Starting phenix.real_space_refine on Tue Jul 29 21:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x3x_32996/07_2025/7x3x_32996.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x3x_32996/07_2025/7x3x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2025/7x3x_32996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2025/7x3x_32996.map" model { file = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2025/7x3x_32996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x3x_32996/07_2025/7x3x_32996.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.85, per 1000 atoms: 0.65 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: 3.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.55 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: 4.07 Time building geometry restraints manager: 3.87 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: 0.940 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.800 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.006 0.001 HIS A 39 PHE 0.012 0.001 PHE D 67 TYR 0.018 0.002 TYR B 88 ARG 0.037 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.10856 ( 757) hydrogen bonds : angle 3.37182 ( 1911) covalent geometry : bond 0.01200 (12843) covalent geometry : angle 0.98230 (18610) *********************** 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 : 1.002 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: 0.8389 (tp) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.3847 time to fit residues: 94.5907 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 : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.078562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.056336 restraints weight = 47561.192| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.39 r_work: 0.3011 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12843 Z= 0.163 Angle : 0.564 7.043 18610 Z= 0.339 Chirality : 0.034 0.214 2127 Planarity : 0.004 0.041 1347 Dihedral : 30.606 168.087 4045 Min Nonbonded Distance : 2.501 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.30), residues: 751 helix: 3.09 (0.22), residues: 543 sheet: None (None), residues: 0 loop : -0.42 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE H 67 TYR 0.010 0.001 TYR D 37 ARG 0.005 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 757) hydrogen bonds : angle 2.70834 ( 1911) covalent geometry : bond 0.00356 (12843) covalent geometry : angle 0.56448 (18610) *********************** 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 140 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8489 (mmm) cc_final: 0.8266 (mmm) REVERT: B 78 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8164 (mtm-85) REVERT: C 56 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8654 (tt0) REVERT: D 48 ASP cc_start: 0.8511 (p0) cc_final: 0.8234 (p0) REVERT: D 80 TYR cc_start: 0.7730 (m-10) cc_final: 0.7491 (m-10) REVERT: E 73 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7442 (mt-10) REVERT: E 120 MET cc_start: 0.7708 (mtt) cc_final: 0.7395 (mtt) REVERT: G 90 ASP cc_start: 0.8681 (t0) cc_final: 0.8456 (t0) outliers start: 4 outliers final: 1 residues processed: 139 average time/residue: 0.2687 time to fit residues: 51.2434 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 39 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 113 HIS F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.072009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049984 restraints weight = 48044.998| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.41 r_work: 0.2834 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12843 Z= 0.196 Angle : 0.583 6.334 18610 Z= 0.348 Chirality : 0.035 0.124 2127 Planarity : 0.004 0.039 1347 Dihedral : 30.888 165.463 4045 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.75 % Allowed : 10.03 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.30), residues: 751 helix: 3.00 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.58 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 82 PHE 0.019 0.002 PHE C 25 TYR 0.019 0.002 TYR D 34 ARG 0.005 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 757) hydrogen bonds : angle 2.84923 ( 1911) covalent geometry : bond 0.00440 (12843) covalent geometry : angle 0.58318 (18610) *********************** 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 138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8676 (pm20) cc_final: 0.8468 (pm20) REVERT: A 120 MET cc_start: 0.8706 (mmm) cc_final: 0.8379 (mmm) REVERT: C 56 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8582 (tm-30) REVERT: D 30 ARG cc_start: 0.7640 (mtp180) cc_final: 0.7431 (mtp180) REVERT: D 48 ASP cc_start: 0.8701 (p0) cc_final: 0.8323 (p0) REVERT: D 80 TYR cc_start: 0.8037 (m-10) cc_final: 0.7611 (m-10) REVERT: D 102 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8351 (tt0) REVERT: E 73 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7871 (mt-10) REVERT: G 90 ASP cc_start: 0.8804 (t0) cc_final: 0.8546 (t0) REVERT: H 30 ARG cc_start: 0.7962 (mtt180) cc_final: 0.7630 (mtp180) REVERT: H 76 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8673 (mtt-85) REVERT: H 102 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8329 (mm-30) outliers start: 11 outliers final: 8 residues processed: 133 average time/residue: 0.2845 time to fit residues: 52.1229 Evaluate side-chains 122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR 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 H residue 113 LYS 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 41 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.068647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047713 restraints weight = 47410.458| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.33 r_work: 0.2778 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12843 Z= 0.211 Angle : 0.589 10.986 18610 Z= 0.347 Chirality : 0.035 0.167 2127 Planarity : 0.005 0.045 1347 Dihedral : 30.792 160.190 4045 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.27 % Allowed : 11.46 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.30), residues: 751 helix: 2.99 (0.21), residues: 543 sheet: None (None), residues: 0 loop : -0.76 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 82 PHE 0.014 0.002 PHE C 25 TYR 0.016 0.002 TYR D 34 ARG 0.005 0.001 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 757) hydrogen bonds : angle 2.80251 ( 1911) covalent geometry : bond 0.00477 (12843) covalent geometry : angle 0.58918 (18610) *********************** 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 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8634 (mmm) cc_final: 0.8248 (mtp) REVERT: B 78 ARG cc_start: 0.8945 (mtm-85) cc_final: 0.8555 (mtm-85) REVERT: C 56 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8631 (tm-30) REVERT: D 48 ASP cc_start: 0.8713 (p0) cc_final: 0.8386 (p0) REVERT: D 80 TYR cc_start: 0.8181 (m-10) cc_final: 0.7816 (m-10) REVERT: D 102 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8388 (tt0) REVERT: E 73 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7961 (mt-10) REVERT: H 30 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7622 (mtt-85) REVERT: H 31 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8579 (mptt) outliers start: 8 outliers final: 7 residues processed: 121 average time/residue: 0.3014 time to fit residues: 49.3997 Evaluate side-chains 117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 52 GLU 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 H residue 113 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 75 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.069091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.047978 restraints weight = 47941.662| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.37 r_work: 0.2794 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.4434 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= 0.157 Angle : 0.535 10.861 18610 Z= 0.321 Chirality : 0.032 0.125 2127 Planarity : 0.004 0.042 1347 Dihedral : 30.550 160.639 4045 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.80 % Allowed : 12.26 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.31), residues: 751 helix: 3.22 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.64 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.013 0.001 TYR D 34 ARG 0.003 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 757) hydrogen bonds : angle 2.56888 ( 1911) covalent geometry : bond 0.00344 (12843) covalent geometry : angle 0.53488 (18610) *********************** 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 132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8697 (pm20) cc_final: 0.8445 (pm20) REVERT: A 120 MET cc_start: 0.8704 (mmm) cc_final: 0.8329 (mmm) REVERT: B 78 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8514 (mtm-85) REVERT: C 56 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 48 ASP cc_start: 0.8677 (p0) cc_final: 0.8380 (p0) REVERT: D 80 TYR cc_start: 0.8063 (m-10) cc_final: 0.7795 (m-10) REVERT: D 102 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8385 (tt0) REVERT: D 105 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8726 (mtpp) REVERT: G 90 ASP cc_start: 0.8803 (t0) cc_final: 0.8582 (t0) REVERT: H 30 ARG cc_start: 0.7836 (mtt180) cc_final: 0.7508 (mtp180) outliers start: 5 outliers final: 2 residues processed: 130 average time/residue: 0.2904 time to fit residues: 52.1246 Evaluate side-chains 118 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain H residue 113 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 79 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044521 restraints weight = 48652.374| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.44 r_work: 0.2698 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12843 Z= 0.244 Angle : 0.614 11.448 18610 Z= 0.361 Chirality : 0.036 0.124 2127 Planarity : 0.005 0.046 1347 Dihedral : 30.902 153.677 4045 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.75 % Allowed : 12.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 751 helix: 2.92 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 82 PHE 0.015 0.002 PHE C 25 TYR 0.016 0.002 TYR D 34 ARG 0.005 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.05257 ( 757) hydrogen bonds : angle 2.93197 ( 1911) covalent geometry : bond 0.00555 (12843) covalent geometry : angle 0.61393 (18610) *********************** 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 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8754 (mmm) cc_final: 0.8332 (mtp) REVERT: C 56 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8731 (tm-30) REVERT: D 48 ASP cc_start: 0.8762 (p0) cc_final: 0.8459 (p0) REVERT: D 80 TYR cc_start: 0.8123 (m-10) cc_final: 0.7839 (m-10) REVERT: D 102 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8441 (tt0) REVERT: D 105 LYS cc_start: 0.9045 (mtmt) cc_final: 0.8734 (mtpp) REVERT: F 24 ASP cc_start: 0.6434 (t0) cc_final: 0.6164 (t0) REVERT: G 90 ASP cc_start: 0.8817 (t0) cc_final: 0.8556 (t0) REVERT: H 30 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7602 (mtp180) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.2821 time to fit residues: 45.5076 Evaluate side-chains 119 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.065599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.044771 restraints weight = 48121.759| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.39 r_work: 0.2706 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12843 Z= 0.203 Angle : 0.572 10.512 18610 Z= 0.339 Chirality : 0.034 0.130 2127 Planarity : 0.004 0.045 1347 Dihedral : 30.594 157.957 4045 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.27 % Allowed : 14.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.31), residues: 751 helix: 3.16 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 46 PHE 0.011 0.001 PHE E 67 TYR 0.011 0.001 TYR D 34 ARG 0.005 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 757) hydrogen bonds : angle 2.65232 ( 1911) covalent geometry : bond 0.00457 (12843) covalent geometry : angle 0.57184 (18610) *********************** 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: 8 poor density : 119 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8672 (mmm) cc_final: 0.8221 (mtp) REVERT: B 78 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8575 (mtm-85) REVERT: C 56 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8732 (tm-30) REVERT: C 90 ASP cc_start: 0.9086 (t0) cc_final: 0.8703 (t0) REVERT: D 48 ASP cc_start: 0.8735 (p0) cc_final: 0.8466 (p0) REVERT: D 80 TYR cc_start: 0.8178 (m-10) cc_final: 0.7940 (m-10) REVERT: D 102 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8378 (tt0) REVERT: D 105 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8791 (ttmm) REVERT: F 24 ASP cc_start: 0.6417 (t0) cc_final: 0.6195 (t0) REVERT: G 90 ASP cc_start: 0.8818 (t0) cc_final: 0.8531 (t0) REVERT: H 30 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7358 (mtt-85) REVERT: H 31 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8454 (mptt) outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 0.2717 time to fit residues: 46.3891 Evaluate side-chains 124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR 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 H residue 113 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.066606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.045831 restraints weight = 48007.976| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.38 r_work: 0.2743 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.5317 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= 0.150 Angle : 0.547 12.826 18610 Z= 0.323 Chirality : 0.032 0.123 2127 Planarity : 0.004 0.047 1347 Dihedral : 30.368 158.186 4045 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.31), residues: 751 helix: 3.21 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 113 PHE 0.011 0.001 PHE E 67 TYR 0.009 0.001 TYR D 34 ARG 0.004 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 757) hydrogen bonds : angle 2.55390 ( 1911) covalent geometry : bond 0.00329 (12843) covalent geometry : angle 0.54726 (18610) *********************** 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 135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8667 (mmm) cc_final: 0.8316 (mmm) REVERT: B 78 ARG cc_start: 0.8916 (mtm-85) cc_final: 0.8496 (mtm-85) REVERT: B 88 TYR cc_start: 0.9231 (m-10) cc_final: 0.8631 (m-80) REVERT: C 56 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8651 (tm-30) REVERT: D 48 ASP cc_start: 0.8699 (p0) cc_final: 0.8484 (p0) REVERT: D 80 TYR cc_start: 0.7882 (m-10) cc_final: 0.7570 (m-10) REVERT: D 102 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8382 (tt0) REVERT: G 90 ASP cc_start: 0.8830 (t0) cc_final: 0.8564 (t0) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.2915 time to fit residues: 50.7459 Evaluate side-chains 125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 62 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.066635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.045997 restraints weight = 47756.295| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.29 r_work: 0.2749 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.5404 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= 0.153 Angle : 0.556 13.025 18610 Z= 0.327 Chirality : 0.032 0.157 2127 Planarity : 0.004 0.045 1347 Dihedral : 30.279 159.122 4045 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.96 % Allowed : 14.81 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.31), residues: 751 helix: 3.25 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.61 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.015 0.001 TYR H 80 ARG 0.006 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 757) hydrogen bonds : angle 2.57177 ( 1911) covalent geometry : bond 0.00337 (12843) covalent geometry : angle 0.55560 (18610) *********************** 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 131 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8655 (mmm) cc_final: 0.8297 (mmm) REVERT: B 78 ARG cc_start: 0.8905 (mtm-85) cc_final: 0.8496 (mtm-85) REVERT: B 88 TYR cc_start: 0.9099 (m-10) cc_final: 0.8454 (m-80) REVERT: C 56 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8636 (tm-30) REVERT: C 90 ASP cc_start: 0.8994 (t0) cc_final: 0.8603 (t0) REVERT: D 80 TYR cc_start: 0.8142 (m-10) cc_final: 0.7561 (m-10) REVERT: D 102 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8388 (tt0) REVERT: G 90 ASP cc_start: 0.8829 (t0) cc_final: 0.8570 (t0) REVERT: H 31 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8606 (mptt) outliers start: 6 outliers final: 5 residues processed: 128 average time/residue: 0.2798 time to fit residues: 49.0663 Evaluate side-chains 122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.062870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.042164 restraints weight = 48169.769| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.35 r_work: 0.2627 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12843 Z= 0.314 Angle : 0.658 13.424 18610 Z= 0.380 Chirality : 0.039 0.198 2127 Planarity : 0.005 0.055 1347 Dihedral : 30.875 151.545 4045 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.27 % Allowed : 14.65 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.31), residues: 751 helix: 2.88 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.71 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 46 PHE 0.015 0.002 PHE E 67 TYR 0.015 0.002 TYR H 80 ARG 0.008 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.05463 ( 757) hydrogen bonds : angle 3.07776 ( 1911) covalent geometry : bond 0.00719 (12843) covalent geometry : angle 0.65755 (18610) ********************** 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 120 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8768 (mmm) cc_final: 0.8395 (mtp) REVERT: C 56 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8899 (tm-30) REVERT: D 80 TYR cc_start: 0.8195 (m-10) cc_final: 0.7920 (m-10) REVERT: G 90 ASP cc_start: 0.8790 (t0) cc_final: 0.8479 (t0) outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 0.3931 time to fit residues: 62.7397 Evaluate side-chains 115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.065143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.044575 restraints weight = 47426.300| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.35 r_work: 0.2702 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.5824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12843 Z= 0.162 Angle : 0.571 13.448 18610 Z= 0.337 Chirality : 0.032 0.165 2127 Planarity : 0.004 0.043 1347 Dihedral : 30.337 157.751 4045 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.96 % Allowed : 14.81 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.31), residues: 751 helix: 3.15 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE E 67 TYR 0.010 0.001 TYR D 34 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 757) hydrogen bonds : angle 2.64920 ( 1911) covalent geometry : bond 0.00359 (12843) covalent geometry : angle 0.57100 (18610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6274.33 seconds wall clock time: 110 minutes 25.76 seconds (6625.76 seconds total)