Starting phenix.real_space_refine on Thu Sep 18 19:33:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvp_47214/09_2025/9dvp_47214_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvp_47214/09_2025/9dvp_47214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dvp_47214/09_2025/9dvp_47214_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvp_47214/09_2025/9dvp_47214_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dvp_47214/09_2025/9dvp_47214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvp_47214/09_2025/9dvp_47214.map" } resolution = 2.81 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 39 5.49 5 S 42 5.16 5 C 6464 2.51 5 N 1569 2.21 5 O 1764 1.98 5 H 9494 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19372 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 9477 Classifications: {'peptide': 570} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 550} Chain breaks: 4 Chain: "B" Number of atoms: 9532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 9532 Classifications: {'peptide': 573} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 553} Chain breaks: 4 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 178 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 183 Unusual residues: {'CLR': 1, 'CPL': 1, 'I8P': 2, 'PO4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.32, per 1000 atoms: 0.17 Number of scatterers: 19372 At special positions: 0 Unit cell: (107.3, 93.525, 123.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 42 16.00 P 39 15.00 O 1764 8.00 N 1569 7.00 C 6464 6.00 H 9494 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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: 1.93 Conformation dependent library (CDL) restraints added in 490.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.534A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 47 through 98 Processing helix chain 'A' and resid 126 through 168 Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 189 through 205 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.548A pdb=" N ALA A 226 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 257 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.295A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 384 through 387 Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.040A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 445 through 471 removed outlier: 3.630A pdb=" N ALA A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 472 through 502 removed outlier: 4.003A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 Processing helix chain 'A' and resid 555 through 582 removed outlier: 4.008A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 618 Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 19 removed outlier: 5.593A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 47 through 98 Processing helix chain 'B' and resid 123 through 168 Processing helix chain 'B' and resid 171 through 179 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.701A pdb=" N ARG B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.320A pdb=" N GLN B 227 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 257 Processing helix chain 'B' and resid 267 through 296 removed outlier: 5.241A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.538A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.108A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 471 removed outlier: 3.528A pdb=" N ALA B 449 " --> pdb=" O TYR B 445 " (cutoff:3.500A) Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 500 removed outlier: 4.361A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.575A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 582 removed outlier: 3.874A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 582 " --> pdb=" O SER B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 618 Proline residue: B 598 - end of helix 723 hydrogen bonds defined for protein. 2136 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: 4.31 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9474 1.03 - 1.23: 28 1.23 - 1.42: 4373 1.42 - 1.62: 5688 1.62 - 1.81: 84 Bond restraints: 19647 Sorted by residual: bond pdb=" O45 I8P B 804 " pdb=" PB5 I8P B 804 " ideal model delta sigma weight residual 1.695 1.583 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" O45 I8P A 803 " pdb=" PB5 I8P A 803 " ideal model delta sigma weight residual 1.695 1.583 0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" O45 I8P A 804 " pdb=" PB5 I8P A 804 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" O45 I8P B 805 " pdb=" PB5 I8P B 805 " ideal model delta sigma weight residual 1.695 1.584 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" O3P CPL B 807 " pdb=" P CPL B 807 " ideal model delta sigma weight residual 1.633 1.739 -0.106 2.00e-02 2.50e+03 2.82e+01 ... (remaining 19642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 35004 3.05 - 6.10: 152 6.10 - 9.14: 74 9.14 - 12.19: 20 12.19 - 15.24: 19 Bond angle restraints: 35269 Sorted by residual: angle pdb=" O1P CPL B 807 " pdb=" P CPL B 807 " pdb=" O2P CPL B 807 " ideal model delta sigma weight residual 119.55 134.79 -15.24 3.00e+00 1.11e-01 2.58e+01 angle pdb=" O1P CPL A 806 " pdb=" P CPL A 806 " pdb=" O2P CPL A 806 " ideal model delta sigma weight residual 119.55 134.73 -15.18 3.00e+00 1.11e-01 2.56e+01 angle pdb=" O65 I8P A 804 " pdb=" PB5 I8P A 804 " pdb=" O75 I8P A 804 " ideal model delta sigma weight residual 113.85 99.76 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O65 I8P B 805 " pdb=" PB5 I8P B 805 " pdb=" O75 I8P B 805 " ideal model delta sigma weight residual 113.85 99.80 14.05 3.00e+00 1.11e-01 2.19e+01 angle pdb=" O65 I8P B 804 " pdb=" PB5 I8P B 804 " pdb=" O75 I8P B 804 " ideal model delta sigma weight residual 113.85 99.81 14.04 3.00e+00 1.11e-01 2.19e+01 ... (remaining 35264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 9146 34.93 - 69.86: 390 69.86 - 104.79: 21 104.79 - 139.72: 10 139.72 - 174.65: 4 Dihedral angle restraints: 9571 sinusoidal: 5166 harmonic: 4405 Sorted by residual: dihedral pdb=" O35 I8P B 805 " pdb=" O45 I8P B 805 " pdb=" PA5 I8P B 805 " pdb=" PB5 I8P B 805 " ideal model delta sinusoidal sigma weight residual -10.77 163.88 -174.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 806 " pdb=" C1 CPL A 806 " pdb=" C2 CPL A 806 " pdb=" O3P CPL A 806 " ideal model delta sinusoidal sigma weight residual 72.09 -75.06 147.15 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" O2 CPL A 806 " pdb=" C1 CPL A 806 " pdb=" C2 CPL A 806 " pdb=" O3P CPL A 806 " ideal model delta sinusoidal sigma weight residual 309.18 164.19 144.99 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 9568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1351 0.072 - 0.145: 111 0.145 - 0.217: 12 0.217 - 0.290: 2 0.290 - 0.362: 8 Chirality restraints: 1484 Sorted by residual: chirality pdb=" C17 CLR A 805 " pdb=" C13 CLR A 805 " pdb=" C16 CLR A 805 " pdb=" C20 CLR A 805 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C17 CLR B 806 " pdb=" C13 CLR B 806 " pdb=" C16 CLR B 806 " pdb=" C20 CLR B 806 " both_signs ideal model delta sigma weight residual False 2.55 2.91 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C2 CPL B 807 " pdb=" C1 CPL B 807 " pdb=" C3 CPL B 807 " pdb=" O2 CPL B 807 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 1481 not shown) Planarity restraints: 2746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 293 " 0.351 9.50e-02 1.11e+02 1.99e-01 5.96e+02 pdb=" NE ARG B 293 " 0.160 2.00e-02 2.50e+03 pdb=" CZ ARG B 293 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG B 293 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 293 " -0.037 2.00e-02 2.50e+03 pdb="HH11 ARG B 293 " -0.334 2.00e-02 2.50e+03 pdb="HH12 ARG B 293 " 0.283 2.00e-02 2.50e+03 pdb="HH21 ARG B 293 " -0.108 2.00e-02 2.50e+03 pdb="HH22 ARG B 293 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 308 " 0.156 9.50e-02 1.11e+02 1.47e-01 4.29e+02 pdb=" NE ARG B 308 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG B 308 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 308 " 0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 308 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B 308 " -0.237 2.00e-02 2.50e+03 pdb="HH12 ARG B 308 " 0.271 2.00e-02 2.50e+03 pdb="HH21 ARG B 308 " 0.072 2.00e-02 2.50e+03 pdb="HH22 ARG B 308 " -0.176 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 604 " 0.064 9.50e-02 1.11e+02 1.10e-01 2.61e+02 pdb=" NE ARG B 604 " 0.113 2.00e-02 2.50e+03 pdb=" CZ ARG B 604 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG B 604 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 604 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG B 604 " -0.225 2.00e-02 2.50e+03 pdb="HH12 ARG B 604 " 0.177 2.00e-02 2.50e+03 pdb="HH21 ARG B 604 " -0.081 2.00e-02 2.50e+03 pdb="HH22 ARG B 604 " -0.017 2.00e-02 2.50e+03 ... (remaining 2743 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.11: 389 2.11 - 2.73: 32359 2.73 - 3.35: 59281 3.35 - 3.98: 71870 3.98 - 4.60: 113128 Nonbonded interactions: 277027 Sorted by model distance: nonbonded pdb=" HG SER B 330 " pdb=" HB2 LEU B 351 " model vdw 1.485 2.270 nonbonded pdb=" O PHE B 379 " pdb=" HG1 THR B 383 " model vdw 1.603 2.450 nonbonded pdb="HE21 GLN B 149 " pdb=" O PHE B 185 " model vdw 1.609 2.450 nonbonded pdb=" O ILE A 271 " pdb=" HH TYR A 352 " model vdw 1.625 2.450 nonbonded pdb=" O THR A 203 " pdb=" H GLY A 209 " model vdw 1.629 2.450 ... (remaining 277022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 \ or name HE2 or name HE3 or name HZ1)) or resid 159 through 802 or resid 804)) selection = (chain 'B' and (resid 1 through 98 or (resid 125 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE2)) or re \ sid 126 through 802 or resid 804)) } 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: 3.660 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.930 Find NCS groups from input model: 0.160 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:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 10155 Z= 0.325 Angle : 1.059 15.241 13814 Z= 0.415 Chirality : 0.047 0.362 1484 Planarity : 0.004 0.057 1651 Dihedral : 19.955 174.648 3960 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.89 % Allowed : 19.43 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.26), residues: 1123 helix: 3.45 (0.17), residues: 864 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 219 TYR 0.017 0.001 TYR B 467 PHE 0.017 0.001 PHE B 605 TRP 0.033 0.001 TRP B 573 HIS 0.002 0.000 HIS B 10 Details of bonding type rmsd covalent geometry : bond 0.00635 (10153) covalent geometry : angle 1.05942 (13810) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.63869 ( 4) hydrogen bonds : bond 0.10603 ( 723) hydrogen bonds : angle 4.53568 ( 2136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7449 (mtmm) cc_final: 0.6412 (mmtm) REVERT: A 152 ASN cc_start: 0.7846 (m-40) cc_final: 0.7376 (m110) REVERT: A 189 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6936 (tttt) REVERT: A 216 LYS cc_start: 0.7330 (ttpp) cc_final: 0.6785 (tmtt) REVERT: A 468 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.6968 (tmm-80) REVERT: A 529 ASP cc_start: 0.8175 (m-30) cc_final: 0.7911 (m-30) REVERT: B 14 GLU cc_start: 0.7175 (mp0) cc_final: 0.6333 (pt0) REVERT: B 16 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6823 (ttp-110) REVERT: B 23 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6209 (mp0) REVERT: B 190 LYS cc_start: 0.7697 (mttm) cc_final: 0.7441 (mttp) REVERT: B 212 GLN cc_start: 0.6819 (tm-30) cc_final: 0.6204 (mp-120) REVERT: B 283 PHE cc_start: 0.8128 (t80) cc_final: 0.7065 (m-80) REVERT: B 304 GLU cc_start: 0.8505 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 394 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7876 (p90) REVERT: B 500 LYS cc_start: 0.6604 (tttt) cc_final: 0.6275 (ttpt) outliers start: 9 outliers final: 4 residues processed: 154 average time/residue: 1.2322 time to fit residues: 203.2601 Evaluate side-chains 112 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 545 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.197576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.138992 restraints weight = 26132.100| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.59 r_work: 0.3283 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10155 Z= 0.143 Angle : 0.500 6.948 13814 Z= 0.260 Chirality : 0.035 0.189 1484 Planarity : 0.004 0.040 1651 Dihedral : 17.406 163.907 1744 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.09 % Allowed : 20.22 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.45 (0.25), residues: 1123 helix: 3.29 (0.16), residues: 864 sheet: None (None), residues: 0 loop : -1.56 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 308 TYR 0.012 0.001 TYR B 148 PHE 0.020 0.001 PHE A 605 TRP 0.008 0.001 TRP B 395 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00308 (10153) covalent geometry : angle 0.49947 (13810) SS BOND : bond 0.00215 ( 2) SS BOND : angle 1.01762 ( 4) hydrogen bonds : bond 0.04548 ( 723) hydrogen bonds : angle 3.96223 ( 2136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7692 (mtmm) cc_final: 0.6752 (mmtm) REVERT: A 216 LYS cc_start: 0.7486 (ttpp) cc_final: 0.6799 (tmtt) REVERT: A 270 ARG cc_start: 0.7939 (mmt180) cc_final: 0.7736 (mmm160) REVERT: A 468 ARG cc_start: 0.7702 (tmm-80) cc_final: 0.6810 (tmm-80) REVERT: A 608 ASN cc_start: 0.8731 (m-40) cc_final: 0.8493 (m-40) REVERT: B 2 LYS cc_start: 0.8204 (pttm) cc_final: 0.7872 (pttt) REVERT: B 14 GLU cc_start: 0.7490 (mp0) cc_final: 0.6557 (pt0) REVERT: B 16 ARG cc_start: 0.7150 (ttp-170) cc_final: 0.6786 (ttp-110) REVERT: B 23 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6174 (mp0) REVERT: B 81 GLN cc_start: 0.7566 (mt0) cc_final: 0.7021 (mt0) REVERT: B 179 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5270 (m170) REVERT: B 190 LYS cc_start: 0.7685 (mttm) cc_final: 0.7448 (mttp) REVERT: B 212 GLN cc_start: 0.7063 (tm-30) cc_final: 0.6354 (mp-120) REVERT: B 304 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7802 (mt-10) REVERT: B 417 TYR cc_start: 0.7396 (t80) cc_final: 0.6074 (m-80) REVERT: B 500 LYS cc_start: 0.6630 (tttt) cc_final: 0.6285 (ttpt) outliers start: 11 outliers final: 4 residues processed: 122 average time/residue: 1.2802 time to fit residues: 167.9311 Evaluate side-chains 115 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN A 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.193390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134363 restraints weight = 25794.560| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.52 r_work: 0.3188 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10155 Z= 0.168 Angle : 0.522 7.368 13814 Z= 0.274 Chirality : 0.036 0.221 1484 Planarity : 0.004 0.076 1651 Dihedral : 16.394 166.947 1739 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.88 % Allowed : 18.33 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.24), residues: 1123 helix: 2.96 (0.16), residues: 867 sheet: None (None), residues: 0 loop : -1.67 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 293 TYR 0.013 0.001 TYR B 352 PHE 0.029 0.002 PHE A 605 TRP 0.010 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00373 (10153) covalent geometry : angle 0.52179 (13810) SS BOND : bond 0.00201 ( 2) SS BOND : angle 0.83742 ( 4) hydrogen bonds : bond 0.04979 ( 723) hydrogen bonds : angle 3.94166 ( 2136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7824 (mtmm) cc_final: 0.6973 (mmtm) REVERT: A 199 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 216 LYS cc_start: 0.7491 (ttpp) cc_final: 0.6875 (tmtt) REVERT: A 468 ARG cc_start: 0.7828 (tmm-80) cc_final: 0.6968 (tmm-80) REVERT: B 2 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7920 (pttt) REVERT: B 14 GLU cc_start: 0.7690 (mp0) cc_final: 0.6731 (pt0) REVERT: B 16 ARG cc_start: 0.7256 (ttp-170) cc_final: 0.6954 (ttp-110) REVERT: B 17 LYS cc_start: 0.8006 (mtpp) cc_final: 0.7306 (ptmt) REVERT: B 23 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6281 (mp0) REVERT: B 81 GLN cc_start: 0.7672 (mt0) cc_final: 0.7116 (mt0) REVERT: B 179 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.5433 (m-70) REVERT: B 190 LYS cc_start: 0.7747 (mttm) cc_final: 0.7530 (mttp) REVERT: B 212 GLN cc_start: 0.7152 (tm-30) cc_final: 0.6824 (tm-30) REVERT: B 216 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7070 (tmtt) REVERT: B 304 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 417 TYR cc_start: 0.7484 (t80) cc_final: 0.6146 (m-80) REVERT: B 576 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8622 (tm-30) outliers start: 19 outliers final: 7 residues processed: 130 average time/residue: 1.1476 time to fit residues: 160.9532 Evaluate side-chains 113 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 179 HIS Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 576 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 401 ASN B 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.192904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.133489 restraints weight = 25758.074| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.55 r_work: 0.3180 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10155 Z= 0.141 Angle : 0.489 8.114 13814 Z= 0.257 Chirality : 0.035 0.204 1484 Planarity : 0.004 0.063 1651 Dihedral : 15.857 167.202 1739 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.78 % Allowed : 18.53 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.25), residues: 1123 helix: 2.96 (0.16), residues: 865 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 293 TYR 0.011 0.001 TYR B 148 PHE 0.023 0.002 PHE B 605 TRP 0.009 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00307 (10153) covalent geometry : angle 0.48921 (13810) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.00984 ( 4) hydrogen bonds : bond 0.04593 ( 723) hydrogen bonds : angle 3.88154 ( 2136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7818 (mtmm) cc_final: 0.6962 (mmtm) REVERT: A 215 MET cc_start: 0.7715 (mmm) cc_final: 0.7342 (mmm) REVERT: A 216 LYS cc_start: 0.7534 (ttpp) cc_final: 0.6905 (tmtt) REVERT: A 468 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.6858 (tmm-80) REVERT: A 618 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.6378 (m-40) REVERT: B 2 LYS cc_start: 0.8189 (pttm) cc_final: 0.7872 (pttt) REVERT: B 16 ARG cc_start: 0.7212 (ttp-170) cc_final: 0.6873 (ttp-110) REVERT: B 17 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7278 (ptmt) REVERT: B 23 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6227 (mp0) REVERT: B 81 GLN cc_start: 0.7616 (mt0) cc_final: 0.7073 (mt0) REVERT: B 179 HIS cc_start: 0.6152 (m90) cc_final: 0.5456 (m-70) REVERT: B 190 LYS cc_start: 0.7746 (mttm) cc_final: 0.7545 (mttp) REVERT: B 212 GLN cc_start: 0.7147 (tm-30) cc_final: 0.6845 (tm-30) REVERT: B 216 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7051 (tmtt) REVERT: B 304 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 417 TYR cc_start: 0.7430 (t80) cc_final: 0.6102 (m-80) REVERT: B 576 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8593 (tm-30) outliers start: 18 outliers final: 8 residues processed: 121 average time/residue: 1.2156 time to fit residues: 158.1506 Evaluate side-chains 110 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 576 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 361 ASN B 441 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.192933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.134555 restraints weight = 25672.613| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.52 r_work: 0.3191 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.135 Angle : 0.485 8.305 13814 Z= 0.254 Chirality : 0.035 0.201 1484 Planarity : 0.004 0.074 1651 Dihedral : 15.357 166.476 1739 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.28 % Allowed : 17.94 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.25), residues: 1123 helix: 2.92 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.72 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 293 TYR 0.011 0.001 TYR B 148 PHE 0.024 0.002 PHE B 605 TRP 0.008 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00292 (10153) covalent geometry : angle 0.48447 (13810) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.98852 ( 4) hydrogen bonds : bond 0.04558 ( 723) hydrogen bonds : angle 3.84209 ( 2136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7849 (mtmm) cc_final: 0.6998 (mmtm) REVERT: A 199 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: A 215 MET cc_start: 0.7656 (mmm) cc_final: 0.7188 (mmm) REVERT: A 216 LYS cc_start: 0.7472 (ttpp) cc_final: 0.6847 (tmtt) REVERT: A 468 ARG cc_start: 0.7868 (tmm-80) cc_final: 0.6944 (tmm-80) REVERT: A 618 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6339 (m-40) REVERT: B 2 LYS cc_start: 0.8265 (pttm) cc_final: 0.7304 (mmmt) REVERT: B 16 ARG cc_start: 0.7277 (ttp-170) cc_final: 0.6961 (ttp-110) REVERT: B 23 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6312 (mp0) REVERT: B 81 GLN cc_start: 0.7624 (mt0) cc_final: 0.7079 (mt0) REVERT: B 179 HIS cc_start: 0.6195 (m90) cc_final: 0.5495 (m-70) REVERT: B 190 LYS cc_start: 0.7761 (mttm) cc_final: 0.7558 (mttp) REVERT: B 212 GLN cc_start: 0.7063 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 216 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7087 (tmtt) REVERT: B 304 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 417 TYR cc_start: 0.7499 (t80) cc_final: 0.6122 (m-80) REVERT: B 576 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8579 (tm-30) outliers start: 23 outliers final: 11 residues processed: 124 average time/residue: 1.2425 time to fit residues: 166.3693 Evaluate side-chains 116 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 576 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 361 ASN B 149 GLN B 401 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.190702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131705 restraints weight = 25569.652| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.51 r_work: 0.3151 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10155 Z= 0.178 Angle : 0.519 8.268 13814 Z= 0.273 Chirality : 0.036 0.207 1484 Planarity : 0.004 0.060 1651 Dihedral : 15.428 165.074 1739 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.48 % Allowed : 17.64 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.24), residues: 1123 helix: 2.73 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.73 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.011 0.001 TYR A 553 PHE 0.027 0.002 PHE A 605 TRP 0.010 0.001 TRP A 528 HIS 0.009 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00404 (10153) covalent geometry : angle 0.51887 (13810) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.01816 ( 4) hydrogen bonds : bond 0.04998 ( 723) hydrogen bonds : angle 3.93209 ( 2136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7030 (mmtm) REVERT: A 199 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 215 MET cc_start: 0.7711 (mmm) cc_final: 0.7395 (mmm) REVERT: A 216 LYS cc_start: 0.7512 (ttpp) cc_final: 0.6887 (tmtt) REVERT: A 468 ARG cc_start: 0.7892 (tmm-80) cc_final: 0.6941 (tmm-80) REVERT: B 2 LYS cc_start: 0.8251 (pttm) cc_final: 0.7358 (mmmt) REVERT: B 16 ARG cc_start: 0.7261 (ttp-170) cc_final: 0.6868 (ttp-110) REVERT: B 17 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7340 (ptmt) REVERT: B 23 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6329 (mp0) REVERT: B 81 GLN cc_start: 0.7690 (mt0) cc_final: 0.7152 (mt0) REVERT: B 179 HIS cc_start: 0.6240 (m90) cc_final: 0.5515 (m-70) REVERT: B 190 LYS cc_start: 0.7770 (mttm) cc_final: 0.7570 (mttp) REVERT: B 212 GLN cc_start: 0.7089 (tm-30) cc_final: 0.6779 (tm-30) REVERT: B 216 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7090 (tmtt) REVERT: B 304 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 417 TYR cc_start: 0.7511 (t80) cc_final: 0.6150 (m-80) REVERT: B 576 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8595 (tm-30) outliers start: 25 outliers final: 13 residues processed: 126 average time/residue: 1.2508 time to fit residues: 169.7629 Evaluate side-chains 115 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 576 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 401 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.189296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.130416 restraints weight = 25629.731| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.51 r_work: 0.3118 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10155 Z= 0.197 Angle : 0.537 8.230 13814 Z= 0.283 Chirality : 0.037 0.207 1484 Planarity : 0.005 0.055 1651 Dihedral : 15.440 163.888 1739 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 17.74 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.55 (0.24), residues: 1123 helix: 2.55 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 176 TYR 0.012 0.002 TYR A 272 PHE 0.027 0.002 PHE A 605 TRP 0.011 0.002 TRP A 528 HIS 0.009 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00448 (10153) covalent geometry : angle 0.53630 (13810) SS BOND : bond 0.00325 ( 2) SS BOND : angle 1.08194 ( 4) hydrogen bonds : bond 0.05166 ( 723) hydrogen bonds : angle 3.99773 ( 2136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7054 (mmtm) REVERT: A 199 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: A 216 LYS cc_start: 0.7505 (ttpp) cc_final: 0.6885 (tmtt) REVERT: A 468 ARG cc_start: 0.7950 (tmm-80) cc_final: 0.6970 (tmm-80) REVERT: B 2 LYS cc_start: 0.8226 (pttm) cc_final: 0.7913 (pttt) REVERT: B 16 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.6881 (ttp-110) REVERT: B 17 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7388 (ptmt) REVERT: B 23 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6264 (mp0) REVERT: B 81 GLN cc_start: 0.7738 (mt0) cc_final: 0.7200 (mt0) REVERT: B 179 HIS cc_start: 0.6239 (m90) cc_final: 0.5505 (m-70) REVERT: B 212 GLN cc_start: 0.7030 (tm-30) cc_final: 0.6723 (tm-30) REVERT: B 216 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7132 (tmtt) REVERT: B 304 GLU cc_start: 0.8630 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 417 TYR cc_start: 0.7517 (t80) cc_final: 0.6159 (m-80) REVERT: B 512 TYR cc_start: 0.8131 (m-10) cc_final: 0.7706 (m-10) REVERT: B 576 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8594 (tm-30) outliers start: 25 outliers final: 14 residues processed: 118 average time/residue: 1.3337 time to fit residues: 169.0387 Evaluate side-chains 110 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 576 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 401 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.190192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.131617 restraints weight = 25741.408| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.52 r_work: 0.3142 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10155 Z= 0.157 Angle : 0.511 8.442 13814 Z= 0.268 Chirality : 0.036 0.202 1484 Planarity : 0.004 0.052 1651 Dihedral : 15.150 162.766 1739 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 18.14 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.24), residues: 1123 helix: 2.63 (0.16), residues: 877 sheet: None (None), residues: 0 loop : -1.70 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 176 TYR 0.011 0.001 TYR A 367 PHE 0.025 0.002 PHE B 605 TRP 0.010 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00350 (10153) covalent geometry : angle 0.51020 (13810) SS BOND : bond 0.00325 ( 2) SS BOND : angle 1.17427 ( 4) hydrogen bonds : bond 0.04827 ( 723) hydrogen bonds : angle 3.94449 ( 2136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7073 (mmtm) REVERT: A 199 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: A 216 LYS cc_start: 0.7486 (ttpp) cc_final: 0.6861 (tmtt) REVERT: A 468 ARG cc_start: 0.7938 (tmm-80) cc_final: 0.6960 (tmm-80) REVERT: B 2 LYS cc_start: 0.8218 (pttm) cc_final: 0.7917 (pttt) REVERT: B 16 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6854 (ttp-110) REVERT: B 17 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7353 (ptmt) REVERT: B 23 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6217 (mp0) REVERT: B 81 GLN cc_start: 0.7688 (mt0) cc_final: 0.7158 (mt0) REVERT: B 179 HIS cc_start: 0.6204 (m90) cc_final: 0.5484 (m-70) REVERT: B 212 GLN cc_start: 0.7008 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 216 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7110 (tmtt) REVERT: B 304 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7896 (mt-10) REVERT: B 417 TYR cc_start: 0.7507 (t80) cc_final: 0.6119 (m-80) REVERT: B 512 TYR cc_start: 0.8112 (m-10) cc_final: 0.7710 (m-10) REVERT: B 576 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8596 (tm-30) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 1.3753 time to fit residues: 171.5550 Evaluate side-chains 110 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 548 ARG Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 576 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 15 optimal weight: 0.0040 chunk 104 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 401 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.191701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.133610 restraints weight = 25677.106| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.51 r_work: 0.3258 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.123 Angle : 0.488 8.705 13814 Z= 0.255 Chirality : 0.034 0.194 1484 Planarity : 0.004 0.050 1651 Dihedral : 14.770 161.421 1739 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.88 % Allowed : 18.73 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.88 (0.25), residues: 1123 helix: 2.81 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.66 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 219 TYR 0.012 0.001 TYR B 148 PHE 0.025 0.001 PHE B 605 TRP 0.010 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00260 (10153) covalent geometry : angle 0.48810 (13810) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.16376 ( 4) hydrogen bonds : bond 0.04445 ( 723) hydrogen bonds : angle 3.86243 ( 2136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7162 (mmtm) REVERT: A 199 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 216 LYS cc_start: 0.7500 (ttpp) cc_final: 0.6883 (tmtt) REVERT: A 468 ARG cc_start: 0.7966 (tmm-80) cc_final: 0.6987 (tmm-80) REVERT: B 2 LYS cc_start: 0.8283 (pttm) cc_final: 0.7445 (mmmt) REVERT: B 16 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6956 (ttp-110) REVERT: B 17 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7399 (ptmt) REVERT: B 23 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6325 (mp0) REVERT: B 81 GLN cc_start: 0.7703 (mt0) cc_final: 0.7163 (mt0) REVERT: B 179 HIS cc_start: 0.6203 (m90) cc_final: 0.5509 (m-70) REVERT: B 212 GLN cc_start: 0.7079 (tm-30) cc_final: 0.6812 (tm-30) REVERT: B 304 GLU cc_start: 0.8588 (mt-10) cc_final: 0.7903 (mt-10) REVERT: B 512 TYR cc_start: 0.8168 (m-10) cc_final: 0.7780 (m-10) REVERT: B 622 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7203 (mt-10) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 1.2800 time to fit residues: 159.8804 Evaluate side-chains 111 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 361 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.191459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133043 restraints weight = 25906.233| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.52 r_work: 0.3249 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10155 Z= 0.132 Angle : 0.496 8.751 13814 Z= 0.259 Chirality : 0.035 0.198 1484 Planarity : 0.005 0.087 1651 Dihedral : 14.702 160.161 1739 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.78 % Allowed : 18.83 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.24), residues: 1123 helix: 2.82 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -1.65 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 219 TYR 0.011 0.001 TYR B 148 PHE 0.025 0.002 PHE B 605 TRP 0.009 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00286 (10153) covalent geometry : angle 0.49584 (13810) SS BOND : bond 0.00293 ( 2) SS BOND : angle 1.14076 ( 4) hydrogen bonds : bond 0.04523 ( 723) hydrogen bonds : angle 3.87136 ( 2136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 158 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7129 (mmtm) REVERT: A 199 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: A 216 LYS cc_start: 0.7485 (ttpp) cc_final: 0.6859 (tmtt) REVERT: A 468 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.6976 (tmm-80) REVERT: B 2 LYS cc_start: 0.8268 (pttm) cc_final: 0.7441 (mmmt) REVERT: B 16 ARG cc_start: 0.7260 (ttp-170) cc_final: 0.6929 (ttp-110) REVERT: B 17 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7405 (ptmt) REVERT: B 23 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6261 (mp0) REVERT: B 81 GLN cc_start: 0.7688 (mt0) cc_final: 0.7150 (mt0) REVERT: B 179 HIS cc_start: 0.6217 (m90) cc_final: 0.5531 (m-70) REVERT: B 212 GLN cc_start: 0.7061 (tm-30) cc_final: 0.6794 (tm-30) REVERT: B 304 GLU cc_start: 0.8564 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 413 MET cc_start: 0.7559 (mmm) cc_final: 0.6679 (mtp) REVERT: B 512 TYR cc_start: 0.8142 (m-10) cc_final: 0.7694 (m-10) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 1.2493 time to fit residues: 152.4527 Evaluate side-chains 109 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 548 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.191173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132714 restraints weight = 25817.620| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.52 r_work: 0.3168 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10155 Z= 0.138 Angle : 0.502 8.844 13814 Z= 0.262 Chirality : 0.035 0.201 1484 Planarity : 0.004 0.078 1651 Dihedral : 14.644 159.013 1739 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.88 % Allowed : 18.83 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.24), residues: 1123 helix: 2.82 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -1.63 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 219 TYR 0.011 0.001 TYR B 148 PHE 0.027 0.002 PHE A 3 TRP 0.010 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00301 (10153) covalent geometry : angle 0.50134 (13810) SS BOND : bond 0.00290 ( 2) SS BOND : angle 1.14513 ( 4) hydrogen bonds : bond 0.04565 ( 723) hydrogen bonds : angle 3.87726 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7340.51 seconds wall clock time: 124 minutes 49.94 seconds (7489.94 seconds total)