Starting phenix.real_space_refine on Fri Jul 3 05:25:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dg3_46822/07_2026/9dg3_46822.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dg3_46822/07_2026/9dg3_46822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dg3_46822/07_2026/9dg3_46822.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dg3_46822/07_2026/9dg3_46822.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dg3_46822/07_2026/9dg3_46822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dg3_46822/07_2026/9dg3_46822.map" } resolution = 3.46 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= 0.008 sd= 0.048 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 17 5.16 5 C 6967 2.51 5 N 2342 2.21 5 O 2934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12553 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 773 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3015 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2971 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "M" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 249 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 405 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 3, 'TRANS': 68} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 95 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11931 SG CYS M 27 29.583 48.634 68.684 1.00205.57 S ATOM 11950 SG CYS M 30 27.941 45.395 67.355 1.00208.97 S ATOM 12028 SG CYS M 41 29.688 45.285 70.695 1.00205.36 S ATOM 12048 SG CYS M 44 31.653 45.682 67.608 1.00195.86 S Time building chain proxies: 2.82, per 1000 atoms: 0.22 Number of scatterers: 12553 At special positions: 0 Unit cell: (103.024, 118.368, 122.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 17 16.00 P 292 15.00 O 2934 8.00 N 2342 7.00 C 6967 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 378.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 44 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 30 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 41 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 27 " Number of angles added : 6 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1616 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 65.6% alpha, 4.2% beta 143 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.103A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.620A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.313A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.583A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 35 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.810A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.472A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.684A 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: 7.470A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'N' and resid 12 through 16 436 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.22 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: 2848 1.34 - 1.46: 4190 1.46 - 1.58: 5715 1.58 - 1.70: 582 1.70 - 1.82: 27 Bond restraints: 13362 Sorted by residual: bond pdb=" C1' DC I 36 " pdb=" N1 DC I 36 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.93e+01 bond pdb=" C3' DC I 128 " pdb=" C2' DC I 128 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG I 115 " pdb=" C2' DG I 115 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" C PHE E 84 " pdb=" N GLN E 85 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.38e-02 5.25e+03 1.17e+01 bond pdb=" C3' DG J 54 " pdb=" C2' DG J 54 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 13357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 18480 2.15 - 4.30: 772 4.30 - 6.45: 60 6.45 - 8.60: 13 8.60 - 10.75: 4 Bond angle restraints: 19329 Sorted by residual: angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 114.16 103.58 10.58 1.48e+00 4.57e-01 5.11e+01 angle pdb=" O4' DG J 120 " pdb=" C4' DG J 120 " pdb=" C3' DG J 120 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 angle pdb=" CB LYS G 36 " pdb=" CG LYS G 36 " pdb=" CD LYS G 36 " ideal model delta sigma weight residual 111.30 122.05 -10.75 2.30e+00 1.89e-01 2.19e+01 angle pdb=" O4' DA J 111 " pdb=" C4' DA J 111 " pdb=" C3' DA J 111 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" O4' DC J 131 " pdb=" C4' DC J 131 " pdb=" C3' DC J 131 " ideal model delta sigma weight residual 106.00 103.31 2.69 6.00e-01 2.78e+00 2.01e+01 ... (remaining 19324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 5268 26.16 - 52.32: 1606 52.32 - 78.48: 382 78.48 - 104.64: 10 104.64 - 130.79: 2 Dihedral angle restraints: 7268 sinusoidal: 4772 harmonic: 2496 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ILE B 26 " pdb=" C ILE B 26 " pdb=" N GLN B 27 " pdb=" CA GLN B 27 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 89.21 130.79 1 3.50e+01 8.16e-04 1.30e+01 ... (remaining 7265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2156 0.110 - 0.220: 70 0.220 - 0.330: 0 0.330 - 0.440: 0 0.440 - 0.550: 3 Chirality restraints: 2229 Sorted by residual: chirality pdb=" P DA J 151 " pdb=" OP1 DA J 151 " pdb=" OP2 DA J 151 " pdb=" O5' DA J 151 " both_signs ideal model delta sigma weight residual True 2.34 -2.88 -0.55 2.00e-01 2.50e+01 7.55e+00 chirality pdb=" P DG J 152 " pdb=" OP1 DG J 152 " pdb=" OP2 DG J 152 " pdb=" O5' DG J 152 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" P DA J 153 " pdb=" OP1 DA J 153 " pdb=" OP2 DA J 153 " pdb=" O5' DA J 153 " both_signs ideal model delta sigma weight residual True 2.34 -2.85 -0.51 2.00e-01 2.50e+01 6.56e+00 ... (remaining 2226 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " -0.036 2.00e-02 2.50e+03 2.27e-02 1.03e+01 pdb=" CG TYR B 88 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 71 " 0.271 9.50e-02 1.11e+02 1.21e-01 9.07e+00 pdb=" NE ARG C 71 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 71 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG C 71 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 71 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " -0.022 2.00e-02 2.50e+03 2.08e-02 8.65e+00 pdb=" CG TYR H 80 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.009 2.00e-02 2.50e+03 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 902 2.73 - 3.27: 11782 3.27 - 3.81: 25710 3.81 - 4.36: 28992 4.36 - 4.90: 41823 Nonbonded interactions: 109209 Sorted by model distance: nonbonded pdb=" O LEU G 85 " pdb=" OD1 ASN G 89 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.220 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.250 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.288 3.040 ... (remaining 109204 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 40 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 134)) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 117)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 1.090 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.140 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 0.076 13366 Z= 0.541 Angle : 0.914 10.752 19335 Z= 0.733 Chirality : 0.053 0.550 2229 Planarity : 0.007 0.121 1440 Dihedral : 28.102 130.794 5652 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.15 % Allowed : 22.19 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.28), residues: 840 helix: 1.54 (0.22), residues: 555 sheet: 1.21 (1.10), residues: 25 loop : -0.35 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 96 TYR 0.052 0.003 TYR B 88 PHE 0.012 0.002 PHE B 100 TRP 0.009 0.002 TRP M 25 HIS 0.008 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.54 (13362) covalent geometry : angle 0.91242 / 0.73 (19329) hydrogen bonds : bond 0.06810 / 4.36 ( 803) hydrogen bonds : angle 4.12141 / 3.07 ( 2016) metal coordination : bond 0.01028 / 0.51 ( 4) metal coordination : angle 3.15875 / 1.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: F 74 GLU cc_start: 0.9157 (tp30) cc_final: 0.8728 (tp30) REVERT: H 31 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8516 (pttm) REVERT: H 65 ASP cc_start: 0.9228 (t0) cc_final: 0.9027 (t0) REVERT: H 80 TYR cc_start: 0.8323 (m-80) cc_final: 0.7947 (m-80) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1237 time to fit residues: 31.0411 Evaluate side-chains 158 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** H 46 HIS ** 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 = 0.3480 r_free = 0.3480 target = 0.054797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040135 restraints weight = 74203.845| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.00 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13366 Z= 0.158 Angle : 0.658 10.341 19335 Z= 0.394 Chirality : 0.045 0.259 2229 Planarity : 0.005 0.056 1440 Dihedral : 30.810 127.674 4132 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.67 % Allowed : 19.91 % Favored : 78.42 % 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: 1.66 (0.28), residues: 840 helix: 1.80 (0.22), residues: 557 sheet: 1.13 (1.10), residues: 25 loop : -0.39 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 76 TYR 0.052 0.002 TYR B 88 PHE 0.010 0.001 PHE B 61 TRP 0.006 0.002 TRP M 25 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.16 (13362) covalent geometry : angle 0.65703 / 0.39 (19329) hydrogen bonds : bond 0.05232 / 3.29 ( 803) hydrogen bonds : angle 3.60288 / 2.67 ( 2016) metal coordination : bond 0.00974 / 0.49 ( 4) metal coordination : angle 2.11759 / 1.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7482 (m-80) cc_final: 0.7258 (m-80) REVERT: C 64 GLU cc_start: 0.8608 (tp30) cc_final: 0.8329 (tm-30) REVERT: C 100 VAL cc_start: 0.9635 (t) cc_final: 0.9289 (p) REVERT: D 65 ASP cc_start: 0.9086 (t0) cc_final: 0.8820 (t0) REVERT: F 53 GLU cc_start: 0.9364 (tp30) cc_final: 0.8945 (mm-30) REVERT: H 31 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8458 (pttm) REVERT: H 65 ASP cc_start: 0.9205 (t0) cc_final: 0.8944 (t0) REVERT: H 68 GLU cc_start: 0.9034 (tp30) cc_final: 0.8771 (tp30) REVERT: H 80 TYR cc_start: 0.8008 (m-10) cc_final: 0.7685 (m-80) outliers start: 11 outliers final: 6 residues processed: 177 average time/residue: 0.1151 time to fit residues: 28.8990 Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 0.0470 chunk 104 optimal weight: 50.0000 chunk 12 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** 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 = 0.3489 r_free = 0.3489 target = 0.054851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.040116 restraints weight = 73876.194| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.90 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13366 Z= 0.152 Angle : 0.623 6.353 19335 Z= 0.374 Chirality : 0.043 0.214 2229 Planarity : 0.005 0.056 1440 Dihedral : 30.839 124.227 4132 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.98 % Allowed : 19.76 % Favored : 78.27 % 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: 1.82 (0.29), residues: 840 helix: 1.93 (0.22), residues: 562 sheet: 1.22 (1.11), residues: 25 loop : -0.41 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 76 TYR 0.044 0.002 TYR B 88 PHE 0.010 0.001 PHE E 78 TRP 0.003 0.001 TRP M 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (13362) covalent geometry : angle 0.62222 / 0.37 (19329) hydrogen bonds : bond 0.04663 / 2.93 ( 803) hydrogen bonds : angle 3.41064 / 2.52 ( 2016) metal coordination : bond 0.00837 / 0.42 ( 4) metal coordination : angle 2.27431 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 0.361 Fit side-chains REVERT: C 64 GLU cc_start: 0.8673 (tp30) cc_final: 0.8333 (tm-30) REVERT: C 90 ASP cc_start: 0.8130 (t0) cc_final: 0.7874 (t0) REVERT: C 95 LYS cc_start: 0.9464 (mtpp) cc_final: 0.9213 (mtpp) REVERT: D 43 LYS cc_start: 0.9352 (mmtm) cc_final: 0.8939 (tppt) REVERT: D 65 ASP cc_start: 0.9064 (t0) cc_final: 0.8816 (t0) REVERT: D 76 ARG cc_start: 0.9224 (ttm110) cc_final: 0.8993 (ttp-110) REVERT: E 76 GLN cc_start: 0.8918 (mp10) cc_final: 0.8627 (mp10) REVERT: E 125 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8744 (mp10) REVERT: F 53 GLU cc_start: 0.9377 (tp30) cc_final: 0.8988 (tp30) REVERT: H 31 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8433 (pttm) REVERT: H 65 ASP cc_start: 0.9168 (t0) cc_final: 0.8928 (t0) REVERT: H 68 GLU cc_start: 0.9079 (tp30) cc_final: 0.8799 (tp30) REVERT: H 80 TYR cc_start: 0.8065 (m-10) cc_final: 0.7793 (m-80) outliers start: 13 outliers final: 7 residues processed: 179 average time/residue: 0.1209 time to fit residues: 30.5105 Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 40.0000 chunk 101 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** 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 = 0.3452 r_free = 0.3452 target = 0.053181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037970 restraints weight = 73148.465| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.94 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13366 Z= 0.188 Angle : 0.644 7.272 19335 Z= 0.378 Chirality : 0.043 0.207 2229 Planarity : 0.005 0.053 1440 Dihedral : 30.885 122.256 4132 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.89 % Allowed : 19.91 % Favored : 77.20 % 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: 2.01 (0.29), residues: 840 helix: 2.08 (0.22), residues: 564 sheet: 1.27 (1.14), residues: 25 loop : -0.37 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.023 0.002 TYR G 57 PHE 0.011 0.001 PHE M 32 TRP 0.037 0.015 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (13362) covalent geometry : angle 0.64148 / 0.38 (19329) hydrogen bonds : bond 0.05152 / 3.33 ( 803) hydrogen bonds : angle 3.41542 / 2.54 ( 2016) metal coordination : bond 0.00887 / 0.44 ( 4) metal coordination : angle 2.99387 / 1.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8794 (tp30) cc_final: 0.8468 (tm-30) REVERT: C 90 ASP cc_start: 0.8136 (t0) cc_final: 0.7684 (t0) REVERT: D 43 LYS cc_start: 0.9384 (mmtm) cc_final: 0.8948 (tppt) REVERT: D 65 ASP cc_start: 0.9112 (t0) cc_final: 0.8814 (t0) REVERT: D 76 ARG cc_start: 0.9324 (ttm110) cc_final: 0.9067 (ttp-110) REVERT: E 76 GLN cc_start: 0.8852 (mp10) cc_final: 0.8557 (mp10) REVERT: F 53 GLU cc_start: 0.9431 (tp30) cc_final: 0.9049 (tp30) REVERT: G 39 TYR cc_start: 0.8522 (m-80) cc_final: 0.7979 (m-80) REVERT: G 91 GLU cc_start: 0.8980 (tp30) cc_final: 0.8754 (tp30) REVERT: G 92 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: H 65 ASP cc_start: 0.9242 (t0) cc_final: 0.8965 (t0) REVERT: H 68 GLU cc_start: 0.9150 (tp30) cc_final: 0.8660 (tp30) REVERT: H 80 TYR cc_start: 0.8075 (m-10) cc_final: 0.7734 (m-80) REVERT: H 102 GLU cc_start: 0.7975 (tp30) cc_final: 0.7743 (tp30) outliers start: 19 outliers final: 9 residues processed: 171 average time/residue: 0.1148 time to fit residues: 27.8327 Evaluate side-chains 164 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 65 optimal weight: 0.0050 chunk 83 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** H 46 HIS ** 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 = 0.3468 r_free = 0.3468 target = 0.053659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038653 restraints weight = 72828.917| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.82 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13366 Z= 0.146 Angle : 0.617 7.042 19335 Z= 0.365 Chirality : 0.042 0.215 2229 Planarity : 0.004 0.053 1440 Dihedral : 30.829 120.660 4132 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.58 % Allowed : 21.28 % Favored : 76.14 % 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: 2.06 (0.29), residues: 840 helix: 2.13 (0.22), residues: 564 sheet: 1.27 (1.15), residues: 25 loop : -0.38 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 76 TYR 0.029 0.002 TYR B 88 PHE 0.007 0.001 PHE E 78 TRP 0.004 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (13362) covalent geometry : angle 0.61571 / 0.36 (19329) hydrogen bonds : bond 0.04584 / 2.95 ( 803) hydrogen bonds : angle 3.27260 / 2.42 ( 2016) metal coordination : bond 0.00817 / 0.41 ( 4) metal coordination : angle 2.34272 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8808 (tp30) cc_final: 0.8473 (tm-30) REVERT: D 43 LYS cc_start: 0.9368 (mmtm) cc_final: 0.8922 (tppt) REVERT: D 65 ASP cc_start: 0.9126 (t0) cc_final: 0.8851 (t0) REVERT: D 76 ARG cc_start: 0.9338 (ttm110) cc_final: 0.9086 (ttp-110) REVERT: E 76 GLN cc_start: 0.8825 (mt0) cc_final: 0.8444 (mp10) REVERT: F 53 GLU cc_start: 0.9380 (tp30) cc_final: 0.8888 (mm-30) REVERT: G 92 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: H 65 ASP cc_start: 0.9308 (t0) cc_final: 0.9021 (t0) REVERT: H 68 GLU cc_start: 0.9158 (tp30) cc_final: 0.8875 (tp30) REVERT: H 102 GLU cc_start: 0.8076 (tp30) cc_final: 0.7792 (tp30) outliers start: 17 outliers final: 9 residues processed: 177 average time/residue: 0.1183 time to fit residues: 29.6578 Evaluate side-chains 168 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 92 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** 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 = 0.3405 r_free = 0.3405 target = 0.051379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.036200 restraints weight = 73975.068| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.91 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.103 13366 Z= 0.276 Angle : 0.710 8.551 19335 Z= 0.403 Chirality : 0.045 0.218 2229 Planarity : 0.005 0.051 1440 Dihedral : 31.018 120.138 4132 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.50 % Allowed : 21.88 % Favored : 74.62 % 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: 1.82 (0.28), residues: 840 helix: 1.96 (0.22), residues: 562 sheet: 1.35 (1.23), residues: 23 loop : -0.50 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 76 TYR 0.051 0.003 TYR H 80 PHE 0.011 0.001 PHE A 104 TRP 0.008 0.002 TRP M 25 HIS 0.008 0.002 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.28 (13362) covalent geometry : angle 0.70724 / 0.40 (19329) hydrogen bonds : bond 0.06700 / 4.40 ( 803) hydrogen bonds : angle 3.62451 / 2.71 ( 2016) metal coordination : bond 0.01673 / 0.84 ( 4) metal coordination : angle 3.80566 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8873 (tp30) cc_final: 0.8573 (tm-30) REVERT: C 90 ASP cc_start: 0.8120 (t0) cc_final: 0.7870 (t0) REVERT: D 43 LYS cc_start: 0.9402 (mmtm) cc_final: 0.9013 (tppt) REVERT: D 76 ARG cc_start: 0.9245 (ttm110) cc_final: 0.9011 (ttp-110) REVERT: F 53 GLU cc_start: 0.9445 (tp30) cc_final: 0.9086 (tp30) REVERT: G 92 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: H 65 ASP cc_start: 0.9303 (t0) cc_final: 0.8997 (t0) REVERT: H 68 GLU cc_start: 0.9168 (tp30) cc_final: 0.8872 (tp30) REVERT: H 102 GLU cc_start: 0.8213 (tp30) cc_final: 0.7249 (tp30) REVERT: H 106 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7019 (m170) outliers start: 23 outliers final: 16 residues processed: 159 average time/residue: 0.1217 time to fit residues: 27.0977 Evaluate side-chains 148 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.051956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036629 restraints weight = 73793.418| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.89 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13366 Z= 0.187 Angle : 0.666 10.399 19335 Z= 0.382 Chirality : 0.043 0.218 2229 Planarity : 0.005 0.051 1440 Dihedral : 31.027 118.051 4132 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.80 % Allowed : 22.95 % Favored : 73.25 % 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: 1.94 (0.28), residues: 840 helix: 2.08 (0.22), residues: 562 sheet: 1.29 (1.21), residues: 23 loop : -0.52 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 52 TYR 0.062 0.003 TYR H 80 PHE 0.007 0.001 PHE B 61 TRP 0.005 0.001 TRP M 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.19 (13362) covalent geometry : angle 0.66442 / 0.38 (19329) hydrogen bonds : bond 0.05177 / 3.37 ( 803) hydrogen bonds : angle 3.47387 / 2.58 ( 2016) metal coordination : bond 0.01161 / 0.58 ( 4) metal coordination : angle 2.87948 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8961 (tmtt) REVERT: C 64 GLU cc_start: 0.8827 (tp30) cc_final: 0.8581 (tm-30) REVERT: D 43 LYS cc_start: 0.9372 (mmtm) cc_final: 0.8985 (tppt) REVERT: D 76 ARG cc_start: 0.9261 (ttm110) cc_final: 0.9059 (ttp-110) REVERT: G 39 TYR cc_start: 0.8504 (m-80) cc_final: 0.8287 (m-80) REVERT: G 92 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: H 65 ASP cc_start: 0.9286 (t0) cc_final: 0.8985 (t0) REVERT: H 68 GLU cc_start: 0.9153 (tp30) cc_final: 0.8897 (tp30) REVERT: H 90 GLU cc_start: 0.8831 (mp0) cc_final: 0.8460 (mp0) REVERT: H 102 GLU cc_start: 0.8119 (tp30) cc_final: 0.7158 (tp30) REVERT: H 106 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7004 (m170) outliers start: 25 outliers final: 19 residues processed: 163 average time/residue: 0.1300 time to fit residues: 29.6544 Evaluate side-chains 163 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain M residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.050499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.034851 restraints weight = 74977.996| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.96 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 13366 Z= 0.263 Angle : 0.727 8.717 19335 Z= 0.407 Chirality : 0.045 0.222 2229 Planarity : 0.005 0.050 1440 Dihedral : 31.156 116.238 4132 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.95 % Allowed : 23.56 % Favored : 72.49 % 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: 1.72 (0.28), residues: 840 helix: 1.96 (0.22), residues: 560 sheet: 1.88 (1.21), residues: 21 loop : -0.76 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 76 TYR 0.059 0.003 TYR H 80 PHE 0.008 0.001 PHE A 104 TRP 0.008 0.002 TRP M 25 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.26 (13362) covalent geometry : angle 0.72447 / 0.41 (19329) hydrogen bonds : bond 0.06637 / 4.39 ( 803) hydrogen bonds : angle 3.70468 / 2.77 ( 2016) metal coordination : bond 0.01628 / 0.81 ( 4) metal coordination : angle 3.76276 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8909 (tp30) cc_final: 0.8667 (tm-30) REVERT: C 90 ASP cc_start: 0.8119 (t0) cc_final: 0.7836 (t0) REVERT: D 43 LYS cc_start: 0.9386 (mmtm) cc_final: 0.8995 (tppt) REVERT: D 76 ARG cc_start: 0.9314 (ttm110) cc_final: 0.9077 (ttp-110) REVERT: F 53 GLU cc_start: 0.9423 (mm-30) cc_final: 0.8928 (mm-30) REVERT: G 92 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: H 65 ASP cc_start: 0.9350 (t0) cc_final: 0.9033 (t0) REVERT: H 68 GLU cc_start: 0.9189 (tp30) cc_final: 0.8869 (tp30) REVERT: H 90 GLU cc_start: 0.8944 (mp0) cc_final: 0.8600 (mp0) REVERT: H 102 GLU cc_start: 0.8291 (tp30) cc_final: 0.7316 (tp30) REVERT: H 106 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7056 (m170) outliers start: 26 outliers final: 20 residues processed: 159 average time/residue: 0.1332 time to fit residues: 29.4899 Evaluate side-chains 159 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 50.0000 chunk 95 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 72 optimal weight: 50.0000 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 86 optimal weight: 50.0000 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.050632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.035351 restraints weight = 74183.247| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.92 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13366 Z= 0.256 Angle : 0.717 10.328 19335 Z= 0.403 Chirality : 0.045 0.222 2229 Planarity : 0.005 0.049 1440 Dihedral : 31.175 114.558 4132 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.34 % Allowed : 24.62 % Favored : 72.04 % 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: 1.69 (0.28), residues: 840 helix: 1.97 (0.22), residues: 559 sheet: 1.92 (1.21), residues: 21 loop : -0.84 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.060 0.003 TYR H 80 PHE 0.007 0.001 PHE B 61 TRP 0.007 0.002 TRP M 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.26 (13362) covalent geometry : angle 0.71434 / 0.40 (19329) hydrogen bonds : bond 0.05959 / 3.93 ( 803) hydrogen bonds : angle 3.67975 / 2.75 ( 2016) metal coordination : bond 0.01478 / 0.74 ( 4) metal coordination : angle 3.48543 / 1.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8902 (tp30) cc_final: 0.8628 (tm-30) REVERT: D 43 LYS cc_start: 0.9357 (mmtm) cc_final: 0.8970 (tppt) REVERT: G 92 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: H 65 ASP cc_start: 0.9367 (t0) cc_final: 0.9043 (t0) REVERT: H 68 GLU cc_start: 0.9191 (tp30) cc_final: 0.8904 (tp30) REVERT: H 90 GLU cc_start: 0.8969 (mp0) cc_final: 0.8619 (mp0) REVERT: H 102 GLU cc_start: 0.8289 (tp30) cc_final: 0.7264 (tp30) REVERT: H 106 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7071 (m170) outliers start: 22 outliers final: 18 residues processed: 159 average time/residue: 0.1277 time to fit residues: 28.1700 Evaluate side-chains 160 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain M residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 91 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 103 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 25 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.051491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.036343 restraints weight = 73855.832| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.86 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13366 Z= 0.170 Angle : 0.678 11.074 19335 Z= 0.386 Chirality : 0.043 0.222 2229 Planarity : 0.004 0.049 1440 Dihedral : 31.082 112.364 4132 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.04 % Allowed : 24.92 % Favored : 72.04 % 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: 1.81 (0.29), residues: 840 helix: 2.04 (0.22), residues: 561 sheet: 2.21 (1.23), residues: 21 loop : -0.79 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.059 0.003 TYR H 80 PHE 0.008 0.001 PHE B 61 TRP 0.005 0.001 TRP M 25 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (13362) covalent geometry : angle 0.67654 / 0.39 (19329) hydrogen bonds : bond 0.04926 / 3.21 ( 803) hydrogen bonds : angle 3.46632 / 2.56 ( 2016) metal coordination : bond 0.00990 / 0.50 ( 4) metal coordination : angle 2.59911 / 1.30 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1680 Ramachandran restraints generated. 840 Oldfield, 0 Emsley, 840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8824 (tp30) cc_final: 0.8597 (tm-30) REVERT: D 43 LYS cc_start: 0.9291 (mmtm) cc_final: 0.8928 (tppt) REVERT: D 65 ASP cc_start: 0.9155 (t0) cc_final: 0.8916 (t0) REVERT: E 76 GLN cc_start: 0.9047 (mt0) cc_final: 0.8834 (mp10) REVERT: E 107 THR cc_start: 0.9349 (m) cc_final: 0.9087 (p) REVERT: F 92 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.9037 (ttp80) REVERT: G 38 ASN cc_start: 0.8923 (p0) cc_final: 0.8639 (p0) REVERT: G 92 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: H 65 ASP cc_start: 0.9249 (t0) cc_final: 0.8975 (t0) REVERT: H 68 GLU cc_start: 0.9158 (tp30) cc_final: 0.8882 (tp30) REVERT: H 90 GLU cc_start: 0.8885 (mp0) cc_final: 0.8563 (mp0) REVERT: H 102 GLU cc_start: 0.8114 (tp30) cc_final: 0.7124 (tp30) REVERT: H 106 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.6942 (m170) outliers start: 20 outliers final: 13 residues processed: 165 average time/residue: 0.1292 time to fit residues: 29.6088 Evaluate side-chains 165 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 106 HIS Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 88 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.051560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.036393 restraints weight = 73652.757| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.87 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 13366 Z= 0.251 Angle : 0.870 59.198 19335 Z= 0.525 Chirality : 0.052 1.344 2229 Planarity : 0.005 0.059 1440 Dihedral : 31.086 112.338 4132 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.69 % Favored : 96.07 % Rotamer: Outliers : 2.43 % Allowed : 26.14 % Favored : 71.43 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.80 (0.28), residues: 840 helix: 2.03 (0.22), residues: 561 sheet: 2.23 (1.23), residues: 21 loop : -0.80 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 47 TYR 0.058 0.003 TYR H 80 PHE 0.009 0.001 PHE B 61 TRP 0.005 0.001 TRP M 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.25 (13362) covalent geometry : angle 0.86918 / 0.52 (19329) hydrogen bonds : bond 0.04931 / 3.22 ( 803) hydrogen bonds : angle 3.46191 / 2.56 ( 2016) metal coordination : bond 0.00992 / 0.50 ( 4) metal coordination : angle 2.61455 / 1.31 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2107.38 seconds wall clock time: 37 minutes 8.03 seconds (2228.03 seconds total)