Starting phenix.real_space_refine on Tue Jun 17 05:57:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dvp_47214/06_2025/9dvp_47214_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dvp_47214/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dvp_47214/06_2025/9dvp_47214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dvp_47214/06_2025/9dvp_47214.map" model { file = "/net/cci-nas-00/data/ceres_data/9dvp_47214/06_2025/9dvp_47214_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dvp_47214/06_2025/9dvp_47214_trim.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.83, per 1000 atoms: 0.61 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: 5.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.47 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: 6.58 Time building geometry restraints manager: 6.47 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 625 or resid 801 thr \ ough 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 625 or resid 801 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: 3.400 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: 0.350 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 44.120 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.050 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:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.820 ------------------------------------------------------------------------------- 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 : 5.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (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 TRP 0.033 0.001 TRP B 573 HIS 0.002 0.000 HIS B 10 PHE 0.017 0.001 PHE B 605 TYR 0.017 0.001 TYR B 467 ARG 0.011 0.000 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.10603 ( 723) hydrogen bonds : angle 4.53568 ( 2136) SS BOND : bond 0.00137 ( 2) SS BOND : angle 0.63869 ( 4) covalent geometry : bond 0.00635 (10153) covalent geometry : angle 1.05942 (13810) *********************** 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 : 1.325 Fit side-chains revert: symmetry clash 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: 0.6413 (mmtm) REVERT: A 216 LYS cc_start: 0.7330 (ttpp) cc_final: 0.6786 (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: 0.7440 (mttp) REVERT: B 212 GLN cc_start: 0.6819 (tm-30) cc_final: 0.6205 (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: 0.7863 (mt-10) REVERT: B 394 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7876 (p90) REVERT: B 468 ARG cc_start: 0.8278 (ttp-170) cc_final: 0.7942 (ttt-90) 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: 2.4886 time to fit residues: 412.6542 Evaluate side-chains 113 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.196551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.137763 restraints weight = 25769.374| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.58 r_work: 0.3281 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10155 Z= 0.140 Angle : 0.501 6.872 13814 Z= 0.259 Chirality : 0.035 0.203 1484 Planarity : 0.004 0.035 1651 Dihedral : 17.455 163.751 1744 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.99 % Allowed : 20.12 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.25), residues: 1123 helix: 3.30 (0.16), residues: 864 sheet: None (None), residues: 0 loop : -1.55 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 395 HIS 0.003 0.001 HIS B 299 PHE 0.020 0.001 PHE B 605 TYR 0.013 0.001 TYR B 148 ARG 0.007 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 723) hydrogen bonds : angle 3.96824 ( 2136) SS BOND : bond 0.00223 ( 2) SS BOND : angle 1.00852 ( 4) covalent geometry : bond 0.00303 (10153) covalent geometry : angle 0.50064 (13810) *********************** 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 129 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7717 (mtmm) cc_final: 0.6776 (mmtm) REVERT: A 152 ASN cc_start: 0.7871 (m-40) cc_final: 0.7235 (m110) REVERT: A 216 LYS cc_start: 0.7497 (ttpp) cc_final: 0.6801 (tmtt) REVERT: A 270 ARG cc_start: 0.7928 (mmt180) cc_final: 0.7723 (mmm160) REVERT: A 468 ARG cc_start: 0.7698 (tmm-80) cc_final: 0.6780 (tmm-80) REVERT: B 2 LYS cc_start: 0.8160 (pttm) cc_final: 0.7831 (pttt) REVERT: B 14 GLU cc_start: 0.7422 (mp0) cc_final: 0.6530 (pt0) REVERT: B 16 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6717 (ttp-110) REVERT: B 17 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7181 (ptmt) REVERT: B 23 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6149 (mp0) REVERT: B 81 GLN cc_start: 0.7514 (mt0) cc_final: 0.6970 (mt0) REVERT: B 179 HIS cc_start: 0.6022 (OUTLIER) cc_final: 0.5246 (m170) REVERT: B 190 LYS cc_start: 0.7668 (mttm) cc_final: 0.7436 (mttp) REVERT: B 212 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6342 (mp-120) REVERT: B 304 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7807 (mt-10) REVERT: B 417 TYR cc_start: 0.7331 (t80) cc_final: 0.6038 (m-80) REVERT: B 500 LYS cc_start: 0.6581 (tttt) cc_final: 0.6235 (ttpt) outliers start: 10 outliers final: 4 residues processed: 124 average time/residue: 2.4494 time to fit residues: 330.4390 Evaluate side-chains 113 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 87 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 B 147 ASN B 441 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.193680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134013 restraints weight = 25531.394| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.55 r_work: 0.3212 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10155 Z= 0.163 Angle : 0.511 7.303 13814 Z= 0.268 Chirality : 0.036 0.221 1484 Planarity : 0.004 0.073 1651 Dihedral : 16.398 166.346 1739 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.88 % Allowed : 18.63 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.24), residues: 1123 helix: 3.03 (0.16), residues: 865 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.007 0.001 HIS B 441 PHE 0.027 0.002 PHE A 605 TYR 0.012 0.001 TYR B 352 ARG 0.008 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04847 ( 723) hydrogen bonds : angle 3.91081 ( 2136) SS BOND : bond 0.00221 ( 2) SS BOND : angle 0.85398 ( 4) covalent geometry : bond 0.00352 (10153) covalent geometry : angle 0.51056 (13810) *********************** 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 135 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7799 (mtmm) cc_final: 0.6938 (mmtm) REVERT: A 215 MET cc_start: 0.7515 (mmm) cc_final: 0.7235 (mmm) REVERT: A 216 LYS cc_start: 0.7529 (ttpp) cc_final: 0.6903 (tmtt) REVERT: A 468 ARG cc_start: 0.7805 (tmm-80) cc_final: 0.6910 (tmm-80) REVERT: B 2 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7884 (pttt) REVERT: B 14 GLU cc_start: 0.7608 (mp0) cc_final: 0.6700 (pt0) REVERT: B 16 ARG cc_start: 0.7223 (ttp-170) cc_final: 0.6871 (ttp-110) REVERT: B 17 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7266 (ptmt) REVERT: B 23 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6225 (mp0) REVERT: B 81 GLN cc_start: 0.7628 (mt0) cc_final: 0.7082 (mt0) REVERT: B 179 HIS cc_start: 0.6114 (OUTLIER) cc_final: 0.5419 (m-70) REVERT: B 190 LYS cc_start: 0.7722 (mttm) cc_final: 0.7506 (mttp) REVERT: B 212 GLN cc_start: 0.7141 (tm-30) cc_final: 0.6824 (tm-30) REVERT: B 216 LYS cc_start: 0.7799 (ttpt) cc_final: 0.7042 (tmtt) REVERT: B 304 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 417 TYR cc_start: 0.7464 (t80) cc_final: 0.6106 (m-80) REVERT: B 576 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8574 (tm-30) outliers start: 19 outliers final: 7 residues processed: 128 average time/residue: 2.2803 time to fit residues: 317.9250 Evaluate side-chains 112 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.192497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133320 restraints weight = 25846.281| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.54 r_work: 0.3200 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2012 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 : 0.488 7.990 13814 Z= 0.256 Chirality : 0.035 0.203 1484 Planarity : 0.004 0.048 1651 Dihedral : 15.905 167.122 1739 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.08 % Allowed : 18.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.25), residues: 1123 helix: 3.00 (0.16), residues: 865 sheet: None (None), residues: 0 loop : -1.62 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 528 HIS 0.007 0.001 HIS B 441 PHE 0.023 0.002 PHE B 605 TYR 0.011 0.001 TYR B 148 ARG 0.007 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04605 ( 723) hydrogen bonds : angle 3.86228 ( 2136) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.96883 ( 4) covalent geometry : bond 0.00309 (10153) covalent geometry : angle 0.48790 (13810) *********************** 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 130 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7831 (mtmm) cc_final: 0.6962 (mmtm) REVERT: A 216 LYS cc_start: 0.7517 (ttpp) cc_final: 0.6902 (tmtt) REVERT: A 468 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.6864 (tmm-80) REVERT: A 618 ASN cc_start: 0.7266 (OUTLIER) cc_final: 0.6381 (m-40) REVERT: B 2 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (pttt) REVERT: B 16 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6869 (ttp-110) REVERT: B 17 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7280 (ptmt) REVERT: B 23 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6218 (mp0) REVERT: B 81 GLN cc_start: 0.7618 (mt0) cc_final: 0.7091 (mt0) REVERT: B 179 HIS cc_start: 0.6122 (m90) cc_final: 0.5432 (m-70) REVERT: B 212 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6831 (tm-30) REVERT: B 216 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7084 (tmtt) REVERT: B 304 GLU cc_start: 0.8584 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 417 TYR cc_start: 0.7461 (t80) cc_final: 0.6120 (m-80) REVERT: B 576 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8593 (tm-30) outliers start: 21 outliers final: 8 residues processed: 125 average time/residue: 2.1637 time to fit residues: 295.0449 Evaluate side-chains 116 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 2 LYS Chi-restraints excluded: chain B residue 394 PHE 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 86 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.193205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134755 restraints weight = 25798.581| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.51 r_work: 0.3208 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2187 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= 0.140 Angle : 0.491 8.207 13814 Z= 0.257 Chirality : 0.035 0.204 1484 Planarity : 0.004 0.072 1651 Dihedral : 15.507 166.755 1739 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.98 % Allowed : 18.53 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.25), residues: 1123 helix: 2.97 (0.16), residues: 867 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 PHE 0.024 0.002 PHE B 605 TYR 0.011 0.001 TYR B 148 ARG 0.010 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 723) hydrogen bonds : angle 3.84802 ( 2136) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.98158 ( 4) covalent geometry : bond 0.00306 (10153) covalent geometry : angle 0.49044 (13810) *********************** 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 126 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7003 (mmtm) REVERT: A 216 LYS cc_start: 0.7539 (ttpp) cc_final: 0.6925 (tmtt) REVERT: A 468 ARG cc_start: 0.7870 (tmm-80) cc_final: 0.6963 (tmm-80) REVERT: A 618 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6398 (m-40) REVERT: B 2 LYS cc_start: 0.8281 (pttm) cc_final: 0.7961 (pttt) REVERT: B 16 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6959 (ttp-110) REVERT: B 23 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6246 (mp0) REVERT: B 81 GLN cc_start: 0.7603 (mt0) cc_final: 0.7064 (mt0) REVERT: B 179 HIS cc_start: 0.6147 (m90) cc_final: 0.5465 (m-70) REVERT: B 212 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6848 (tm-30) REVERT: B 216 LYS cc_start: 0.7785 (ttpt) cc_final: 0.7069 (tmtt) REVERT: B 304 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 417 TYR cc_start: 0.7492 (t80) cc_final: 0.6113 (m-80) REVERT: B 576 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8598 (tm-30) outliers start: 20 outliers final: 10 residues processed: 122 average time/residue: 2.2575 time to fit residues: 298.7500 Evaluate side-chains 114 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 394 PHE 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 548 ARG Chi-restraints excluded: chain B residue 576 GLN Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.9564 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.192237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133642 restraints weight = 25804.234| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.52 r_work: 0.3193 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2320 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= 0.146 Angle : 0.494 8.323 13814 Z= 0.259 Chirality : 0.035 0.202 1484 Planarity : 0.004 0.059 1651 Dihedral : 15.301 165.603 1739 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.08 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.25), residues: 1123 helix: 2.88 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.009 0.001 HIS B 441 PHE 0.024 0.002 PHE B 605 TYR 0.011 0.001 TYR B 148 ARG 0.004 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 723) hydrogen bonds : angle 3.85837 ( 2136) SS BOND : bond 0.00273 ( 2) SS BOND : angle 0.98653 ( 4) covalent geometry : bond 0.00322 (10153) covalent geometry : angle 0.49353 (13810) *********************** 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 125 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7025 (mmtm) REVERT: A 216 LYS cc_start: 0.7505 (ttpp) cc_final: 0.6869 (tmtt) REVERT: A 468 ARG cc_start: 0.7892 (tmm-80) cc_final: 0.6937 (tmm-80) REVERT: A 618 ASN cc_start: 0.7303 (OUTLIER) cc_final: 0.6409 (m-40) REVERT: B 2 LYS cc_start: 0.8259 (pttm) cc_final: 0.7313 (mmmt) REVERT: B 16 ARG cc_start: 0.7283 (ttp-170) cc_final: 0.6897 (ttp-110) REVERT: B 17 LYS cc_start: 0.8007 (mtpp) cc_final: 0.7337 (ptmt) REVERT: B 23 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6290 (mp0) REVERT: B 81 GLN cc_start: 0.7613 (mt0) cc_final: 0.7078 (mt0) REVERT: B 179 HIS cc_start: 0.6189 (m90) cc_final: 0.5496 (m-70) REVERT: B 212 GLN cc_start: 0.7043 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 216 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7081 (tmtt) REVERT: B 304 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 417 TYR cc_start: 0.7490 (t80) cc_final: 0.6133 (m-80) REVERT: B 576 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8586 (tm-30) outliers start: 21 outliers final: 9 residues processed: 122 average time/residue: 2.2313 time to fit residues: 297.1611 Evaluate side-chains 112 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 401 ASN B 441 HIS B 618 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.192563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.134068 restraints weight = 25658.847| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.52 r_work: 0.3187 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.136 Angle : 0.488 8.409 13814 Z= 0.255 Chirality : 0.035 0.200 1484 Planarity : 0.004 0.053 1651 Dihedral : 15.072 164.801 1739 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.08 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.25), residues: 1123 helix: 2.88 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.69 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.009 0.001 HIS B 441 PHE 0.024 0.002 PHE B 605 TYR 0.011 0.001 TYR B 148 ARG 0.007 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 723) hydrogen bonds : angle 3.84201 ( 2136) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.03709 ( 4) covalent geometry : bond 0.00295 (10153) covalent geometry : angle 0.48782 (13810) *********************** 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 124 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7015 (mmtm) REVERT: A 216 LYS cc_start: 0.7495 (ttpp) cc_final: 0.6851 (tmtt) REVERT: A 468 ARG cc_start: 0.7892 (tmm-80) cc_final: 0.6925 (tmm-80) REVERT: A 618 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6329 (m-40) REVERT: B 2 LYS cc_start: 0.8252 (pttm) cc_final: 0.7309 (mmmt) REVERT: B 16 ARG cc_start: 0.7266 (ttp-170) cc_final: 0.6881 (ttp-110) REVERT: B 17 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7341 (ptmt) REVERT: B 23 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6277 (mp0) REVERT: B 81 GLN cc_start: 0.7624 (mt0) cc_final: 0.7087 (mt0) REVERT: B 179 HIS cc_start: 0.6185 (m90) cc_final: 0.5490 (m-70) REVERT: B 212 GLN cc_start: 0.7051 (tm-30) cc_final: 0.6757 (tm-30) REVERT: B 216 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7077 (tmtt) REVERT: B 304 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7868 (mt-10) REVERT: B 512 TYR cc_start: 0.8120 (m-10) cc_final: 0.7766 (m-10) REVERT: B 576 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8582 (tm-30) REVERT: B 622 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6880 (mt-10) outliers start: 21 outliers final: 11 residues processed: 121 average time/residue: 2.3667 time to fit residues: 311.1824 Evaluate side-chains 114 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.471 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 622 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.191565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.132860 restraints weight = 25773.868| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.52 r_work: 0.3166 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10155 Z= 0.149 Angle : 0.500 8.426 13814 Z= 0.263 Chirality : 0.035 0.200 1484 Planarity : 0.004 0.048 1651 Dihedral : 15.003 163.155 1739 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.25), residues: 1123 helix: 2.84 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.68 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.008 0.001 HIS B 441 PHE 0.026 0.002 PHE A 605 TYR 0.010 0.001 TYR B 148 ARG 0.006 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 723) hydrogen bonds : angle 3.86666 ( 2136) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.00987 ( 4) covalent geometry : bond 0.00330 (10153) covalent geometry : angle 0.50006 (13810) *********************** 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 124 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7033 (mmtm) REVERT: A 216 LYS cc_start: 0.7501 (ttpp) cc_final: 0.6856 (tmtt) REVERT: A 468 ARG cc_start: 0.7904 (tmm-80) cc_final: 0.6921 (tmm-80) REVERT: A 618 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6370 (m-40) REVERT: B 2 LYS cc_start: 0.8242 (pttm) cc_final: 0.7328 (mmmt) REVERT: B 16 ARG cc_start: 0.7246 (ttp-170) cc_final: 0.6862 (ttp-110) REVERT: B 17 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7367 (ptmt) REVERT: B 23 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6277 (mp0) REVERT: B 81 GLN cc_start: 0.7668 (mt0) cc_final: 0.7137 (mt0) REVERT: B 179 HIS cc_start: 0.6221 (m90) cc_final: 0.5538 (m-70) REVERT: B 212 GLN cc_start: 0.7056 (tm-30) cc_final: 0.6744 (tm-30) REVERT: B 216 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7112 (tmtt) REVERT: B 304 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 417 TYR cc_start: 0.7429 (t80) cc_final: 0.6115 (m-80) REVERT: B 512 TYR cc_start: 0.8114 (m-10) cc_final: 0.7767 (m-10) REVERT: B 576 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8568 (tm-30) outliers start: 23 outliers final: 10 residues processed: 121 average time/residue: 2.3827 time to fit residues: 312.1900 Evaluate side-chains 107 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.192438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.133997 restraints weight = 25710.676| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.52 r_work: 0.3269 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2541 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= 0.128 Angle : 0.487 8.619 13814 Z= 0.254 Chirality : 0.035 0.197 1484 Planarity : 0.004 0.047 1651 Dihedral : 14.779 162.136 1739 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.59 % Allowed : 18.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.99 (0.25), residues: 1123 helix: 2.91 (0.16), residues: 874 sheet: None (None), residues: 0 loop : -1.70 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.007 0.001 HIS B 441 PHE 0.024 0.001 PHE B 605 TYR 0.011 0.001 TYR B 148 ARG 0.006 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 723) hydrogen bonds : angle 3.84030 ( 2136) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.07426 ( 4) covalent geometry : bond 0.00275 (10153) covalent geometry : angle 0.48626 (13810) *********************** 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 113 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7178 (mmtm) REVERT: A 216 LYS cc_start: 0.7561 (ttpp) cc_final: 0.6925 (tmtt) REVERT: A 468 ARG cc_start: 0.7932 (tmm-80) cc_final: 0.6968 (tmm-80) REVERT: B 2 LYS cc_start: 0.8300 (pttm) cc_final: 0.7440 (mmmt) REVERT: B 16 ARG cc_start: 0.7290 (ttp-170) cc_final: 0.6934 (ttp-110) REVERT: B 17 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7408 (ptmt) REVERT: B 23 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6321 (mp0) REVERT: B 81 GLN cc_start: 0.7685 (mt0) cc_final: 0.7152 (mt0) REVERT: B 179 HIS cc_start: 0.6206 (m90) cc_final: 0.5557 (m-70) REVERT: B 212 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6797 (tm-30) REVERT: B 304 GLU cc_start: 0.8581 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 512 TYR cc_start: 0.8148 (m-10) cc_final: 0.7753 (m-10) outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 2.3706 time to fit residues: 282.7240 Evaluate side-chains 108 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 441 HIS Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 515 ILE 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 3 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN B 618 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.189491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.130561 restraints weight = 25718.290| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.52 r_work: 0.3218 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10155 Z= 0.216 Angle : 0.552 8.313 13814 Z= 0.289 Chirality : 0.037 0.208 1484 Planarity : 0.004 0.053 1651 Dihedral : 15.147 160.714 1739 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.68 % Allowed : 18.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.24), residues: 1123 helix: 2.62 (0.16), residues: 876 sheet: None (None), residues: 0 loop : -1.79 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 528 HIS 0.022 0.002 HIS B 441 PHE 0.027 0.002 PHE A 605 TYR 0.013 0.002 TYR A 272 ARG 0.009 0.001 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 723) hydrogen bonds : angle 3.98355 ( 2136) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.95429 ( 4) covalent geometry : bond 0.00500 (10153) covalent geometry : angle 0.55201 (13810) ********************** 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 115 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7168 (mmtm) REVERT: A 216 LYS cc_start: 0.7557 (ttpp) cc_final: 0.6938 (tmtt) REVERT: A 468 ARG cc_start: 0.7961 (tmm-80) cc_final: 0.6975 (tmm-80) REVERT: B 2 LYS cc_start: 0.8292 (pttm) cc_final: 0.8009 (pttt) REVERT: B 16 ARG cc_start: 0.7275 (ttp-170) cc_final: 0.6940 (ttp-110) REVERT: B 17 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7415 (ptmt) REVERT: B 23 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6262 (mp0) REVERT: B 81 GLN cc_start: 0.7749 (mt0) cc_final: 0.7231 (mt0) REVERT: B 179 HIS cc_start: 0.6245 (m90) cc_final: 0.5559 (m-70) REVERT: B 212 GLN cc_start: 0.7075 (tm-30) cc_final: 0.6780 (tm-30) REVERT: B 216 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7159 (tmtt) REVERT: B 304 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 417 TYR cc_start: 0.7483 (t80) cc_final: 0.6159 (m-80) REVERT: B 512 TYR cc_start: 0.8151 (m-10) cc_final: 0.7765 (m-10) REVERT: B 576 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8564 (tm-30) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 2.3855 time to fit residues: 292.2666 Evaluate side-chains 108 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.191773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133112 restraints weight = 25761.887| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.52 r_work: 0.3257 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.131 Angle : 0.501 8.733 13814 Z= 0.262 Chirality : 0.035 0.196 1484 Planarity : 0.004 0.052 1651 Dihedral : 14.795 160.339 1739 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.59 % Allowed : 18.93 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.24), residues: 1123 helix: 2.76 (0.16), residues: 875 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 528 HIS 0.006 0.001 HIS B 441 PHE 0.025 0.001 PHE A 3 TYR 0.011 0.001 TYR B 148 ARG 0.008 0.001 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.04533 ( 723) hydrogen bonds : angle 3.90208 ( 2136) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.97108 ( 4) covalent geometry : bond 0.00281 (10153) covalent geometry : angle 0.50072 (13810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14133.04 seconds wall clock time: 239 minutes 19.00 seconds (14359.00 seconds total)