Starting phenix.real_space_refine on Wed Feb 4 01:12:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kyc_62644/02_2026/9kyc_62644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kyc_62644/02_2026/9kyc_62644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kyc_62644/02_2026/9kyc_62644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kyc_62644/02_2026/9kyc_62644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kyc_62644/02_2026/9kyc_62644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kyc_62644/02_2026/9kyc_62644.map" } resolution = 2.94 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= 0.096 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: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5293 2.51 5 N 1408 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1937 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 232} Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1780 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 902 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "E" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 909 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "G" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 932 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Time building chain proxies: 1.66, per 1000 atoms: 0.20 Number of scatterers: 8324 At special positions: 0 Unit cell: (86.92, 85.86, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1591 8.00 N 1408 7.00 C 5293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 49 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 113 " distance=2.01 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS D 47 " distance=2.03 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 110 " distance=2.00 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS E 47 " distance=2.03 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 110 " distance=2.04 Simple disulfide: pdb=" SG CYS F 32 " - pdb=" SG CYS F 49 " distance=2.03 Simple disulfide: pdb=" SG CYS F 107 " - pdb=" SG CYS F 113 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 49 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.51 Conformation dependent library (CDL) restraints added in 257.0 milliseconds 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 20.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 181 through 192 Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 58 through 70 removed outlier: 3.855A pdb=" N THR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 108 through 119 removed outlier: 4.202A pdb=" N MET B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 200 removed outlier: 6.348A pdb=" N ILE B 197 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR B 198 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 199 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 200' Processing helix chain 'B' and resid 219 through 227 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.531A pdb=" N GLN C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.977A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 74 " --> pdb=" O TYR C 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 69 through 74' Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'D' and resid 58 through 72 Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'E' and resid 58 through 73 removed outlier: 3.527A pdb=" N MET E 62 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 94 Processing helix chain 'F' and resid 60 through 74 removed outlier: 3.707A pdb=" N GLN F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 96 Processing helix chain 'G' and resid 57 through 59 No H-bonds generated for 'chain 'G' and resid 57 through 59' Processing helix chain 'G' and resid 60 through 74 removed outlier: 3.712A pdb=" N GLN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 removed outlier: 3.606A pdb=" N THR G 95 " --> pdb=" O PRO G 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.128A pdb=" N VAL A 11 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 114 through 115 removed outlier: 5.915A pdb=" N TRP A 172 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 9 through 13 removed outlier: 7.328A pdb=" N LEU B 79 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA B 137 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG B 81 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 135 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 83 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N GLN B 133 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE B 154 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA B 135 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER B 152 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA B 137 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'B' and resid 191 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 15 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 15 current: chain 'C' and resid 29 through 35 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'C' and resid 100 through 106 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 100 through 106 current: chain 'D' and resid 28 through 36 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 49 current: chain 'D' and resid 99 through 104 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 99 through 104 current: chain 'E' and resid 30 through 36 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 44 through 48 current: chain 'E' and resid 98 through 104 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 98 through 104 current: chain 'F' and resid 30 through 37 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 48 through 51 current: chain 'F' and resid 100 through 106 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 100 through 106 current: chain 'G' and resid 28 through 37 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 46 through 51 current: chain 'G' and resid 100 through 106 194 hydrogen bonds defined for protein. 528 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1365 1.32 - 1.45: 2535 1.45 - 1.58: 4601 1.58 - 1.71: 0 1.71 - 1.84: 40 Bond restraints: 8541 Sorted by residual: bond pdb=" CA SER C 106 " pdb=" CB SER C 106 " ideal model delta sigma weight residual 1.529 1.459 0.070 1.58e-02 4.01e+03 1.98e+01 bond pdb=" CA SER E 27 " pdb=" CB SER E 27 " ideal model delta sigma weight residual 1.534 1.464 0.070 1.77e-02 3.19e+03 1.56e+01 bond pdb=" CA SER G 97 " pdb=" CB SER G 97 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.57e-02 4.06e+03 1.54e+01 bond pdb=" CA SER D 104 " pdb=" CB SER D 104 " ideal model delta sigma weight residual 1.530 1.472 0.058 1.48e-02 4.57e+03 1.54e+01 bond pdb=" CA SER D 106 " pdb=" CB SER D 106 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.66e-02 3.63e+03 1.27e+01 ... (remaining 8536 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 11398 3.00 - 6.00: 195 6.00 - 8.99: 27 8.99 - 11.99: 3 11.99 - 14.99: 1 Bond angle restraints: 11624 Sorted by residual: angle pdb=" N PRO A 127 " pdb=" CA PRO A 127 " pdb=" C PRO A 127 " ideal model delta sigma weight residual 112.47 127.46 -14.99 2.06e+00 2.36e-01 5.29e+01 angle pdb=" N ASP C 5 " pdb=" CA ASP C 5 " pdb=" C ASP C 5 " ideal model delta sigma weight residual 111.71 103.63 8.08 1.15e+00 7.56e-01 4.94e+01 angle pdb=" N GLU F 7 " pdb=" CA GLU F 7 " pdb=" C GLU F 7 " ideal model delta sigma weight residual 113.55 105.48 8.07 1.26e+00 6.30e-01 4.10e+01 angle pdb=" N LYS D 54 " pdb=" CA LYS D 54 " pdb=" C LYS D 54 " ideal model delta sigma weight residual 113.18 105.61 7.57 1.21e+00 6.83e-01 3.91e+01 angle pdb=" N SER C 41 " pdb=" CA SER C 41 " pdb=" C SER C 41 " ideal model delta sigma weight residual 112.72 104.33 8.39 1.36e+00 5.41e-01 3.81e+01 ... (remaining 11619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4265 17.89 - 35.78: 549 35.78 - 53.68: 171 53.68 - 71.57: 27 71.57 - 89.46: 10 Dihedral angle restraints: 5022 sinusoidal: 1939 harmonic: 3083 Sorted by residual: dihedral pdb=" CB CYS C 107 " pdb=" SG CYS C 107 " pdb=" SG CYS C 113 " pdb=" CB CYS C 113 " ideal model delta sinusoidal sigma weight residual -86.00 -134.70 48.70 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CB CYS E 31 " pdb=" SG CYS E 31 " pdb=" SG CYS E 47 " pdb=" CB CYS E 47 " ideal model delta sinusoidal sigma weight residual -86.00 -133.17 47.17 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CB CYS E 105 " pdb=" SG CYS E 105 " pdb=" SG CYS E 110 " pdb=" CB CYS E 110 " ideal model delta sinusoidal sigma weight residual 93.00 48.90 44.10 1 1.00e+01 1.00e-02 2.71e+01 ... (remaining 5019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1088 0.075 - 0.149: 154 0.149 - 0.224: 17 0.224 - 0.298: 5 0.298 - 0.373: 3 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA ASP G 5 " pdb=" N ASP G 5 " pdb=" C ASP G 5 " pdb=" CB ASP G 5 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1264 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 125 " -0.028 2.00e-02 2.50e+03 5.63e-02 3.18e+01 pdb=" C SER A 125 " 0.097 2.00e-02 2.50e+03 pdb=" O SER A 125 " -0.038 2.00e-02 2.50e+03 pdb=" N ARG A 126 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 1 " -0.024 2.00e-02 2.50e+03 4.72e-02 2.23e+01 pdb=" C GLU F 1 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU F 1 " -0.030 2.00e-02 2.50e+03 pdb=" N TRP F 2 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 29 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C TYR E 29 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR E 29 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE E 30 " -0.023 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1658 2.77 - 3.31: 7956 3.31 - 3.84: 14337 3.84 - 4.37: 17589 4.37 - 4.90: 29766 Nonbonded interactions: 71306 Sorted by model distance: nonbonded pdb=" ND1 HIS E 20 " pdb=" OG SER F 105 " model vdw 2.242 3.120 nonbonded pdb=" OD1 ASN E 87 " pdb=" OG SER E 89 " model vdw 2.242 3.040 nonbonded pdb=" O ASN B 179 " pdb=" ND2 ASN B 179 " model vdw 2.245 3.120 nonbonded pdb=" OD1 ASP A 8 " pdb=" OG SER B 126 " model vdw 2.246 3.040 nonbonded pdb=" O SER A 239 " pdb=" OG SER A 239 " model vdw 2.246 3.040 ... (remaining 71301 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 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 115) } 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: 0.270 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.005 0.070 8552 Z= 0.327 Angle : 0.961 14.988 11646 Z= 0.619 Chirality : 0.057 0.373 1267 Planarity : 0.006 0.078 1503 Dihedral : 17.526 89.461 3017 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 1.05 % Allowed : 10.04 % Favored : 88.91 % Rotamer: Outliers : 5.03 % Allowed : 29.18 % Favored : 65.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.04 % 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: -2.41 (0.25), residues: 1046 helix: -2.14 (0.34), residues: 212 sheet: -0.76 (0.29), residues: 278 loop : -1.80 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 126 TYR 0.044 0.001 TYR E 29 PHE 0.010 0.001 PHE E 111 TRP 0.011 0.001 TRP G 2 HIS 0.008 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8541) covalent geometry : angle 0.96081 (11624) SS BOND : bond 0.01230 ( 11) SS BOND : angle 1.17267 ( 22) hydrogen bonds : bond 0.18796 ( 194) hydrogen bonds : angle 8.47620 ( 528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6173 (p90) REVERT: C 54 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: C 82 TYR cc_start: 0.7645 (p90) cc_final: 0.7412 (p90) REVERT: E 26 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7907 (mmt-90) REVERT: F 11 TYR cc_start: 0.8497 (p90) cc_final: 0.8267 (p90) REVERT: F 94 ASN cc_start: 0.7966 (m110) cc_final: 0.7451 (m110) REVERT: G 97 SER cc_start: 0.8849 (m) cc_final: 0.8400 (p) outliers start: 46 outliers final: 38 residues processed: 167 average time/residue: 0.3454 time to fit residues: 63.1896 Evaluate side-chains 165 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 127 PRO Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 107 CYS Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 110 CYS Chi-restraints excluded: chain E residue 26 ARG Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 60 ASN B 181 GLN C 14 HIS C 76 GLN ** D 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN F 8 ASN G 94 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.186128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136010 restraints weight = 9224.510| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.70 r_work: 0.3445 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8552 Z= 0.117 Angle : 0.606 7.796 11646 Z= 0.320 Chirality : 0.046 0.159 1267 Planarity : 0.005 0.061 1503 Dihedral : 8.195 69.775 1220 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.60 % Favored : 90.82 % Rotamer: Outliers : 7.10 % Allowed : 23.93 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.04 (0.24), residues: 1046 helix: -1.39 (0.35), residues: 204 sheet: -0.61 (0.28), residues: 281 loop : -1.74 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 205 TYR 0.022 0.001 TYR F 6 PHE 0.011 0.001 PHE G 31 TRP 0.005 0.001 TRP A 27 HIS 0.005 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8541) covalent geometry : angle 0.60463 (11624) SS BOND : bond 0.00455 ( 11) SS BOND : angle 1.14592 ( 22) hydrogen bonds : bond 0.03449 ( 194) hydrogen bonds : angle 5.50835 ( 528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 139 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.5922 (ttm170) cc_final: 0.5320 (tpp-160) REVERT: B 148 LYS cc_start: 0.7929 (ptmm) cc_final: 0.7706 (ptmt) REVERT: B 157 ASP cc_start: 0.7413 (t0) cc_final: 0.7076 (t0) REVERT: C 6 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6503 (p90) REVERT: D 26 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7521 (mpp-170) REVERT: F 94 ASN cc_start: 0.8041 (m110) cc_final: 0.7474 (m-40) outliers start: 65 outliers final: 30 residues processed: 188 average time/residue: 0.3025 time to fit residues: 62.2888 Evaluate side-chains 150 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 47 CYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 76 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS B 118 GLN D 23 GLN E 87 ASN F 8 ASN ** F 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128659 restraints weight = 9305.482| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.76 r_work: 0.3350 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8552 Z= 0.176 Angle : 0.614 7.292 11646 Z= 0.326 Chirality : 0.046 0.152 1267 Planarity : 0.005 0.060 1503 Dihedral : 6.838 58.359 1187 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.70 % Favored : 90.92 % Rotamer: Outliers : 6.12 % Allowed : 25.68 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.02 (0.24), residues: 1046 helix: -1.24 (0.34), residues: 203 sheet: -0.75 (0.27), residues: 293 loop : -1.69 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 42 TYR 0.023 0.001 TYR A 92 PHE 0.009 0.001 PHE B 187 TRP 0.006 0.001 TRP A 172 HIS 0.005 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8541) covalent geometry : angle 0.61227 (11624) SS BOND : bond 0.00479 ( 11) SS BOND : angle 1.27010 ( 22) hydrogen bonds : bond 0.03688 ( 194) hydrogen bonds : angle 5.35092 ( 528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.4849 (pmt170) cc_final: 0.4615 (pmt-80) REVERT: A 180 ARG cc_start: 0.5991 (ttm170) cc_final: 0.5419 (tpt170) REVERT: A 187 SER cc_start: 0.5126 (OUTLIER) cc_final: 0.4702 (m) REVERT: B 157 ASP cc_start: 0.7472 (t0) cc_final: 0.7073 (t0) REVERT: B 175 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: C 6 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6438 (p90) REVERT: D 26 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7547 (mpp-170) REVERT: D 53 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8824 (p) REVERT: F 94 ASN cc_start: 0.8064 (m110) cc_final: 0.7499 (m-40) REVERT: F 99 ASN cc_start: 0.8624 (m-40) cc_final: 0.8258 (m-40) outliers start: 56 outliers final: 33 residues processed: 163 average time/residue: 0.3280 time to fit residues: 58.3944 Evaluate side-chains 157 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN F 8 ASN ** F 89 ASN ** 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 = 0.3854 r_free = 0.3854 target = 0.164850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116168 restraints weight = 9569.798| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.49 r_work: 0.3096 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8552 Z= 0.177 Angle : 0.598 7.563 11646 Z= 0.320 Chirality : 0.047 0.150 1267 Planarity : 0.005 0.061 1503 Dihedral : 6.019 57.158 1178 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.08 % Favored : 90.73 % Rotamer: Outliers : 6.56 % Allowed : 25.14 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.24), residues: 1046 helix: -1.13 (0.34), residues: 206 sheet: -0.62 (0.27), residues: 282 loop : -1.70 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.021 0.001 TYR A 92 PHE 0.013 0.001 PHE E 90 TRP 0.007 0.001 TRP A 27 HIS 0.005 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8541) covalent geometry : angle 0.59601 (11624) SS BOND : bond 0.00487 ( 11) SS BOND : angle 1.38412 ( 22) hydrogen bonds : bond 0.03598 ( 194) hydrogen bonds : angle 5.24205 ( 528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 125 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8757 (m-80) cc_final: 0.8182 (m-80) REVERT: A 61 ARG cc_start: 0.4762 (OUTLIER) cc_final: 0.4438 (pmt-80) REVERT: A 180 ARG cc_start: 0.5871 (ttm170) cc_final: 0.5319 (tpt170) REVERT: A 184 ARG cc_start: 0.7166 (mtt90) cc_final: 0.5832 (mmp-170) REVERT: A 187 SER cc_start: 0.5225 (OUTLIER) cc_final: 0.4475 (m) REVERT: B 148 LYS cc_start: 0.7882 (ptmm) cc_final: 0.7597 (ptmt) REVERT: B 157 ASP cc_start: 0.7322 (t0) cc_final: 0.6865 (t0) REVERT: B 175 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 6 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.6402 (p90) REVERT: D 26 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7329 (mpp-170) REVERT: D 53 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8740 (p) REVERT: E 87 ASN cc_start: 0.7587 (t0) cc_final: 0.7363 (t0) REVERT: F 94 ASN cc_start: 0.7863 (m110) cc_final: 0.7207 (m110) REVERT: F 99 ASN cc_start: 0.8641 (m-40) cc_final: 0.8297 (m-40) REVERT: G 56 VAL cc_start: 0.8244 (m) cc_final: 0.7938 (p) outliers start: 60 outliers final: 34 residues processed: 173 average time/residue: 0.3545 time to fit residues: 66.6671 Evaluate side-chains 166 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 23 GLN ** F 89 ASN ** 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 = 0.3886 r_free = 0.3886 target = 0.168213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.120158 restraints weight = 9420.373| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.47 r_work: 0.3214 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8552 Z= 0.119 Angle : 0.571 8.923 11646 Z= 0.304 Chirality : 0.045 0.148 1267 Planarity : 0.004 0.059 1503 Dihedral : 5.832 58.888 1177 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.89 % Favored : 90.82 % Rotamer: Outliers : 5.36 % Allowed : 26.45 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.24), residues: 1046 helix: -0.84 (0.35), residues: 204 sheet: -0.43 (0.28), residues: 275 loop : -1.59 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.018 0.001 TYR F 6 PHE 0.013 0.001 PHE E 90 TRP 0.007 0.001 TRP A 172 HIS 0.004 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8541) covalent geometry : angle 0.56925 (11624) SS BOND : bond 0.00425 ( 11) SS BOND : angle 1.21620 ( 22) hydrogen bonds : bond 0.03250 ( 194) hydrogen bonds : angle 5.05032 ( 528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8820 (m-80) cc_final: 0.8242 (m-80) REVERT: A 61 ARG cc_start: 0.4793 (OUTLIER) cc_final: 0.4489 (pmt-80) REVERT: A 180 ARG cc_start: 0.6032 (ttm170) cc_final: 0.5415 (tpp-160) REVERT: A 184 ARG cc_start: 0.6931 (mtt90) cc_final: 0.6687 (mpp-170) REVERT: A 190 MET cc_start: 0.6342 (mtm) cc_final: 0.5981 (mpt) REVERT: B 157 ASP cc_start: 0.7407 (t0) cc_final: 0.6904 (t0) REVERT: B 175 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: C 6 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6420 (p90) REVERT: D 26 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7423 (mpp-170) REVERT: F 94 ASN cc_start: 0.7996 (m110) cc_final: 0.7372 (m-40) REVERT: F 99 ASN cc_start: 0.8573 (m-40) cc_final: 0.8258 (m-40) REVERT: G 56 VAL cc_start: 0.8466 (m) cc_final: 0.8169 (p) outliers start: 49 outliers final: 31 residues processed: 166 average time/residue: 0.3687 time to fit residues: 67.0049 Evaluate side-chains 156 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 87 ASN ** F 89 ASN ** 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 = 0.3868 r_free = 0.3868 target = 0.166583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118248 restraints weight = 9307.865| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.46 r_work: 0.3153 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8552 Z= 0.143 Angle : 0.581 9.288 11646 Z= 0.309 Chirality : 0.046 0.141 1267 Planarity : 0.004 0.058 1503 Dihedral : 5.767 55.971 1175 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.27 % Favored : 90.54 % Rotamer: Outliers : 5.46 % Allowed : 26.34 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.24), residues: 1046 helix: -0.86 (0.34), residues: 209 sheet: -0.42 (0.28), residues: 275 loop : -1.61 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.020 0.001 TYR A 92 PHE 0.012 0.001 PHE E 90 TRP 0.007 0.001 TRP A 27 HIS 0.004 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8541) covalent geometry : angle 0.57873 (11624) SS BOND : bond 0.00442 ( 11) SS BOND : angle 1.21120 ( 22) hydrogen bonds : bond 0.03323 ( 194) hydrogen bonds : angle 5.03863 ( 528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.8774 (m-80) cc_final: 0.8169 (m-80) REVERT: A 61 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4434 (pmt-80) REVERT: A 180 ARG cc_start: 0.6186 (ttm170) cc_final: 0.5303 (tpt170) REVERT: B 157 ASP cc_start: 0.7417 (t0) cc_final: 0.6915 (t0) REVERT: B 175 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: C 6 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.6337 (p90) REVERT: D 26 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7376 (mpp-170) REVERT: F 94 ASN cc_start: 0.8032 (m110) cc_final: 0.7421 (m110) REVERT: F 99 ASN cc_start: 0.8545 (m-40) cc_final: 0.8171 (m-40) REVERT: G 56 VAL cc_start: 0.8425 (m) cc_final: 0.8142 (p) outliers start: 50 outliers final: 34 residues processed: 160 average time/residue: 0.3885 time to fit residues: 67.7730 Evaluate side-chains 157 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 99 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 48 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: E 87 ASN ** F 89 ASN ** 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 = 0.3866 r_free = 0.3866 target = 0.166202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117671 restraints weight = 9486.973| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.49 r_work: 0.3177 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8552 Z= 0.146 Angle : 0.579 9.635 11646 Z= 0.308 Chirality : 0.046 0.155 1267 Planarity : 0.004 0.057 1503 Dihedral : 5.708 55.854 1175 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.08 % Favored : 90.73 % Rotamer: Outliers : 5.25 % Allowed : 27.32 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.24), residues: 1046 helix: -0.80 (0.34), residues: 209 sheet: -0.44 (0.28), residues: 275 loop : -1.60 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.021 0.001 TYR B 99 PHE 0.012 0.001 PHE E 90 TRP 0.007 0.001 TRP A 27 HIS 0.004 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8541) covalent geometry : angle 0.57714 (11624) SS BOND : bond 0.00429 ( 11) SS BOND : angle 1.17881 ( 22) hydrogen bonds : bond 0.03339 ( 194) hydrogen bonds : angle 5.05341 ( 528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 124 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ARG cc_start: 0.4646 (OUTLIER) cc_final: 0.4324 (pmt-80) REVERT: A 84 ARG cc_start: 0.5228 (mmm160) cc_final: 0.4990 (mmm160) REVERT: A 180 ARG cc_start: 0.6198 (ttm170) cc_final: 0.5286 (tpp-160) REVERT: B 148 LYS cc_start: 0.7840 (ptmm) cc_final: 0.7558 (ptmt) REVERT: B 157 ASP cc_start: 0.7520 (t0) cc_final: 0.7003 (t0) REVERT: C 6 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.6332 (p90) REVERT: D 26 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7394 (mpp-170) REVERT: F 94 ASN cc_start: 0.8021 (m110) cc_final: 0.7424 (m110) REVERT: F 99 ASN cc_start: 0.8550 (m-40) cc_final: 0.8201 (m-40) REVERT: G 56 VAL cc_start: 0.8432 (m) cc_final: 0.8150 (p) REVERT: G 94 ASN cc_start: 0.8156 (m110) cc_final: 0.7535 (t0) outliers start: 48 outliers final: 33 residues processed: 162 average time/residue: 0.3853 time to fit residues: 67.8722 Evaluate side-chains 156 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 250 HIS Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN ** F 89 ASN ** 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 = 0.3851 r_free = 0.3851 target = 0.164235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.115713 restraints weight = 9368.365| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.50 r_work: 0.3067 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8552 Z= 0.209 Angle : 0.623 9.485 11646 Z= 0.330 Chirality : 0.047 0.150 1267 Planarity : 0.004 0.059 1503 Dihedral : 5.841 56.122 1173 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.75 % Favored : 90.06 % Rotamer: Outliers : 4.81 % Allowed : 27.65 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1046 helix: -0.86 (0.35), residues: 207 sheet: -0.52 (0.28), residues: 277 loop : -1.60 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 233 TYR 0.022 0.002 TYR B 99 PHE 0.012 0.001 PHE B 225 TRP 0.006 0.001 TRP A 27 HIS 0.005 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8541) covalent geometry : angle 0.62047 (11624) SS BOND : bond 0.00547 ( 11) SS BOND : angle 1.32699 ( 22) hydrogen bonds : bond 0.03702 ( 194) hydrogen bonds : angle 5.16121 ( 528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.6195 (ttm170) cc_final: 0.5302 (tpt170) REVERT: B 148 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7513 (ptmt) REVERT: B 157 ASP cc_start: 0.7480 (t0) cc_final: 0.6955 (t0) REVERT: C 6 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6453 (p90) REVERT: D 26 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7340 (mpp-170) REVERT: F 90 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7119 (tp-100) REVERT: F 94 ASN cc_start: 0.7967 (m110) cc_final: 0.7180 (m-40) REVERT: G 56 VAL cc_start: 0.8303 (m) cc_final: 0.8008 (p) REVERT: G 94 ASN cc_start: 0.8234 (m110) cc_final: 0.7609 (t0) outliers start: 44 outliers final: 33 residues processed: 157 average time/residue: 0.3425 time to fit residues: 58.7377 Evaluate side-chains 152 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN ** F 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.166243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117899 restraints weight = 9475.552| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.48 r_work: 0.3150 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8552 Z= 0.139 Angle : 0.597 8.483 11646 Z= 0.315 Chirality : 0.046 0.155 1267 Planarity : 0.004 0.057 1503 Dihedral : 5.663 55.979 1173 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.80 % Favored : 91.01 % Rotamer: Outliers : 4.15 % Allowed : 28.52 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.24), residues: 1046 helix: -0.79 (0.34), residues: 208 sheet: -0.51 (0.28), residues: 278 loop : -1.58 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.021 0.001 TYR B 99 PHE 0.012 0.001 PHE B 225 TRP 0.007 0.001 TRP C 2 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8541) covalent geometry : angle 0.59527 (11624) SS BOND : bond 0.00406 ( 11) SS BOND : angle 1.14073 ( 22) hydrogen bonds : bond 0.03363 ( 194) hydrogen bonds : angle 5.07536 ( 528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.6156 (ttm170) cc_final: 0.5234 (tpp-160) REVERT: A 190 MET cc_start: 0.5917 (mtm) cc_final: 0.5540 (mpt) REVERT: B 148 LYS cc_start: 0.7744 (ptmm) cc_final: 0.7449 (ptmt) REVERT: B 157 ASP cc_start: 0.7543 (t0) cc_final: 0.7019 (t0) REVERT: C 6 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6368 (p90) REVERT: C 54 GLU cc_start: 0.8578 (tt0) cc_final: 0.8147 (tt0) REVERT: D 26 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7373 (mpp-170) REVERT: F 94 ASN cc_start: 0.8111 (m110) cc_final: 0.7534 (m110) REVERT: F 99 ASN cc_start: 0.8556 (m-40) cc_final: 0.8167 (m-40) REVERT: G 56 VAL cc_start: 0.8441 (m) cc_final: 0.8157 (p) REVERT: G 94 ASN cc_start: 0.8093 (m110) cc_final: 0.7465 (t0) outliers start: 38 outliers final: 31 residues processed: 143 average time/residue: 0.3484 time to fit residues: 54.6433 Evaluate side-chains 147 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS A 250 HIS E 87 ASN ** F 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115340 restraints weight = 9406.358| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.46 r_work: 0.3082 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8552 Z= 0.184 Angle : 0.621 10.279 11646 Z= 0.327 Chirality : 0.047 0.157 1267 Planarity : 0.004 0.058 1503 Dihedral : 5.797 56.256 1173 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.94 % Favored : 89.87 % Rotamer: Outliers : 4.15 % Allowed : 28.63 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.24), residues: 1046 helix: -0.83 (0.34), residues: 208 sheet: -0.60 (0.28), residues: 280 loop : -1.56 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.023 0.002 TYR B 99 PHE 0.012 0.001 PHE B 225 TRP 0.007 0.001 TRP D 55 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8541) covalent geometry : angle 0.61874 (11624) SS BOND : bond 0.00489 ( 11) SS BOND : angle 1.28063 ( 22) hydrogen bonds : bond 0.03611 ( 194) hydrogen bonds : angle 5.11618 ( 528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2092 Ramachandran restraints generated. 1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.6282 (ttm170) cc_final: 0.5367 (tpt170) REVERT: A 190 MET cc_start: 0.5882 (mtm) cc_final: 0.5468 (mpt) REVERT: B 6 ILE cc_start: 0.6729 (mm) cc_final: 0.6265 (mm) REVERT: B 148 LYS cc_start: 0.7822 (ptmm) cc_final: 0.7519 (ptmt) REVERT: B 157 ASP cc_start: 0.7583 (t0) cc_final: 0.7075 (t0) REVERT: C 6 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6386 (p90) REVERT: C 54 GLU cc_start: 0.8604 (tt0) cc_final: 0.8237 (tt0) REVERT: D 18 ASP cc_start: 0.8845 (m-30) cc_final: 0.8642 (m-30) REVERT: D 26 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7369 (mpp-170) REVERT: F 94 ASN cc_start: 0.8084 (m110) cc_final: 0.7473 (m110) REVERT: G 7 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6102 (tm-30) REVERT: G 56 VAL cc_start: 0.8328 (m) cc_final: 0.8037 (p) REVERT: G 94 ASN cc_start: 0.8155 (m110) cc_final: 0.7541 (t0) outliers start: 38 outliers final: 33 residues processed: 146 average time/residue: 0.3950 time to fit residues: 62.9057 Evaluate side-chains 149 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 45 MET Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain B residue 78 ASN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 6 TYR Chi-restraints excluded: chain C residue 32 CYS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 113 CYS Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain E residue 31 CYS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 98 THR Chi-restraints excluded: chain G residue 7 GLU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 76 GLN Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 0.0570 chunk 40 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS E 87 ASN ** F 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 ASN F 99 ASN G 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.169221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121176 restraints weight = 9344.602| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.47 r_work: 0.3226 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8552 Z= 0.111 Angle : 0.580 8.616 11646 Z= 0.306 Chirality : 0.045 0.150 1267 Planarity : 0.004 0.056 1503 Dihedral : 5.527 57.564 1173 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.60 % Favored : 91.20 % Rotamer: Outliers : 4.26 % Allowed : 28.85 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.24), residues: 1046 helix: -0.58 (0.35), residues: 207 sheet: -0.81 (0.26), residues: 297 loop : -1.54 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.022 0.001 TYR B 99 PHE 0.011 0.001 PHE E 90 TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS E 20 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8541) covalent geometry : angle 0.57840 (11624) SS BOND : bond 0.00335 ( 11) SS BOND : angle 1.01700 ( 22) hydrogen bonds : bond 0.03175 ( 194) hydrogen bonds : angle 4.90489 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2908.57 seconds wall clock time: 50 minutes 23.46 seconds (3023.46 seconds total)