Starting phenix.real_space_refine on Wed Mar 4 07:02:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x3x_32996/03_2026/7x3x_32996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x3x_32996/03_2026/7x3x_32996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x3x_32996/03_2026/7x3x_32996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x3x_32996/03_2026/7x3x_32996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x3x_32996/03_2026/7x3x_32996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x3x_32996/03_2026/7x3x_32996.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 292 5.49 5 S 12 5.16 5 C 6647 2.51 5 N 2257 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12036 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 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: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 62 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Time building chain proxies: 2.41, per 1000 atoms: 0.20 Number of scatterers: 12036 At special positions: 0 Unit cell: (93.095, 125.57, 116.91, 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 12 16.00 P 292 15.00 O 2828 8.00 N 2257 7.00 C 6647 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: 0.80 Conformation dependent library (CDL) restraints added in 262.6 milliseconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1444 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 70.9% alpha, 2.6% beta 137 base pairs and 225 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.754A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (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 25 through 29 removed outlier: 3.969A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.810A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.485A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain '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 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.686A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.802A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.422A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.603A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain '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 101 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.706A 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: 7.886A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.123A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.991A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.547A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 406 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 351 hydrogen bonds 702 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 225 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 1258 1.27 - 1.41: 3834 1.41 - 1.55: 7099 1.55 - 1.69: 624 1.69 - 1.83: 28 Bond restraints: 12843 Sorted by residual: bond pdb=" C3' DA I 90 " pdb=" O3' DA I 90 " ideal model delta sigma weight residual 1.422 1.823 -0.401 3.00e-02 1.11e+03 1.78e+02 bond pdb=" C1' DT I 89 " pdb=" N1 DT I 89 " ideal model delta sigma weight residual 1.490 1.125 0.365 3.00e-02 1.11e+03 1.48e+02 bond pdb=" C1' DT I 87 " pdb=" N1 DT I 87 " ideal model delta sigma weight residual 1.490 1.830 -0.340 3.00e-02 1.11e+03 1.28e+02 bond pdb=" O5' DA I 91 " pdb=" C5' DA I 91 " ideal model delta sigma weight residual 1.423 1.700 -0.277 3.00e-02 1.11e+03 8.50e+01 bond pdb=" C1' DC J 54 " pdb=" N1 DC J 54 " ideal model delta sigma weight residual 1.490 1.233 0.257 3.00e-02 1.11e+03 7.35e+01 ... (remaining 12838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 18462 4.17 - 8.35: 103 8.35 - 12.52: 33 12.52 - 16.69: 7 16.69 - 20.87: 5 Bond angle restraints: 18610 Sorted by residual: angle pdb=" C2' DG J 55 " pdb=" C1' DG J 55 " pdb=" N9 DG J 55 " ideal model delta sigma weight residual 113.50 96.41 17.09 1.50e+00 4.44e-01 1.30e+02 angle pdb=" C1' DG J 55 " pdb=" N9 DG J 55 " pdb=" C8 DG J 55 " ideal model delta sigma weight residual 127.00 113.23 13.77 1.50e+00 4.44e-01 8.42e+01 angle pdb=" C5' DA I 90 " pdb=" C4' DA I 90 " pdb=" O4' DA I 90 " ideal model delta sigma weight residual 109.40 96.23 13.17 1.50e+00 4.44e-01 7.70e+01 angle pdb=" O4' DT I 88 " pdb=" C1' DT I 88 " pdb=" N1 DT I 88 " ideal model delta sigma weight residual 108.40 121.03 -12.63 1.50e+00 4.44e-01 7.09e+01 angle pdb=" O3' DG J 52 " pdb=" P DG J 53 " pdb=" O5' DG J 53 " ideal model delta sigma weight residual 104.00 116.10 -12.10 1.50e+00 4.44e-01 6.51e+01 ... (remaining 18605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 5604 35.19 - 70.37: 1333 70.37 - 105.56: 27 105.56 - 140.74: 1 140.74 - 175.92: 2 Dihedral angle restraints: 6967 sinusoidal: 4733 harmonic: 2234 Sorted by residual: dihedral pdb=" CA LYS B 20 " pdb=" C LYS B 20 " pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA ARG B 19 " pdb=" C ARG B 19 " pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 44.08 175.92 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 6964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2090 0.159 - 0.317: 22 0.317 - 0.476: 9 0.476 - 0.634: 2 0.634 - 0.793: 4 Chirality restraints: 2127 Sorted by residual: chirality pdb=" P DT I 89 " pdb=" OP1 DT I 89 " pdb=" OP2 DT I 89 " pdb=" O5' DT I 89 " both_signs ideal model delta sigma weight residual True 2.35 -1.55 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C1' DT I 89 " pdb=" O4' DT I 89 " pdb=" C2' DT I 89 " pdb=" N1 DT I 89 " both_signs ideal model delta sigma weight residual False 2.47 1.79 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1' DA I 90 " pdb=" O4' DA I 90 " pdb=" C2' DA I 90 " pdb=" N9 DA I 90 " both_signs ideal model delta sigma weight residual False 2.42 1.77 0.65 2.00e-01 2.50e+01 1.07e+01 ... (remaining 2124 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 55 " 0.071 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" N9 DG J 55 " -0.203 2.00e-02 2.50e+03 pdb=" C8 DG J 55 " 0.030 2.00e-02 2.50e+03 pdb=" N7 DG J 55 " 0.065 2.00e-02 2.50e+03 pdb=" C5 DG J 55 " 0.012 2.00e-02 2.50e+03 pdb=" C6 DG J 55 " 0.035 2.00e-02 2.50e+03 pdb=" O6 DG J 55 " -0.053 2.00e-02 2.50e+03 pdb=" N1 DG J 55 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 55 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG J 55 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DG J 55 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG J 55 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 54 " 0.074 2.00e-02 2.50e+03 4.96e-02 5.54e+01 pdb=" N1 DC J 54 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DC J 54 " -0.062 2.00e-02 2.50e+03 pdb=" O2 DC J 54 " 0.033 2.00e-02 2.50e+03 pdb=" N3 DC J 54 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DC J 54 " -0.052 2.00e-02 2.50e+03 pdb=" N4 DC J 54 " 0.081 2.00e-02 2.50e+03 pdb=" C5 DC J 54 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 54 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 89 " 0.064 2.00e-02 2.50e+03 4.21e-02 4.43e+01 pdb=" N1 DT I 89 " -0.102 2.00e-02 2.50e+03 pdb=" C2 DT I 89 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DT I 89 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DT I 89 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DT I 89 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 89 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DT I 89 " 0.016 2.00e-02 2.50e+03 pdb=" C7 DT I 89 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 89 " -0.015 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 40 2.54 - 3.13: 8386 3.13 - 3.72: 21654 3.72 - 4.31: 28955 4.31 - 4.90: 42283 Nonbonded interactions: 101318 Sorted by model distance: nonbonded pdb=" O5' DA I 90 " pdb=" O4' DA I 90 " model vdw 1.947 2.432 nonbonded pdb=" O4' DT I 89 " pdb=" C2 DT I 89 " model vdw 2.120 2.608 nonbonded pdb=" C1' DT I 89 " pdb=" O2 DT I 89 " model vdw 2.194 2.776 nonbonded pdb=" OE2 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.206 3.120 nonbonded pdb=" O4' DT I 89 " pdb=" O2 DT I 89 " model vdw 2.206 3.040 ... (remaining 101313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 19 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 19 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 118)) 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 118)) } 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.770 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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 : 0.012 0.401 12843 Z= 0.504 Angle : 0.982 20.866 18610 Z= 0.564 Chirality : 0.062 0.793 2127 Planarity : 0.006 0.068 1347 Dihedral : 27.916 175.925 5523 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.16 % Allowed : 0.64 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 2.89 (0.30), residues: 751 helix: 2.82 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.54 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 19 TYR 0.018 0.002 TYR B 88 PHE 0.012 0.001 PHE D 67 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.01200 (12843) covalent geometry : angle 0.98230 (18610) hydrogen bonds : bond 0.10856 ( 757) hydrogen bonds : angle 3.37182 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7865 (mt) cc_final: 0.7564 (mt) REVERT: C 41 GLU cc_start: 0.7525 (tt0) cc_final: 0.7219 (tt0) REVERT: C 99 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8033 (mmm160) REVERT: D 39 TYR cc_start: 0.8208 (t80) cc_final: 0.7930 (t80) REVERT: D 48 ASP cc_start: 0.8250 (p0) cc_final: 0.8002 (p0) REVERT: D 73 GLU cc_start: 0.8095 (tp30) cc_final: 0.7815 (tp30) REVERT: D 82 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8498 (mmtt) REVERT: D 102 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7925 (mt-10) REVERT: G 90 ASP cc_start: 0.8076 (t0) cc_final: 0.7660 (t0) REVERT: G 95 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8672 (ttmm) REVERT: H 36 ILE cc_start: 0.8634 (mt) cc_final: 0.8324 (tp) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1694 time to fit residues: 41.2748 Evaluate side-chains 127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 93 GLN C 24 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.079221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.057071 restraints weight = 47775.278| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.37 r_work: 0.3033 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12843 Z= 0.158 Angle : 0.559 6.611 18610 Z= 0.336 Chirality : 0.034 0.214 2127 Planarity : 0.004 0.041 1347 Dihedral : 30.571 168.353 4045 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.64 % Allowed : 9.08 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.30), residues: 751 helix: 3.10 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.009 0.001 TYR D 37 PHE 0.009 0.001 PHE H 67 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd covalent geometry : bond 0.00341 (12843) covalent geometry : angle 0.55913 (18610) hydrogen bonds : bond 0.04202 ( 757) hydrogen bonds : angle 2.69162 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8440 (mmm) cc_final: 0.8233 (mmm) REVERT: B 78 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8121 (mtm-85) REVERT: C 56 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8654 (tt0) REVERT: D 48 ASP cc_start: 0.8487 (p0) cc_final: 0.8214 (p0) REVERT: D 80 TYR cc_start: 0.7705 (m-10) cc_final: 0.7484 (m-10) REVERT: E 73 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7503 (mt-10) REVERT: E 120 MET cc_start: 0.7683 (mtt) cc_final: 0.7345 (mtt) REVERT: G 90 ASP cc_start: 0.8683 (t0) cc_final: 0.8466 (t0) outliers start: 4 outliers final: 1 residues processed: 144 average time/residue: 0.1296 time to fit residues: 25.6487 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN D 79 HIS F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.068021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046566 restraints weight = 49287.410| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.35 r_work: 0.2745 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 12843 Z= 0.311 Angle : 0.691 6.187 18610 Z= 0.405 Chirality : 0.041 0.160 2127 Planarity : 0.005 0.045 1347 Dihedral : 31.520 158.025 4045 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.23 % Allowed : 10.35 % Favored : 87.42 % 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: 2.50 (0.30), residues: 751 helix: 2.50 (0.21), residues: 545 sheet: None (None), residues: 0 loop : -0.76 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 29 TYR 0.029 0.003 TYR D 34 PHE 0.033 0.002 PHE C 25 HIS 0.007 0.002 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00708 (12843) covalent geometry : angle 0.69097 (18610) hydrogen bonds : bond 0.06470 ( 757) hydrogen bonds : angle 3.30736 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8888 (pm20) cc_final: 0.8641 (pm20) REVERT: B 93 GLN cc_start: 0.8925 (mt0) cc_final: 0.8688 (mt0) REVERT: C 56 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8875 (tm-30) REVERT: D 48 ASP cc_start: 0.8797 (p0) cc_final: 0.8569 (p0) REVERT: D 80 TYR cc_start: 0.8169 (m-10) cc_final: 0.7753 (m-10) REVERT: D 102 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8251 (tt0) REVERT: E 73 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7927 (mt-10) REVERT: G 90 ASP cc_start: 0.8810 (t0) cc_final: 0.8508 (t0) REVERT: H 31 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8413 (mptt) REVERT: H 102 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8733 (mm-30) outliers start: 14 outliers final: 7 residues processed: 127 average time/residue: 0.1318 time to fit residues: 22.9552 Evaluate side-chains 115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.068857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047711 restraints weight = 48146.360| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.37 r_work: 0.2781 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12843 Z= 0.174 Angle : 0.559 9.718 18610 Z= 0.335 Chirality : 0.033 0.123 2127 Planarity : 0.004 0.044 1347 Dihedral : 30.774 161.646 4045 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.96 % Allowed : 12.26 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.30), residues: 751 helix: 3.04 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.76 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.010 0.001 TYR D 34 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (12843) covalent geometry : angle 0.55927 (18610) hydrogen bonds : bond 0.03930 ( 757) hydrogen bonds : angle 2.69589 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8955 (mtm-85) cc_final: 0.8542 (mtm-85) REVERT: C 56 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8656 (tm-30) REVERT: D 48 ASP cc_start: 0.8642 (p0) cc_final: 0.8332 (p0) REVERT: D 80 TYR cc_start: 0.8142 (m-10) cc_final: 0.7847 (m-10) REVERT: D 102 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8251 (tt0) REVERT: G 90 ASP cc_start: 0.8933 (t0) cc_final: 0.8716 (t0) REVERT: H 31 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8576 (mptt) outliers start: 6 outliers final: 3 residues processed: 128 average time/residue: 0.1276 time to fit residues: 22.5303 Evaluate side-chains 115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN ** E 113 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 = 0.3598 r_free = 0.3598 target = 0.069257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048144 restraints weight = 48184.669| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.39 r_work: 0.2806 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12843 Z= 0.153 Angle : 0.536 10.238 18610 Z= 0.320 Chirality : 0.032 0.121 2127 Planarity : 0.004 0.040 1347 Dihedral : 30.476 161.354 4045 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.43 % Allowed : 13.06 % Favored : 85.51 % 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: 3.37 (0.31), residues: 751 helix: 3.25 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.74 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 116 TYR 0.013 0.001 TYR D 34 PHE 0.008 0.001 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (12843) covalent geometry : angle 0.53619 (18610) hydrogen bonds : bond 0.03632 ( 757) hydrogen bonds : angle 2.54565 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8521 (mtp) cc_final: 0.8109 (mtp) REVERT: B 78 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8479 (mtm-85) REVERT: C 56 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8632 (tm-30) REVERT: D 48 ASP cc_start: 0.8660 (p0) cc_final: 0.8356 (p0) REVERT: D 80 TYR cc_start: 0.8110 (m-10) cc_final: 0.7722 (m-10) REVERT: D 102 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8241 (tt0) REVERT: E 73 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8258 (mt-10) REVERT: H 31 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8617 (mptt) REVERT: H 102 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8278 (mm-30) REVERT: H 105 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8675 (mtmm) outliers start: 9 outliers final: 5 residues processed: 129 average time/residue: 0.1307 time to fit residues: 23.3211 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** E 113 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 = 0.3556 r_free = 0.3556 target = 0.067492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046493 restraints weight = 48081.409| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.35 r_work: 0.2749 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12843 Z= 0.179 Angle : 0.557 11.754 18610 Z= 0.330 Chirality : 0.033 0.120 2127 Planarity : 0.004 0.041 1347 Dihedral : 30.529 157.364 4045 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.91 % Allowed : 13.54 % Favored : 84.55 % 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: 3.36 (0.31), residues: 751 helix: 3.23 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.013 0.001 TYR D 34 PHE 0.011 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (12843) covalent geometry : angle 0.55688 (18610) hydrogen bonds : bond 0.03961 ( 757) hydrogen bonds : angle 2.64076 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8999 (mtm-85) cc_final: 0.8554 (mtm-85) REVERT: C 56 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8713 (tm-30) REVERT: D 48 ASP cc_start: 0.8672 (p0) cc_final: 0.8428 (p0) REVERT: D 80 TYR cc_start: 0.8080 (m-10) cc_final: 0.7790 (m-10) REVERT: D 102 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8136 (tt0) REVERT: D 105 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8848 (tttm) REVERT: E 120 MET cc_start: 0.8332 (mtt) cc_final: 0.8075 (mtt) REVERT: F 24 ASP cc_start: 0.6147 (t0) cc_final: 0.5893 (t0) REVERT: G 90 ASP cc_start: 0.8789 (t0) cc_final: 0.8569 (t0) outliers start: 12 outliers final: 9 residues processed: 128 average time/residue: 0.1315 time to fit residues: 23.1410 Evaluate side-chains 126 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.062897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042010 restraints weight = 48188.031| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.34 r_work: 0.2622 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12843 Z= 0.325 Angle : 0.676 11.605 18610 Z= 0.395 Chirality : 0.040 0.217 2127 Planarity : 0.005 0.053 1347 Dihedral : 31.277 164.748 4045 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.91 % Allowed : 13.69 % Favored : 84.39 % 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: 2.76 (0.30), residues: 751 helix: 2.73 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 88 TYR 0.015 0.002 TYR B 88 PHE 0.016 0.002 PHE C 25 HIS 0.005 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00744 (12843) covalent geometry : angle 0.67557 (18610) hydrogen bonds : bond 0.06056 ( 757) hydrogen bonds : angle 3.17856 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8974 (tm-30) REVERT: C 90 ASP cc_start: 0.9170 (t0) cc_final: 0.8923 (t0) REVERT: D 48 ASP cc_start: 0.8891 (p0) cc_final: 0.8584 (p0) REVERT: D 80 TYR cc_start: 0.8176 (m-10) cc_final: 0.7875 (m-10) REVERT: D 102 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8239 (tt0) REVERT: G 90 ASP cc_start: 0.8722 (t0) cc_final: 0.8437 (t0) outliers start: 12 outliers final: 9 residues processed: 119 average time/residue: 0.1249 time to fit residues: 20.4002 Evaluate side-chains 117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 110 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 93 GLN ** 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 = 0.3508 r_free = 0.3508 target = 0.065169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044515 restraints weight = 47683.109| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.35 r_work: 0.2700 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12843 Z= 0.154 Angle : 0.558 10.611 18610 Z= 0.334 Chirality : 0.033 0.164 2127 Planarity : 0.004 0.043 1347 Dihedral : 30.518 156.950 4045 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.80 % Allowed : 14.17 % Favored : 85.03 % 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: 3.25 (0.31), residues: 751 helix: 3.15 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.78 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 116 TYR 0.010 0.001 TYR D 37 PHE 0.011 0.002 PHE E 67 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00333 (12843) covalent geometry : angle 0.55834 (18610) hydrogen bonds : bond 0.03693 ( 757) hydrogen bonds : angle 2.62943 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8637 (mtp) cc_final: 0.8296 (mtp) REVERT: B 78 ARG cc_start: 0.8980 (mtm-85) cc_final: 0.8546 (mtm-85) REVERT: B 88 TYR cc_start: 0.9193 (m-10) cc_final: 0.8592 (m-80) REVERT: C 56 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8772 (tm-30) REVERT: D 80 TYR cc_start: 0.8192 (m-10) cc_final: 0.7738 (m-10) REVERT: D 102 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8100 (tt0) REVERT: E 73 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 90 ASP cc_start: 0.8812 (t0) cc_final: 0.8503 (t0) outliers start: 5 outliers final: 4 residues processed: 127 average time/residue: 0.1170 time to fit residues: 21.0862 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 110 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.064686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.043964 restraints weight = 47545.526| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.35 r_work: 0.2681 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12843 Z= 0.181 Angle : 0.573 11.321 18610 Z= 0.338 Chirality : 0.033 0.146 2127 Planarity : 0.004 0.042 1347 Dihedral : 30.493 155.384 4045 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.96 % Allowed : 14.65 % Favored : 84.39 % 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: 3.33 (0.31), residues: 751 helix: 3.20 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.011 0.001 TYR D 34 PHE 0.012 0.002 PHE E 67 HIS 0.002 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00407 (12843) covalent geometry : angle 0.57264 (18610) hydrogen bonds : bond 0.04013 ( 757) hydrogen bonds : angle 2.69667 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 78 ARG cc_start: 0.9010 (mtm-85) cc_final: 0.8558 (mtm-85) REVERT: C 56 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 90 ASP cc_start: 0.9035 (t0) cc_final: 0.8691 (t0) REVERT: D 80 TYR cc_start: 0.8209 (m-10) cc_final: 0.7899 (m-10) REVERT: D 102 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8121 (tt0) REVERT: E 73 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8486 (mt-10) REVERT: G 90 ASP cc_start: 0.8781 (t0) cc_final: 0.8521 (t0) outliers start: 6 outliers final: 3 residues processed: 121 average time/residue: 0.1200 time to fit residues: 20.5384 Evaluate side-chains 121 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.064997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.044658 restraints weight = 48234.395| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.21 r_work: 0.2729 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12843 Z= 0.172 Angle : 0.569 12.063 18610 Z= 0.335 Chirality : 0.033 0.171 2127 Planarity : 0.004 0.041 1347 Dihedral : 30.356 157.419 4045 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.64 % Allowed : 14.97 % Favored : 84.39 % 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: 3.32 (0.31), residues: 751 helix: 3.19 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.010 0.001 TYR D 34 PHE 0.011 0.001 PHE E 67 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00383 (12843) covalent geometry : angle 0.56880 (18610) hydrogen bonds : bond 0.03782 ( 757) hydrogen bonds : angle 2.65110 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 124 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8948 (mtm-85) cc_final: 0.8529 (mtm-85) REVERT: B 88 TYR cc_start: 0.9151 (m-10) cc_final: 0.8527 (m-80) REVERT: C 56 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8748 (tm-30) REVERT: D 80 TYR cc_start: 0.8149 (m-10) cc_final: 0.7658 (m-10) REVERT: D 102 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8119 (tt0) REVERT: E 73 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8347 (mt-10) REVERT: G 90 ASP cc_start: 0.8725 (t0) cc_final: 0.8503 (t0) outliers start: 4 outliers final: 4 residues processed: 125 average time/residue: 0.1326 time to fit residues: 22.8398 Evaluate side-chains 123 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 18 optimal weight: 0.0170 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.066252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046215 restraints weight = 47913.506| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.17 r_work: 0.2775 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12843 Z= 0.148 Angle : 0.552 13.295 18610 Z= 0.327 Chirality : 0.032 0.149 2127 Planarity : 0.004 0.063 1347 Dihedral : 30.155 159.403 4045 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.48 % Allowed : 15.13 % Favored : 84.39 % 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: 3.40 (0.31), residues: 751 helix: 3.25 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.010 0.001 TYR H 37 PHE 0.010 0.001 PHE E 67 HIS 0.002 0.000 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00322 (12843) covalent geometry : angle 0.55231 (18610) hydrogen bonds : bond 0.03474 ( 757) hydrogen bonds : angle 2.54423 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.06 seconds wall clock time: 50 minutes 55.53 seconds (3055.53 seconds total)