Starting phenix.real_space_refine on Sat Aug 23 00:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wba_37418/08_2025/8wba_37418.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wba_37418/08_2025/8wba_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_37418/08_2025/8wba_37418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wba_37418/08_2025/8wba_37418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wba_37418/08_2025/8wba_37418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wba_37418/08_2025/8wba_37418.map" } 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-2.0-5787/lib/python3.9/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: 2.39, per 1000 atoms: 0.28 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: 0.89 Conformation dependent library (CDL) restraints added in 335.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.24 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: 1.49 Time building geometry restraints manager: 1.15 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: 4425 16.36 - 32.71: 648 32.71 - 49.07: 172 49.07 - 65.42: 30 65.42 - 81.78: 15 Dihedral angle restraints: 5290 sinusoidal: 2130 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 5287 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: 1.060 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.700 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 : 16.646 81.777 3256 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 aren 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 covalent geometry : bond 0.00224 ( 8828) covalent geometry : angle 0.53717 (11978) SS BOND : bond 0.00096 ( 2) SS BOND : angle 0.28483 ( 4) hydrogen bonds : bond 0.12331 ( 529) hydrogen bonds : angle 5.47708 ( 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 : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.0944 time to fit residues: 17.5423 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 : 0.329 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 413 GLN A 461 GLN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.167875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124248 restraints weight = 9445.270| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.02 r_work: 0.3188 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8830 Z= 0.191 Angle : 0.576 9.219 11982 Z= 0.281 Chirality : 0.041 0.227 1434 Planarity : 0.005 0.045 1458 Dihedral : 6.043 59.688 1340 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.38 % Allowed : 21.15 % 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 aren not related in a simple way. whole: 1.27 (0.26), residues: 1086 helix: 1.51 (0.19), residues: 698 sheet: -2.59 (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 0.010 0.001 TYR A 526 PHE 0.030 0.002 PHE A 275 TRP 0.011 0.001 TRP A 447 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8828) covalent geometry : angle 0.57566 (11978) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.47711 ( 4) hydrogen bonds : bond 0.03623 ( 529) hydrogen bonds : angle 4.68287 ( 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 180 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 139 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7533 (mmmt) REVERT: A 256 LYS cc_start: 0.8386 (mmtt) cc_final: 0.7958 (mmmm) REVERT: B 274 MET cc_start: 0.8012 (mmm) cc_final: 0.7338 (mmt) REVERT: B 291 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7814 (ttpt) REVERT: B 517 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8256 (mm) REVERT: B 630 ILE cc_start: 0.7781 (mp) cc_final: 0.7479 (mp) REVERT: B 636 TRP cc_start: 0.8396 (m100) cc_final: 0.8033 (m100) outliers start: 41 outliers final: 23 residues processed: 166 average time/residue: 0.0836 time to fit residues: 20.1482 Evaluate side-chains 158 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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: 1.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 HIS ** 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 = 0.3900 r_free = 0.3900 target = 0.167544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.124038 restraints weight = 9355.896| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.00 r_work: 0.3188 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8830 Z= 0.161 Angle : 0.550 8.108 11982 Z= 0.270 Chirality : 0.040 0.221 1434 Planarity : 0.004 0.045 1458 Dihedral : 5.842 57.389 1338 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.38 % Allowed : 22.01 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.26), residues: 1086 helix: 1.57 (0.19), residues: 696 sheet: -1.91 (0.69), residues: 48 loop : 0.07 (0.38), residues: 342 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 0.042 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 covalent geometry : bond 0.00380 ( 8828) covalent geometry : angle 0.54987 (11978) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.29300 ( 4) hydrogen bonds : bond 0.03319 ( 529) hydrogen bonds : angle 4.51907 ( 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 183 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7900 (mmmt) cc_final: 0.7643 (mmmt) REVERT: A 256 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7963 (mmmm) REVERT: B 291 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7764 (ttpt) REVERT: B 517 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 630 ILE cc_start: 0.7955 (mp) cc_final: 0.7634 (mp) outliers start: 41 outliers final: 27 residues processed: 162 average time/residue: 0.0867 time to fit residues: 20.2311 Evaluate side-chains 164 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 450 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 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: 0.5980 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.0030 chunk 72 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3921 r_free = 0.3921 target = 0.169453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125695 restraints weight = 9467.997| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.08 r_work: 0.3204 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8830 Z= 0.130 Angle : 0.523 7.608 11982 Z= 0.256 Chirality : 0.040 0.221 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.692 56.108 1338 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.59 % Allowed : 22.65 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.26), residues: 1086 helix: 1.72 (0.19), residues: 696 sheet: -1.85 (0.69), residues: 48 loop : 0.06 (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 B 584 PHE 0.032 0.001 PHE A 275 TRP 0.013 0.001 TRP A 575 HIS 0.005 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8828) covalent geometry : angle 0.52261 (11978) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.24881 ( 4) hydrogen bonds : bond 0.03044 ( 529) hydrogen bonds : angle 4.33258 ( 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: 43 poor density : 142 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7824 (mmmt) cc_final: 0.7478 (mmmt) REVERT: A 256 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7877 (mmmm) REVERT: A 508 TYR cc_start: 0.7577 (m-10) cc_final: 0.6356 (t80) REVERT: A 568 LYS cc_start: 0.8552 (mttp) cc_final: 0.8071 (mptt) REVERT: B 291 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7640 (ttpt) REVERT: B 517 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (mm) REVERT: B 630 ILE cc_start: 0.7911 (mp) cc_final: 0.7588 (mp) REVERT: B 636 TRP cc_start: 0.8375 (m100) cc_final: 0.8005 (m100) outliers start: 43 outliers final: 30 residues processed: 168 average time/residue: 0.0856 time to fit residues: 20.8167 Evaluate side-chains 167 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 100 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.167168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122901 restraints weight = 9510.721| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.09 r_work: 0.3164 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8830 Z= 0.203 Angle : 0.582 7.930 11982 Z= 0.284 Chirality : 0.041 0.217 1434 Planarity : 0.004 0.048 1458 Dihedral : 5.863 56.132 1338 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.49 % Allowed : 23.61 % 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 aren not related in a simple way. whole: 1.23 (0.26), residues: 1086 helix: 1.44 (0.19), residues: 700 sheet: -1.88 (0.70), residues: 48 loop : 0.09 (0.39), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.010 0.002 TYR A 526 PHE 0.045 0.002 PHE A 275 TRP 0.013 0.002 TRP A 575 HIS 0.005 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8828) covalent geometry : angle 0.58215 (11978) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.25527 ( 4) hydrogen bonds : bond 0.03458 ( 529) hydrogen bonds : angle 4.49154 ( 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 179 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7308 (mmmt) REVERT: A 256 LYS cc_start: 0.8397 (mmtt) cc_final: 0.7912 (mmmm) REVERT: B 264 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8141 (mm) REVERT: B 291 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7738 (ttpt) REVERT: B 517 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8275 (mm) REVERT: B 630 ILE cc_start: 0.7934 (mp) cc_final: 0.7615 (mp) outliers start: 42 outliers final: 35 residues processed: 163 average time/residue: 0.0855 time to fit residues: 20.2193 Evaluate side-chains 173 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 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 645 MET 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 264 ILE 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 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: 0.9980 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.168535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124902 restraints weight = 9420.541| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.07 r_work: 0.3196 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8830 Z= 0.138 Angle : 0.536 7.784 11982 Z= 0.263 Chirality : 0.040 0.214 1434 Planarity : 0.004 0.050 1458 Dihedral : 5.709 55.892 1338 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.70 % Allowed : 23.82 % Favored : 71.47 % 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 aren not related in a simple way. whole: 1.42 (0.26), residues: 1086 helix: 1.62 (0.19), residues: 700 sheet: -1.79 (0.71), residues: 48 loop : 0.07 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 436 TYR 0.010 0.001 TYR B 584 PHE 0.041 0.002 PHE A 275 TRP 0.016 0.001 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8828) covalent geometry : angle 0.53649 (11978) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.24329 ( 4) hydrogen bonds : bond 0.03115 ( 529) hydrogen bonds : angle 4.31293 ( 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 186 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7292 (mmmt) REVERT: A 136 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7023 (mmmt) REVERT: A 256 LYS cc_start: 0.8358 (mmtt) cc_final: 0.7880 (mmmm) REVERT: B 291 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7727 (ttpt) REVERT: B 517 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8283 (mm) REVERT: B 630 ILE cc_start: 0.7928 (mp) cc_final: 0.7611 (mp) REVERT: B 636 TRP cc_start: 0.8392 (m100) cc_final: 0.8036 (m100) outliers start: 44 outliers final: 36 residues processed: 169 average time/residue: 0.0874 time to fit residues: 21.1509 Evaluate side-chains 174 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 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 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 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.0000 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.169666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126464 restraints weight = 9424.655| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.06 r_work: 0.3216 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1469 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= 0.134 Angle : 0.529 7.176 11982 Z= 0.259 Chirality : 0.040 0.211 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.643 55.815 1338 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.56 % Allowed : 22.76 % 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 aren not related in a simple way. whole: 1.49 (0.26), residues: 1086 helix: 1.68 (0.19), residues: 700 sheet: -1.71 (0.72), residues: 48 loop : 0.07 (0.38), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 270 TYR 0.009 0.001 TYR A 584 PHE 0.038 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 covalent geometry : bond 0.00314 ( 8828) covalent geometry : angle 0.52939 (11978) SS BOND : bond 0.00109 ( 2) SS BOND : angle 0.21250 ( 4) hydrogen bonds : bond 0.03058 ( 529) hydrogen bonds : angle 4.23688 ( 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 188 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7703 (mmmt) cc_final: 0.7290 (mmmt) REVERT: A 136 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7036 (mmmt) REVERT: A 256 LYS cc_start: 0.8356 (mmtt) cc_final: 0.7871 (mmmm) REVERT: B 291 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7724 (ttpt) REVERT: B 508 TYR cc_start: 0.6321 (t80) cc_final: 0.5954 (t80) REVERT: B 517 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8239 (mm) REVERT: B 630 ILE cc_start: 0.7927 (mp) cc_final: 0.7600 (mp) REVERT: B 636 TRP cc_start: 0.8377 (m100) cc_final: 0.8003 (m100) outliers start: 52 outliers final: 39 residues processed: 168 average time/residue: 0.0885 time to fit residues: 21.3200 Evaluate side-chains 173 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 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 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 645 MET 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 461 GLN 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: 0.8980 chunk 19 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3902 r_free = 0.3902 target = 0.167536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123735 restraints weight = 9429.446| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.06 r_work: 0.3186 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1679 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= 0.189 Angle : 0.579 7.752 11982 Z= 0.282 Chirality : 0.041 0.216 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.761 55.846 1338 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.81 % Allowed : 23.29 % 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 aren not related in a simple way. whole: 1.35 (0.26), residues: 1086 helix: 1.47 (0.19), residues: 704 sheet: -1.66 (0.72), residues: 48 loop : 0.24 (0.39), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 401 TYR 0.010 0.001 TYR A 526 PHE 0.040 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 covalent geometry : bond 0.00448 ( 8828) covalent geometry : angle 0.57939 (11978) SS BOND : bond 0.00135 ( 2) SS BOND : angle 0.19578 ( 4) hydrogen bonds : bond 0.03378 ( 529) hydrogen bonds : angle 4.39168 ( 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 177 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7704 (mmmt) cc_final: 0.7243 (mmmt) REVERT: A 256 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7889 (mmmm) REVERT: A 517 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7991 (mp) REVERT: B 291 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7744 (ttpt) REVERT: B 517 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8325 (mm) REVERT: B 630 ILE cc_start: 0.7931 (mp) cc_final: 0.7612 (mp) REVERT: B 636 TRP cc_start: 0.8409 (m100) cc_final: 0.8031 (m100) outliers start: 45 outliers final: 38 residues processed: 162 average time/residue: 0.0840 time to fit residues: 19.8008 Evaluate side-chains 169 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 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 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 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 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 581 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 645 MET 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 461 GLN 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: 6.9990 chunk 13 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.169518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126327 restraints weight = 9353.578| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.06 r_work: 0.3206 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1608 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= 0.137 Angle : 0.545 7.771 11982 Z= 0.265 Chirality : 0.040 0.212 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.637 56.056 1338 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.38 % Allowed : 23.50 % 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 aren not related in a simple way. whole: 1.48 (0.27), residues: 1086 helix: 1.63 (0.19), residues: 704 sheet: -2.10 (0.57), residues: 70 loop : 0.45 (0.41), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 401 TYR 0.009 0.001 TYR B 584 PHE 0.039 0.002 PHE A 275 TRP 0.020 0.002 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8828) covalent geometry : angle 0.54505 (11978) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.20259 ( 4) hydrogen bonds : bond 0.03106 ( 529) hydrogen bonds : angle 4.26347 ( 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 175 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7169 (mmmt) REVERT: A 256 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7861 (mmmm) REVERT: B 291 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7741 (ttpt) REVERT: B 508 TYR cc_start: 0.6190 (t80) cc_final: 0.5862 (t80) REVERT: B 517 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8248 (mm) REVERT: B 630 ILE cc_start: 0.7943 (mp) cc_final: 0.7618 (mp) REVERT: B 636 TRP cc_start: 0.8411 (m100) cc_final: 0.8027 (m100) outliers start: 41 outliers final: 36 residues processed: 159 average time/residue: 0.0843 time to fit residues: 19.4137 Evaluate side-chains 171 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 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 645 MET 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 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 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: 2.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.170211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126890 restraints weight = 9418.670| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.08 r_work: 0.3211 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8830 Z= 0.135 Angle : 0.545 7.944 11982 Z= 0.266 Chirality : 0.040 0.210 1434 Planarity : 0.004 0.050 1458 Dihedral : 5.499 56.427 1336 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.38 % Allowed : 23.82 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.27), residues: 1086 helix: 1.71 (0.19), residues: 702 sheet: -2.05 (0.58), residues: 70 loop : 0.45 (0.41), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.009 0.001 TYR A 584 PHE 0.039 0.001 PHE A 275 TRP 0.022 0.002 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8828) covalent geometry : angle 0.54544 (11978) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.20269 ( 4) hydrogen bonds : bond 0.03043 ( 529) hydrogen bonds : angle 4.21678 ( 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 177 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7191 (mmmt) REVERT: A 256 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7848 (mmmm) REVERT: B 264 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7994 (mm) REVERT: B 291 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7734 (ttpt) REVERT: B 508 TYR cc_start: 0.6118 (t80) cc_final: 0.5783 (t80) REVERT: B 517 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8236 (mm) REVERT: B 630 ILE cc_start: 0.7960 (mp) cc_final: 0.7619 (mp) REVERT: B 636 TRP cc_start: 0.8403 (m100) cc_final: 0.8022 (m100) outliers start: 41 outliers final: 37 residues processed: 162 average time/residue: 0.0902 time to fit residues: 20.8298 Evaluate side-chains 173 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 134 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 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 645 MET 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 249 LEU Chi-restraints excluded: chain B residue 264 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 548 SER 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 34 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.168433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124838 restraints weight = 9422.276| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.07 r_work: 0.3182 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8830 Z= 0.165 Angle : 0.565 8.078 11982 Z= 0.276 Chirality : 0.041 0.213 1434 Planarity : 0.004 0.049 1458 Dihedral : 5.613 57.293 1336 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.38 % Allowed : 23.61 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.26), residues: 1086 helix: 1.56 (0.19), residues: 704 sheet: -2.01 (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 A 410 TYR 0.009 0.001 TYR A 584 PHE 0.042 0.002 PHE A 275 TRP 0.020 0.002 TRP A 575 HIS 0.007 0.001 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8828) covalent geometry : angle 0.56531 (11978) SS BOND : bond 0.00108 ( 2) SS BOND : angle 0.18312 ( 4) hydrogen bonds : bond 0.03226 ( 529) hydrogen bonds : angle 4.29254 ( 1560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.65 seconds wall clock time: 43 minutes 9.12 seconds (2589.12 seconds total)