Starting phenix.real_space_refine on Thu Jul 2 13:32:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8wba_37418/07_2026/8wba_37418.cif" } resolution = 3.1 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= -0.002 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5646 2.51 5 N 1430 2.21 5 O 1512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8646 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4288 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 4 Chain: "B" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4288 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 18, 'TRANS': 534} Chain breaks: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.38, per 1000 atoms: 0.16 Number of scatterers: 8646 At special positions: 0 Unit cell: (68.2, 105.6, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1512 8.00 N 1430 7.00 C 5646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 622 " distance=2.03 Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 622 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 299.0 milliseconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 66.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.538A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 174 through 189 Processing helix chain 'A' and resid 190 through 194 removed outlier: 4.184A pdb=" N LYS A 193 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 Processing helix chain 'A' and resid 238 through 255 Processing helix chain 'A' and resid 268 through 275 removed outlier: 3.596A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 357 removed outlier: 4.832A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Proline residue: A 351 - end of helix Processing helix chain 'A' and resid 379 through 406 removed outlier: 4.569A pdb=" N LYS A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 Processing helix chain 'A' and resid 432 through 456 Proline residue: A 451 - end of helix removed outlier: 3.683A pdb=" N VAL A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.620A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ILE A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 Processing helix chain 'A' and resid 493 through 508 removed outlier: 4.020A pdb=" N TRP A 505 " --> pdb=" O THR A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.746A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 561 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.635A pdb=" N VAL A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 660 removed outlier: 3.753A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 174 through 189 Processing helix chain 'B' and resid 190 through 194 removed outlier: 4.082A pdb=" N LYS B 193 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.514A pdb=" N GLU B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 255 Processing helix chain 'B' and resid 268 through 275 removed outlier: 3.650A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 311 through 321 Processing helix chain 'B' and resid 338 through 357 removed outlier: 4.612A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix Processing helix chain 'B' and resid 379 through 405 removed outlier: 4.583A pdb=" N LYS B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU B 400 " --> pdb=" O ARG B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 432 through 456 Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 457 through 472 removed outlier: 4.979A pdb=" N ALA B 464 " --> pdb=" O PRO B 460 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 Processing helix chain 'B' and resid 493 through 508 removed outlier: 4.170A pdb=" N TRP B 505 " --> pdb=" O THR B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.628A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 561 Processing helix chain 'B' and resid 573 through 578 removed outlier: 4.232A pdb=" N LYS B 577 " --> pdb=" O MET B 573 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 573 through 578' Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 597 through 605 Processing helix chain 'B' and resid 619 through 625 removed outlier: 3.539A pdb=" N VAL B 625 " --> pdb=" O GLY B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 660 removed outlier: 3.629A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.209A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 230 removed outlier: 6.171A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N PHE A 96 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 279 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA A 98 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 281 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 100 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 288 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 282 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N CYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 91 removed outlier: 5.401A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 100 removed outlier: 5.938A pdb=" N SER B 282 " --> pdb=" O CYS B 286 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N CYS B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.632A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 529 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.87 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1502 1.33 - 1.45: 2237 1.45 - 1.57: 4996 1.57 - 1.69: 1 1.69 - 1.81: 92 Bond restraints: 8828 Sorted by residual: bond pdb=" CBE Y01 A 702 " pdb=" CBI Y01 A 702 " ideal model delta sigma weight residual 1.550 1.570 -0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" CB MET B 603 " pdb=" CG MET B 603 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.87e-01 bond pdb=" CB PHE A 516 " pdb=" CG PHE A 516 " ideal model delta sigma weight residual 1.502 1.522 -0.020 2.30e-02 1.89e+03 7.79e-01 bond pdb=" CB MET A 603 " pdb=" CG MET A 603 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.99e-01 bond pdb=" CB PHE B 516 " pdb=" CG PHE B 516 " ideal model delta sigma weight residual 1.502 1.520 -0.018 2.30e-02 1.89e+03 6.18e-01 ... (remaining 8823 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 11787 1.80 - 3.59: 156 3.59 - 5.39: 28 5.39 - 7.19: 2 7.19 - 8.99: 5 Bond angle restraints: 11978 Sorted by residual: angle pdb=" CB MET B 603 " pdb=" CG MET B 603 " pdb=" SD MET B 603 " ideal model delta sigma weight residual 112.70 121.32 -8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" CA PHE B 308 " pdb=" C PHE B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 117.82 120.00 -2.18 7.80e-01 1.64e+00 7.83e+00 angle pdb=" CB MET A 603 " pdb=" CG MET A 603 " pdb=" SD MET A 603 " ideal model delta sigma weight residual 112.70 120.70 -8.00 3.00e+00 1.11e-01 7.10e+00 angle pdb=" CA LEU A 161 " pdb=" CB LEU A 161 " pdb=" CG LEU A 161 " ideal model delta sigma weight residual 116.30 107.31 8.99 3.50e+00 8.16e-02 6.59e+00 angle pdb=" CA ILE A 541 " pdb=" CB ILE A 541 " pdb=" CG1 ILE A 541 " ideal model delta sigma weight residual 110.40 114.68 -4.28 1.70e+00 3.46e-01 6.33e+00 ... (remaining 11973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4322 16.36 - 32.71: 639 32.71 - 49.07: 168 49.07 - 65.42: 30 65.42 - 81.78: 15 Dihedral angle restraints: 5174 sinusoidal: 2014 harmonic: 3160 Sorted by residual: dihedral pdb=" CB CYS A 606 " pdb=" SG CYS A 606 " pdb=" SG CYS A 622 " pdb=" CB CYS A 622 " ideal model delta sinusoidal sigma weight residual 93.00 142.65 -49.65 1 1.00e+01 1.00e-02 3.38e+01 dihedral pdb=" CA ASP A 148 " pdb=" CB ASP A 148 " pdb=" CG ASP A 148 " pdb=" OD1 ASP A 148 " ideal model delta sinusoidal sigma weight residual -30.00 -89.28 59.28 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 607 " pdb=" CB ASP A 607 " pdb=" CG ASP A 607 " pdb=" OD1 ASP A 607 " ideal model delta sinusoidal sigma weight residual -30.00 -89.14 59.14 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 5171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1223 0.055 - 0.110: 190 0.110 - 0.165: 18 0.165 - 0.220: 1 0.220 - 0.275: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CG LEU A 517 " pdb=" CB LEU A 517 " pdb=" CD1 LEU A 517 " pdb=" CD2 LEU A 517 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CBB Y01 A 702 " pdb=" CAC Y01 A 702 " pdb=" CAO Y01 A 702 " pdb=" CBE Y01 A 702 " both_signs ideal model delta sigma weight residual False 2.58 2.34 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBE Y01 A 702 " pdb=" CAP Y01 A 702 " pdb=" CBB Y01 A 702 " pdb=" CBI Y01 A 702 " both_signs ideal model delta sigma weight residual False 2.57 2.40 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 1431 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 514 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 515 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 515 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 515 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 275 " 0.017 2.00e-02 2.50e+03 1.53e-02 4.11e+00 pdb=" CG PHE B 275 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 275 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 275 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 275 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 275 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 275 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 514 " 0.034 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO B 515 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 515 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 515 " 0.029 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2394 2.81 - 3.33: 8736 3.33 - 3.86: 15301 3.86 - 4.38: 17514 4.38 - 4.90: 30572 Nonbonded interactions: 74517 Sorted by model distance: nonbonded pdb=" NH1 ARG B 168 " pdb=" O HIS B 219 " model vdw 2.289 3.120 nonbonded pdb=" O ALA A 464 " pdb=" OG1 THR A 467 " model vdw 2.352 3.040 nonbonded pdb=" OG SER A 452 " pdb=" O SER A 530 " model vdw 2.357 3.040 nonbonded pdb=" N ILE B 129 " pdb=" O GLY B 132 " model vdw 2.393 3.120 nonbonded pdb=" OE1 GLU A 232 " pdb=" OG SER A 235 " model vdw 2.395 3.040 ... (remaining 74512 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 35 through 660) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.590 Find NCS groups from input model: 0.110 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.002 0.028 8830 Z= 0.107 Angle : 0.537 8.987 11982 Z= 0.267 Chirality : 0.040 0.275 1434 Planarity : 0.004 0.054 1458 Dihedral : 16.812 81.777 3140 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.32 % Allowed : 25.85 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.27), residues: 1086 helix: 1.82 (0.20), residues: 676 sheet: -2.57 (0.55), residues: 68 loop : 0.39 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 401 TYR 0.009 0.001 TYR B 584 PHE 0.035 0.002 PHE B 275 TRP 0.022 0.001 TRP A 575 HIS 0.004 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 8828) covalent geometry : angle 0.53717 / 0.27 (11978) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.28483 / 0.14 ( 4) hydrogen bonds : bond 0.12331 / 8.24 ( 529) hydrogen bonds : angle 5.47708 / 4.04 ( 1560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.0702 time to fit residues: 13.1449 Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 601 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 GLN A 461 GLN ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.168392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124975 restraints weight = 9415.239| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.00 r_work: 0.3185 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8830 Z= 0.191 Angle : 0.584 9.262 11982 Z= 0.284 Chirality : 0.042 0.228 1434 Planarity : 0.005 0.045 1458 Dihedral : 5.476 58.910 1224 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.49 % Allowed : 21.05 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.26), residues: 1086 helix: 1.48 (0.19), residues: 698 sheet: -2.61 (0.66), residues: 44 loop : 0.11 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 510 TYR 0.011 0.002 TYR B 526 PHE 0.030 0.002 PHE A 275 TRP 0.011 0.001 TRP A 447 HIS 0.007 0.002 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 8828) covalent geometry : angle 0.58358 / 0.28 (11978) SS BOND : bond 0.00188 / 0.10 ( 2) SS BOND : angle 0.45999 / 0.26 ( 4) hydrogen bonds : bond 0.03592 / 2.41 ( 529) hydrogen bonds : angle 4.68005 / 3.45 ( 1560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 142 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7803 (mmmt) cc_final: 0.7384 (mmmt) REVERT: A 256 LYS cc_start: 0.8397 (mmtt) cc_final: 0.7982 (mmmm) REVERT: B 274 MET cc_start: 0.8049 (mmm) cc_final: 0.7359 (mmt) REVERT: B 291 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7839 (ttpt) REVERT: B 517 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8249 (mm) REVERT: B 630 ILE cc_start: 0.7804 (mp) cc_final: 0.7497 (mp) REVERT: B 636 TRP cc_start: 0.8404 (m100) cc_final: 0.8061 (m100) outliers start: 42 outliers final: 23 residues processed: 169 average time/residue: 0.0640 time to fit residues: 15.6556 Evaluate side-chains 160 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.168988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125251 restraints weight = 9317.764| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.06 r_work: 0.3215 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8830 Z= 0.146 Angle : 0.541 7.924 11982 Z= 0.265 Chirality : 0.040 0.229 1434 Planarity : 0.004 0.045 1458 Dihedral : 5.237 57.142 1222 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.17 % Allowed : 22.12 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.26), residues: 1086 helix: 1.65 (0.19), residues: 694 sheet: -1.91 (0.70), residues: 48 loop : 0.05 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.009 0.001 TYR A 526 PHE 0.043 0.002 PHE A 275 TRP 0.011 0.001 TRP B 575 HIS 0.006 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8828) covalent geometry : angle 0.54148 / 0.27 (11978) SS BOND : bond 0.00125 / 0.07 ( 2) SS BOND : angle 0.30561 / 0.17 ( 4) hydrogen bonds : bond 0.03242 / 2.16 ( 529) hydrogen bonds : angle 4.46734 / 3.28 ( 1560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7642 (mmmt) REVERT: A 256 LYS cc_start: 0.8362 (mmtt) cc_final: 0.7882 (mmmm) REVERT: B 291 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7691 (ttpt) REVERT: B 517 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8217 (mm) REVERT: B 630 ILE cc_start: 0.7893 (mp) cc_final: 0.7580 (mp) REVERT: B 636 TRP cc_start: 0.8390 (m100) cc_final: 0.8033 (m100) outliers start: 39 outliers final: 27 residues processed: 162 average time/residue: 0.0692 time to fit residues: 16.4681 Evaluate side-chains 163 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126689 restraints weight = 9444.283| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.08 r_work: 0.3207 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8830 Z= 0.133 Angle : 0.526 7.560 11982 Z= 0.257 Chirality : 0.040 0.229 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.157 56.037 1222 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.49 % Allowed : 22.97 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1086 helix: 1.72 (0.19), residues: 696 sheet: -1.82 (0.70), residues: 48 loop : 0.05 (0.38), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 436 TYR 0.009 0.001 TYR A 526 PHE 0.037 0.001 PHE B 275 TRP 0.014 0.001 TRP A 575 HIS 0.006 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 8828) covalent geometry : angle 0.52578 / 0.26 (11978) SS BOND : bond 0.00102 / 0.05 ( 2) SS BOND : angle 0.26936 / 0.14 ( 4) hydrogen bonds : bond 0.03032 / 2.03 ( 529) hydrogen bonds : angle 4.31347 / 3.16 ( 1560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 143 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7711 (mmmt) cc_final: 0.7369 (mmmt) REVERT: A 256 LYS cc_start: 0.8352 (mmtt) cc_final: 0.7883 (mmmm) REVERT: B 291 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7604 (ttpt) REVERT: B 508 TYR cc_start: 0.6332 (t80) cc_final: 0.6061 (t80) REVERT: B 517 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8222 (mm) REVERT: B 630 ILE cc_start: 0.7912 (mp) cc_final: 0.7589 (mp) REVERT: B 636 TRP cc_start: 0.8373 (m100) cc_final: 0.8019 (m100) outliers start: 42 outliers final: 31 residues processed: 168 average time/residue: 0.0634 time to fit residues: 15.5672 Evaluate side-chains 170 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 154 HIS B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.167874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123773 restraints weight = 9501.204| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.08 r_work: 0.3179 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8830 Z= 0.182 Angle : 0.566 7.871 11982 Z= 0.276 Chirality : 0.041 0.225 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.281 55.392 1222 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.02 % Allowed : 23.08 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1086 helix: 1.51 (0.19), residues: 700 sheet: -1.87 (0.69), residues: 48 loop : 0.08 (0.39), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 410 TYR 0.010 0.001 TYR A 526 PHE 0.043 0.002 PHE A 275 TRP 0.014 0.002 TRP A 575 HIS 0.005 0.001 HIS B 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 8828) covalent geometry : angle 0.56600 / 0.28 (11978) SS BOND : bond 0.00134 / 0.07 ( 2) SS BOND : angle 0.26140 / 0.14 ( 4) hydrogen bonds : bond 0.03351 / 2.23 ( 529) hydrogen bonds : angle 4.42981 / 3.24 ( 1560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7310 (mmmt) REVERT: A 256 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7903 (mmmm) REVERT: B 291 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7757 (ttpt) REVERT: B 517 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8298 (mm) REVERT: B 630 ILE cc_start: 0.7930 (mp) cc_final: 0.7604 (mp) REVERT: B 636 TRP cc_start: 0.8494 (m100) cc_final: 0.8207 (m100) outliers start: 47 outliers final: 36 residues processed: 170 average time/residue: 0.0675 time to fit residues: 16.7048 Evaluate side-chains 172 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 68 optimal weight: 0.0870 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 104 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.171238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128378 restraints weight = 9362.462| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.05 r_work: 0.3245 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8830 Z= 0.109 Angle : 0.512 7.612 11982 Z= 0.250 Chirality : 0.039 0.217 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.067 55.008 1222 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.38 % Allowed : 24.04 % Favored : 71.58 % 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 are not related in a simple way. whole: 1.63 (0.27), residues: 1086 helix: 1.83 (0.19), residues: 698 sheet: -1.72 (0.71), residues: 48 loop : 0.05 (0.38), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.010 0.001 TYR B 584 PHE 0.034 0.001 PHE A 275 TRP 0.016 0.001 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8828) covalent geometry : angle 0.51177 / 0.25 (11978) SS BOND : bond 0.00095 / 0.05 ( 2) SS BOND : angle 0.26178 / 0.14 ( 4) hydrogen bonds : bond 0.02871 / 1.92 ( 529) hydrogen bonds : angle 4.17650 / 3.05 ( 1560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7724 (mmmt) cc_final: 0.7261 (mmmt) REVERT: A 136 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7024 (mmmt) REVERT: A 256 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7843 (mmmm) REVERT: B 291 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7644 (ttpt) REVERT: B 508 TYR cc_start: 0.6292 (t80) cc_final: 0.5962 (t80) REVERT: B 517 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 630 ILE cc_start: 0.7956 (mp) cc_final: 0.7641 (mp) REVERT: B 636 TRP cc_start: 0.8416 (m100) cc_final: 0.8101 (m100) outliers start: 41 outliers final: 28 residues processed: 169 average time/residue: 0.0766 time to fit residues: 18.7004 Evaluate side-chains 167 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.0000 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127822 restraints weight = 9397.375| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.05 r_work: 0.3234 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8830 Z= 0.121 Angle : 0.518 7.149 11982 Z= 0.252 Chirality : 0.039 0.217 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.016 54.703 1222 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.38 % Allowed : 23.93 % Favored : 71.69 % 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 are not related in a simple way. whole: 1.68 (0.27), residues: 1086 helix: 1.80 (0.19), residues: 700 sheet: -1.66 (0.72), residues: 48 loop : 0.20 (0.39), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 401 TYR 0.009 0.001 TYR A 584 PHE 0.033 0.001 PHE A 275 TRP 0.018 0.001 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 8828) covalent geometry : angle 0.51764 / 0.25 (11978) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 0.21328 / 0.11 ( 4) hydrogen bonds : bond 0.02919 / 1.96 ( 529) hydrogen bonds : angle 4.13862 / 3.02 ( 1560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7269 (mmmt) REVERT: A 136 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7044 (mmmt) REVERT: A 256 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7838 (mmmm) REVERT: A 517 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8062 (mp) REVERT: B 291 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7658 (ttpt) REVERT: B 508 TYR cc_start: 0.6262 (t80) cc_final: 0.5917 (t80) REVERT: B 517 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8221 (mm) REVERT: B 630 ILE cc_start: 0.7931 (mp) cc_final: 0.7603 (mp) REVERT: B 636 TRP cc_start: 0.8424 (m100) cc_final: 0.8104 (m100) outliers start: 41 outliers final: 33 residues processed: 168 average time/residue: 0.0766 time to fit residues: 18.7184 Evaluate side-chains 173 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123457 restraints weight = 9409.370| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.07 r_work: 0.3182 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8830 Z= 0.195 Angle : 0.582 7.761 11982 Z= 0.284 Chirality : 0.042 0.223 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.230 54.459 1222 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.59 % Allowed : 23.29 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.26), residues: 1086 helix: 1.50 (0.19), residues: 704 sheet: -1.63 (0.73), residues: 48 loop : 0.26 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 410 TYR 0.010 0.002 TYR A 526 PHE 0.044 0.002 PHE A 275 TRP 0.018 0.002 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 ( 8828) covalent geometry : angle 0.58235 / 0.28 (11978) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.20861 / 0.12 ( 4) hydrogen bonds : bond 0.03396 / 2.27 ( 529) hydrogen bonds : angle 4.37169 / 3.19 ( 1560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7728 (mmmt) cc_final: 0.7264 (mmmt) REVERT: A 136 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7044 (mmmt) REVERT: A 256 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7950 (mmmm) REVERT: B 291 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7805 (ttpt) REVERT: B 508 TYR cc_start: 0.6370 (t80) cc_final: 0.6052 (t80) REVERT: B 517 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8333 (mm) REVERT: B 630 ILE cc_start: 0.7941 (mp) cc_final: 0.7601 (mp) REVERT: B 636 TRP cc_start: 0.8520 (m100) cc_final: 0.8220 (m100) outliers start: 43 outliers final: 34 residues processed: 161 average time/residue: 0.0692 time to fit residues: 16.5151 Evaluate side-chains 168 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126091 restraints weight = 9350.656| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8830 Z= 0.138 Angle : 0.542 7.718 11982 Z= 0.264 Chirality : 0.040 0.218 1434 Planarity : 0.004 0.050 1458 Dihedral : 5.021 54.836 1220 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.38 % Allowed : 23.29 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.27), residues: 1086 helix: 1.66 (0.19), residues: 702 sheet: -1.98 (0.58), residues: 70 loop : 0.46 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.009 0.001 TYR B 584 PHE 0.041 0.001 PHE A 275 TRP 0.020 0.001 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8828) covalent geometry : angle 0.54190 / 0.26 (11978) SS BOND : bond 0.00102 / 0.05 ( 2) SS BOND : angle 0.19948 / 0.10 ( 4) hydrogen bonds : bond 0.03080 / 2.06 ( 529) hydrogen bonds : angle 4.23438 / 3.09 ( 1560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7168 (mmmt) REVERT: A 256 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7869 (mmmm) REVERT: B 291 LYS cc_start: 0.8305 (ttmm) cc_final: 0.7762 (ttpt) REVERT: B 508 TYR cc_start: 0.6175 (t80) cc_final: 0.5843 (t80) REVERT: B 517 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8250 (mm) REVERT: B 630 ILE cc_start: 0.7909 (mp) cc_final: 0.7578 (mp) REVERT: B 636 TRP cc_start: 0.8475 (m100) cc_final: 0.8177 (m100) outliers start: 41 outliers final: 37 residues processed: 164 average time/residue: 0.0698 time to fit residues: 16.8017 Evaluate side-chains 171 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.169141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125789 restraints weight = 9441.353| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.07 r_work: 0.3199 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8830 Z= 0.154 Angle : 0.560 8.094 11982 Z= 0.272 Chirality : 0.041 0.218 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.063 55.174 1220 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.38 % Allowed : 23.18 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.27), residues: 1086 helix: 1.60 (0.19), residues: 704 sheet: -1.98 (0.58), residues: 70 loop : 0.46 (0.41), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 401 TYR 0.009 0.001 TYR A 526 PHE 0.042 0.002 PHE A 275 TRP 0.021 0.002 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 8828) covalent geometry : angle 0.55971 / 0.27 (11978) SS BOND : bond 0.00103 / 0.05 ( 2) SS BOND : angle 0.18861 / 0.10 ( 4) hydrogen bonds : bond 0.03153 / 2.11 ( 529) hydrogen bonds : angle 4.24995 / 3.10 ( 1560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7645 (mmmt) cc_final: 0.7159 (mmmt) REVERT: A 256 LYS cc_start: 0.8380 (mmtt) cc_final: 0.7895 (mmmm) REVERT: B 291 LYS cc_start: 0.8313 (ttmm) cc_final: 0.7770 (ttpt) REVERT: B 508 TYR cc_start: 0.6323 (t80) cc_final: 0.5977 (t80) REVERT: B 517 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8252 (mm) REVERT: B 630 ILE cc_start: 0.7950 (mp) cc_final: 0.7609 (mp) REVERT: B 636 TRP cc_start: 0.8501 (m100) cc_final: 0.8215 (m100) outliers start: 41 outliers final: 36 residues processed: 159 average time/residue: 0.0727 time to fit residues: 16.9162 Evaluate side-chains 169 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 461 GLN Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 660 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.168839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125775 restraints weight = 9420.141| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.05 r_work: 0.3206 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8830 Z= 0.151 Angle : 0.555 7.998 11982 Z= 0.271 Chirality : 0.041 0.217 1434 Planarity : 0.004 0.050 1458 Dihedral : 5.075 55.599 1220 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.17 % Allowed : 23.50 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.27), residues: 1086 helix: 1.60 (0.19), residues: 704 sheet: -1.98 (0.59), residues: 70 loop : 0.47 (0.41), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 141 TYR 0.009 0.001 TYR A 526 PHE 0.042 0.002 PHE B 275 TRP 0.021 0.002 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8828) covalent geometry : angle 0.55529 / 0.27 (11978) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 0.18944 / 0.10 ( 4) hydrogen bonds : bond 0.03129 / 2.09 ( 529) hydrogen bonds : angle 4.23881 / 3.09 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.86 seconds wall clock time: 35 minutes 48.90 seconds (2148.90 seconds total)