 0.19372 / 0.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.221 Fit side-chains REVERT: B 41 SER cc_start: 0.9331 (t) cc_final: 0.8985 (p) REVERT: D 16 ASN cc_start: 0.6488 (OUTLIER) cc_final: 0.6279 (p0) REVERT: E 172 MET cc_start: 0.8156 (ttm) cc_final: 0.7925 (ttp) REVERT: H 31 ASP cc_start: 0.8517 (p0) cc_final: 0.8278 (p0) REVERT: H 100 TYR cc_start: 0.8661 (t80) cc_final: 0.8334 (t80) REVERT: G 169 LYS cc_start: 0.6727 (mmtp) cc_final: 0.6394 (mtpt) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.0873 time to fit residues: 10.8982 Evaluate side-chains 85 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 16 ASN Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain H residue 27 GLN Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain G residue 137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.128242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093319 restraints weight = 17886.695| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.28 r_work: 0.3118 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11316 Z= 0.136 Angle : 0.587 7.949 16301 Z= 0.348 Chirality : 0.041 0.288 1891 Planarity : 0.003 0.040 1211 Dihedral : 30.150 170.418 3430 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.34 % Allowed : 17.20 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.16 (0.31), residues: 748 helix: 2.50 (0.23), residues: 494 sheet: None (None), residues: 0 loop : -0.79 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 18 TYR 0.020 0.001 TYR H 81 PHE 0.031 0.002 PHE G 152 HIS 0.003 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (11312) covalent geometry : angle 0.58763 / 0.35 (16289) hydrogen bonds : bond 0.04465 / 3.06 ( 641) hydrogen bonds : angle 2.70894 / 1.89 ( 1628) link_TRANS : bond 0.00073 / 0.04 ( 4) link_TRANS : angle 0.15473 / 0.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.253 Fit side-chains REVERT: B 41 SER cc_start: 0.9315 (t) cc_final: 0.9014 (p) REVERT: E 172 MET cc_start: 0.8133 (ttm) cc_final: 0.7895 (ttp) REVERT: H 31 ASP cc_start: 0.8516 (p0) cc_final: 0.8280 (p0) REVERT: H 100 TYR cc_start: 0.8646 (t80) cc_final: 0.8317 (t80) REVERT: G 169 LYS cc_start: 0.6697 (mmtp) cc_final: 0.6361 (mtpt) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.0857 time to fit residues: 10.7539 Evaluate side-chains 86 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 182 GLN Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092964 restraints weight = 17911.846| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.28 r_work: 0.3111 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11316 Z= 0.145 Angle : 0.591 7.778 16301 Z= 0.349 Chirality : 0.041 0.284 1891 Planarity : 0.003 0.043 1211 Dihedral : 30.119 170.374 3430 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.17 % Allowed : 17.53 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.17 (0.31), residues: 748 helix: 2.49 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.80 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.020 0.001 TYR H 81 PHE 0.033 0.002 PHE G 152 HIS 0.003 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (11312) covalent geometry : angle 0.59136 / 0.35 (16289) hydrogen bonds : bond 0.04447 / 3.05 ( 641) hydrogen bonds : angle 2.69381 / 1.89 ( 1628) link_TRANS : bond 0.00074 / 0.04 ( 4) link_TRANS : angle 0.14750 / 0.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.174 Fit side-chains REVERT: B 41 SER cc_start: 0.9311 (t) cc_final: 0.9022 (p) REVERT: E 172 MET cc_start: 0.8170 (ttm) cc_final: 0.7926 (ttp) REVERT: E 206 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7973 (mm-30) REVERT: H 31 ASP cc_start: 0.8520 (p0) cc_final: 0.8286 (p0) REVERT: H 100 TYR cc_start: 0.8662 (t80) cc_final: 0.8421 (t80) REVERT: G 169 LYS cc_start: 0.6705 (mmtp) cc_final: 0.6363 (mtpt) outliers start: 13 outliers final: 12 residues processed: 83 average time/residue: 0.0949 time to fit residues: 11.5141 Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.128242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.093420 restraints weight = 17934.732| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.28 r_work: 0.3121 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11316 Z= 0.139 Angle : 0.579 7.876 16301 Z= 0.344 Chirality : 0.041 0.284 1891 Planarity : 0.003 0.044 1211 Dihedral : 30.077 169.985 3430 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 18.03 % Favored : 79.80 % 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: 2.31 (0.31), residues: 748 helix: 2.58 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 129 TYR 0.022 0.001 TYR H 81 PHE 0.036 0.002 PHE G 152 HIS 0.003 0.001 HIS D 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (11312) covalent geometry : angle 0.57905 / 0.34 (16289) hydrogen bonds : bond 0.04316 / 2.96 ( 641) hydrogen bonds : angle 2.63918 / 1.85 ( 1628) link_TRANS : bond 0.00073 / 0.04 ( 4) link_TRANS : angle 0.16787 / 0.10 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.281 Fit side-chains REVERT: B 41 SER cc_start: 0.9301 (t) cc_final: 0.9015 (p) REVERT: E 172 MET cc_start: 0.8171 (ttm) cc_final: 0.7932 (ttp) REVERT: E 206 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8041 (mm-30) REVERT: H 31 ASP cc_start: 0.8512 (p0) cc_final: 0.8277 (p0) REVERT: H 100 TYR cc_start: 0.8648 (t80) cc_final: 0.8385 (t80) REVERT: G 169 LYS cc_start: 0.6687 (mmtp) cc_final: 0.6350 (mtpt) outliers start: 13 outliers final: 12 residues processed: 84 average time/residue: 0.0957 time to fit residues: 11.7852 Evaluate side-chains 87 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 195 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 16 ASN ** E 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 ASN H 27 GLN G 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.089236 restraints weight = 17815.580| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.26 r_work: 0.3060 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11316 Z= 0.206 Angle : 0.685 7.812 16301 Z= 0.383 Chirality : 0.046 0.281 1891 Planarity : 0.004 0.042 1211 Dihedral : 30.256 171.252 3430 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.50 % Allowed : 18.03 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.90 (0.30), residues: 748 helix: 2.24 (0.23), residues: 496 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 129 TYR 0.034 0.002 TYR H 81 PHE 0.048 0.004 PHE G 152 HIS 0.004 0.001 HIS G 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (11312) covalent geometry : angle 0.68546 / 0.38 (16289) hydrogen bonds : bond 0.05103 / 3.48 ( 641) hydrogen bonds : angle 2.96084 / 2.07 ( 1628) link_TRANS : bond 0.00116 / 0.06 ( 4) link_TRANS : angle 0.34151 / 0.15 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1906.85 seconds wall clock time: 33 minutes 27.75 seconds (2007.75 seconds total)