Starting phenix.real_space_refine on Sun Oct 12 03:53:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soi_40658/10_2025/8soi_40658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soi_40658/10_2025/8soi_40658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8soi_40658/10_2025/8soi_40658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soi_40658/10_2025/8soi_40658.map" model { file = "/net/cci-nas-00/data/ceres_data/8soi_40658/10_2025/8soi_40658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soi_40658/10_2025/8soi_40658.cif" } resolution = 4.2 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= 0.032 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: 5 Type Number sf(0) Gaussians S 80 5.16 5 C 6514 2.51 5 N 1786 2.21 5 O 1863 1.98 5 H 10465 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20708 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 8222 Classifications: {'peptide': 505} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486} Chain breaks: 1 Chain: "B" Number of atoms: 8393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8393 Classifications: {'peptide': 515} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 497} Chain breaks: 1 Chain: "C" Number of atoms: 3302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 3302 Classifications: {'peptide': 205} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain: "D" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 791 Classifications: {'peptide': 51} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain breaks: 1 Time building chain proxies: 3.73, per 1000 atoms: 0.18 Number of scatterers: 20708 At special positions: 0 Unit cell: (133.35, 150.15, 195.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 O 1863 8.00 N 1786 7.00 C 6514 6.00 H 10465 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 379 " distance=2.04 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: 2.01 Conformation dependent library (CDL) restraints added in 560.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 75.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.763A pdb=" N VAL A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 23 " --> pdb=" O GLU A 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 18 through 23' Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 111 through 180 removed outlier: 3.609A pdb=" N GLU A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 148 " --> pdb=" O HIS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 320 through 335 Processing helix chain 'A' and resid 336 through 355 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.594A pdb=" N LYS A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 403 removed outlier: 3.863A pdb=" N GLN A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 543 removed outlier: 4.290A pdb=" N ASP A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.566A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.729A pdb=" N VAL B 22 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.737A pdb=" N ASP B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 200 removed outlier: 3.725A pdb=" N GLU B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 321 through 335 Processing helix chain 'B' and resid 336 through 355 Proline residue: B 342 - end of helix Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 364 through 404 removed outlier: 3.643A pdb=" N GLY B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 491 removed outlier: 4.367A pdb=" N LYS B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 543 removed outlier: 3.678A pdb=" N LYS B 511 " --> pdb=" O LYS B 507 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 removed outlier: 3.511A pdb=" N SER B 587 " --> pdb=" O GLN B 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 841 through 864 removed outlier: 3.734A pdb=" N ARG C 845 " --> pdb=" O THR C 841 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 859 " --> pdb=" O GLN C 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 891 removed outlier: 4.315A pdb=" N ASP C 885 " --> pdb=" O SER C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 923 removed outlier: 4.043A pdb=" N GLY C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 971 removed outlier: 4.165A pdb=" N GLN C 934 " --> pdb=" O SER C 930 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ARG C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N PHE C 960 " --> pdb=" O ARG C 956 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU C 967 " --> pdb=" O ASP C 963 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C 970 " --> pdb=" O ARG C 966 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 971 " --> pdb=" O LEU C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 997 Processing helix chain 'C' and resid 1002 through 1021 removed outlier: 3.953A pdb=" N ARG C1006 " --> pdb=" O GLY C1002 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HIS C1019 " --> pdb=" O GLU C1015 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C1020 " --> pdb=" O GLY C1016 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1044 Processing helix chain 'D' and resid 463 through 471 Processing helix chain 'D' and resid 488 through 514 Proline residue: D 496 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 4.156A pdb=" N LEU A 3 " --> pdb=" O PHE A 16 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR A 4 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU A 73 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE A 6 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ASN A 75 " --> pdb=" O PHE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 16 783 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10425 1.04 - 1.24: 1339 1.24 - 1.44: 2980 1.44 - 1.64: 6022 1.64 - 1.84: 118 Bond restraints: 20884 Sorted by residual: bond pdb=" N ASP D 462 " pdb=" H1 ASP D 462 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CB LEU B 430 " pdb=" CG LEU B 430 " ideal model delta sigma weight residual 1.530 1.507 0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C ILE A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.326 1.342 -0.016 1.44e-02 4.82e+03 1.20e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.844 -0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CG MET B 154 " pdb=" SD MET B 154 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 1.01e+00 ... (remaining 20879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.10: 37846 7.10 - 14.19: 1 14.19 - 21.29: 0 21.29 - 28.38: 0 28.38 - 35.48: 3 Bond angle restraints: 37850 Sorted by residual: angle pdb=" CB SER A 176 " pdb=" CA SER A 176 " pdb=" HA SER A 176 " ideal model delta sigma weight residual 109.00 73.52 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C SER A 176 " pdb=" CA SER A 176 " pdb=" HA SER A 176 " ideal model delta sigma weight residual 109.00 74.77 34.23 3.00e+00 1.11e-01 1.30e+02 angle pdb=" N SER A 176 " pdb=" CA SER A 176 " pdb=" HA SER A 176 " ideal model delta sigma weight residual 110.00 75.90 34.10 3.00e+00 1.11e-01 1.29e+02 angle pdb=" CA GLU B 443 " pdb=" CB GLU B 443 " pdb=" CG GLU B 443 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 8.99e+00 angle pdb=" N GLU B 206 " pdb=" CA GLU B 206 " pdb=" C GLU B 206 " ideal model delta sigma weight residual 112.87 109.61 3.26 1.20e+00 6.94e-01 7.36e+00 ... (remaining 37845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8690 17.84 - 35.67: 746 35.67 - 53.51: 206 53.51 - 71.34: 55 71.34 - 89.18: 16 Dihedral angle restraints: 9713 sinusoidal: 5371 harmonic: 4342 Sorted by residual: dihedral pdb=" CA LEU B 585 " pdb=" C LEU B 585 " pdb=" N GLN B 586 " pdb=" CA GLN B 586 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA CYS B 216 " pdb=" C CYS B 216 " pdb=" N LEU B 217 " pdb=" CA LEU B 217 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual 93.00 55.40 37.60 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 9710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1492 0.067 - 0.134: 110 0.134 - 0.201: 3 0.201 - 0.268: 0 0.268 - 0.335: 1 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA SER A 176 " pdb=" N SER A 176 " pdb=" C SER A 176 " pdb=" CB SER A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA CYS B 133 " pdb=" N CYS B 133 " pdb=" C CYS B 133 " pdb=" CB CYS B 133 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CG LEU A 365 " pdb=" CB LEU A 365 " pdb=" CD1 LEU A 365 " pdb=" CD2 LEU A 365 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1603 not shown) Planarity restraints: 3019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 141 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C HIS B 141 " -0.041 2.00e-02 2.50e+03 pdb=" O HIS B 141 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP B 142 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 594 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO B 595 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 595 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 595 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1007 " -0.010 2.00e-02 2.50e+03 8.69e-03 2.26e+00 pdb=" CG TYR C1007 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR C1007 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C1007 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C1007 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C1007 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C1007 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C1007 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR C1007 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR C1007 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR C1007 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR C1007 " -0.002 2.00e-02 2.50e+03 ... (remaining 3016 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 721 2.15 - 2.76: 40533 2.76 - 3.38: 60814 3.38 - 3.99: 71886 3.99 - 4.60: 115162 Nonbonded interactions: 289116 Sorted by model distance: nonbonded pdb=" O ALA B 361 " pdb="HH21 ARG B 451 " model vdw 1.539 2.450 nonbonded pdb="HH22 ARG A 535 " pdb=" OD2 ASP B 571 " model vdw 1.540 2.450 nonbonded pdb=" O PHE D 512 " pdb=" H THR D 515 " model vdw 1.566 2.450 nonbonded pdb=" O ARG A 58 " pdb=" HG1 THR A 61 " model vdw 1.577 2.450 nonbonded pdb=" OD2 ASP A 571 " pdb="HH22 ARG B 535 " model vdw 1.579 2.450 ... (remaining 289111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 132 or (resid 133 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 134 through 378 or (resid 379 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 380 through 597)) selection = (chain 'B' and (resid 1 through 208 or resid 304 through 460 or (resid 461 and ( \ name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name \ HD2 or name HE1 or name HE2)) or resid 462 through 597)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.390 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: 0.140 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.170 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 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 : 0.003 0.036 10420 Z= 0.155 Angle : 0.601 7.631 14043 Z= 0.331 Chirality : 0.036 0.335 1606 Planarity : 0.003 0.043 1790 Dihedral : 15.468 89.178 3965 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 13.32 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.61 (0.24), residues: 1262 helix: 1.75 (0.17), residues: 878 sheet: -0.21 (0.88), residues: 28 loop : -0.50 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 505 TYR 0.025 0.002 TYR C1007 PHE 0.017 0.002 PHE B 74 TRP 0.017 0.002 TRP B 150 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00316 (10419) covalent geometry : angle 0.59857 (14041) SS BOND : bond 0.00464 ( 1) SS BOND : angle 4.26258 ( 2) hydrogen bonds : bond 0.10222 ( 783) hydrogen bonds : angle 5.15774 ( 2313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.7533 (tp30) cc_final: 0.6709 (tp30) outliers start: 1 outliers final: 1 residues processed: 154 average time/residue: 0.2603 time to fit residues: 54.8861 Evaluate side-chains 152 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS B 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.174620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.153129 restraints weight = 81008.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.155906 restraints weight = 48275.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.157116 restraints weight = 32469.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.158455 restraints weight = 25668.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158738 restraints weight = 21754.169| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10420 Z= 0.182 Angle : 0.592 6.972 14043 Z= 0.329 Chirality : 0.037 0.342 1606 Planarity : 0.004 0.090 1790 Dihedral : 5.068 26.435 1372 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 0.09 % Allowed : 1.58 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.39 (0.23), residues: 1262 helix: 1.73 (0.17), residues: 878 sheet: -1.33 (0.98), residues: 24 loop : -0.93 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 548 TYR 0.020 0.002 TYR D 467 PHE 0.020 0.002 PHE A 393 TRP 0.014 0.002 TRP B 516 HIS 0.012 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00382 (10419) covalent geometry : angle 0.58929 (14041) SS BOND : bond 0.01304 ( 1) SS BOND : angle 5.02854 ( 2) hydrogen bonds : bond 0.05481 ( 783) hydrogen bonds : angle 4.75479 ( 2313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 459 MET cc_start: 0.6100 (ttp) cc_final: 0.5810 (ttp) REVERT: A 508 MET cc_start: 0.7923 (ttp) cc_final: 0.7648 (mtp) REVERT: B 140 VAL cc_start: 0.8679 (t) cc_final: 0.8321 (t) REVERT: B 154 MET cc_start: 0.7418 (mtt) cc_final: 0.7028 (mtt) REVERT: B 175 TYR cc_start: 0.6209 (m-80) cc_final: 0.5830 (m-80) REVERT: C 1033 CYS cc_start: 0.7890 (m) cc_final: 0.7635 (m) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.2487 time to fit residues: 65.1419 Evaluate side-chains 151 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.173815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151881 restraints weight = 80399.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155113 restraints weight = 43844.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.157992 restraints weight = 29435.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.158418 restraints weight = 19113.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158479 restraints weight = 16986.130| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10420 Z= 0.186 Angle : 0.586 11.238 14043 Z= 0.325 Chirality : 0.036 0.345 1606 Planarity : 0.004 0.094 1790 Dihedral : 5.016 26.829 1372 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.45 (0.24), residues: 1262 helix: 1.80 (0.17), residues: 875 sheet: -0.65 (0.93), residues: 33 loop : -1.00 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.014 0.001 TYR B 370 PHE 0.024 0.002 PHE A 542 TRP 0.015 0.002 TRP B 516 HIS 0.006 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00396 (10419) covalent geometry : angle 0.58238 (14041) SS BOND : bond 0.00979 ( 1) SS BOND : angle 5.23400 ( 2) hydrogen bonds : bond 0.05397 ( 783) hydrogen bonds : angle 4.66592 ( 2313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.6516 (m-80) cc_final: 0.6162 (m-10) REVERT: A 6 PHE cc_start: 0.7477 (t80) cc_final: 0.7123 (t80) REVERT: A 148 GLN cc_start: 0.7734 (mt0) cc_final: 0.7484 (mt0) REVERT: A 435 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 459 MET cc_start: 0.6230 (ttp) cc_final: 0.5995 (ttp) REVERT: A 508 MET cc_start: 0.7923 (ttp) cc_final: 0.7568 (mtp) REVERT: B 24 THR cc_start: 0.6215 (t) cc_final: 0.5884 (t) REVERT: B 140 VAL cc_start: 0.8792 (t) cc_final: 0.8424 (t) REVERT: C 1033 CYS cc_start: 0.7889 (m) cc_final: 0.7551 (t) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2588 time to fit residues: 64.1979 Evaluate side-chains 154 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 66 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 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 = 0.4292 r_free = 0.4292 target = 0.170201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.147797 restraints weight = 80557.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.151237 restraints weight = 43010.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.152941 restraints weight = 29795.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.153807 restraints weight = 21447.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.154431 restraints weight = 18345.634| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10420 Z= 0.277 Angle : 0.658 8.887 14043 Z= 0.371 Chirality : 0.039 0.362 1606 Planarity : 0.005 0.061 1790 Dihedral : 5.228 30.230 1372 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.36 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.08 (0.24), residues: 1262 helix: 1.54 (0.17), residues: 880 sheet: -0.93 (1.30), residues: 20 loop : -1.23 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 58 TYR 0.016 0.002 TYR B 370 PHE 0.026 0.003 PHE A 542 TRP 0.021 0.002 TRP B 516 HIS 0.007 0.001 HIS A 141 Details of bonding type rmsd covalent geometry : bond 0.00601 (10419) covalent geometry : angle 0.65674 (14041) SS BOND : bond 0.01108 ( 1) SS BOND : angle 3.42322 ( 2) hydrogen bonds : bond 0.05642 ( 783) hydrogen bonds : angle 4.90425 ( 2313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.6584 (m-80) cc_final: 0.6251 (m-10) REVERT: A 6 PHE cc_start: 0.7439 (t80) cc_final: 0.7019 (t80) REVERT: A 148 GLN cc_start: 0.7777 (mt0) cc_final: 0.7487 (mt0) REVERT: A 435 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 459 MET cc_start: 0.6387 (ttp) cc_final: 0.6135 (ttp) REVERT: A 508 MET cc_start: 0.8006 (ttp) cc_final: 0.7617 (mtp) REVERT: B 140 VAL cc_start: 0.8928 (t) cc_final: 0.8668 (t) REVERT: B 175 TYR cc_start: 0.6306 (m-80) cc_final: 0.4965 (m-80) REVERT: B 459 MET cc_start: 0.0636 (ttt) cc_final: 0.0374 (ttm) REVERT: C 1033 CYS cc_start: 0.7708 (m) cc_final: 0.7433 (m) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2492 time to fit residues: 63.1029 Evaluate side-chains 160 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.173077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.150953 restraints weight = 80279.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.154327 restraints weight = 41977.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.156056 restraints weight = 28567.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156846 restraints weight = 20954.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.158045 restraints weight = 17836.461| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10420 Z= 0.168 Angle : 0.578 9.572 14043 Z= 0.321 Chirality : 0.036 0.343 1606 Planarity : 0.004 0.081 1790 Dihedral : 5.135 28.180 1372 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.49 % Favored : 96.35 % Rotamer: Outliers : 0.09 % Allowed : 1.14 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.26 (0.24), residues: 1262 helix: 1.71 (0.17), residues: 878 sheet: -1.75 (1.00), residues: 27 loop : -1.17 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 543 TYR 0.038 0.002 TYR B 175 PHE 0.021 0.002 PHE A 538 TRP 0.014 0.002 TRP B 516 HIS 0.017 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00361 (10419) covalent geometry : angle 0.57644 (14041) SS BOND : bond 0.00517 ( 1) SS BOND : angle 3.61733 ( 2) hydrogen bonds : bond 0.05280 ( 783) hydrogen bonds : angle 4.67317 ( 2313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 TYR cc_start: 0.6503 (m-80) cc_final: 0.6259 (m-10) REVERT: A 6 PHE cc_start: 0.7359 (t80) cc_final: 0.6907 (t80) REVERT: A 145 LEU cc_start: 0.8681 (tp) cc_final: 0.8481 (tp) REVERT: A 148 GLN cc_start: 0.7757 (mt0) cc_final: 0.7479 (mt0) REVERT: A 435 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 459 MET cc_start: 0.6351 (ttp) cc_final: 0.6094 (ttp) REVERT: A 508 MET cc_start: 0.8002 (ttp) cc_final: 0.7590 (mtp) REVERT: B 24 THR cc_start: 0.6920 (t) cc_final: 0.6635 (t) REVERT: B 140 VAL cc_start: 0.8816 (t) cc_final: 0.8462 (t) REVERT: B 158 GLU cc_start: 0.8241 (tt0) cc_final: 0.7604 (tm-30) REVERT: B 162 ASN cc_start: 0.8259 (m110) cc_final: 0.7870 (m110) REVERT: C 1033 CYS cc_start: 0.7577 (m) cc_final: 0.7357 (m) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2663 time to fit residues: 67.5413 Evaluate side-chains 163 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.173565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.151374 restraints weight = 80348.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154500 restraints weight = 43814.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157247 restraints weight = 30147.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157466 restraints weight = 20477.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.157845 restraints weight = 18647.961| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10420 Z= 0.161 Angle : 0.552 8.223 14043 Z= 0.307 Chirality : 0.035 0.343 1606 Planarity : 0.004 0.048 1790 Dihedral : 5.005 27.017 1372 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.72 % Rotamer: Outliers : 0.09 % Allowed : 1.05 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.45 (0.24), residues: 1262 helix: 1.90 (0.17), residues: 872 sheet: -2.15 (0.84), residues: 32 loop : -1.09 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 506 TYR 0.024 0.002 TYR B 175 PHE 0.022 0.002 PHE D 466 TRP 0.014 0.002 TRP B 516 HIS 0.008 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00343 (10419) covalent geometry : angle 0.55048 (14041) SS BOND : bond 0.00422 ( 1) SS BOND : angle 3.34321 ( 2) hydrogen bonds : bond 0.05104 ( 783) hydrogen bonds : angle 4.57781 ( 2313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7344 (t80) cc_final: 0.6975 (t80) REVERT: A 148 GLN cc_start: 0.7751 (mt0) cc_final: 0.7461 (mt0) REVERT: A 435 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 459 MET cc_start: 0.6353 (ttp) cc_final: 0.5956 (ttp) REVERT: A 508 MET cc_start: 0.7963 (ttp) cc_final: 0.7541 (mtp) REVERT: A 525 LYS cc_start: 0.7893 (tttm) cc_final: 0.7529 (pttt) REVERT: A 598 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7114 (mtt-85) REVERT: B 24 THR cc_start: 0.6701 (t) cc_final: 0.6363 (t) REVERT: B 140 VAL cc_start: 0.8790 (t) cc_final: 0.8451 (t) REVERT: B 158 GLU cc_start: 0.8282 (tt0) cc_final: 0.7585 (tm-30) REVERT: B 162 ASN cc_start: 0.8351 (m110) cc_final: 0.7989 (m110) REVERT: C 1033 CYS cc_start: 0.7719 (m) cc_final: 0.7452 (m) REVERT: D 466 PHE cc_start: 0.6878 (t80) cc_final: 0.6633 (t80) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.2567 time to fit residues: 64.7451 Evaluate side-chains 161 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 117 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.173748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151805 restraints weight = 80336.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155520 restraints weight = 42404.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156568 restraints weight = 28453.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.157664 restraints weight = 21669.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.158401 restraints weight = 17868.987| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 10420 Z= 0.168 Angle : 0.551 7.680 14043 Z= 0.307 Chirality : 0.036 0.344 1606 Planarity : 0.004 0.049 1790 Dihedral : 4.982 28.745 1372 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.47 (0.24), residues: 1262 helix: 1.91 (0.17), residues: 872 sheet: -2.06 (0.85), residues: 32 loop : -1.09 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 505 TYR 0.019 0.002 TYR B 175 PHE 0.031 0.002 PHE B 171 TRP 0.014 0.001 TRP B 516 HIS 0.007 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00364 (10419) covalent geometry : angle 0.54794 (14041) SS BOND : bond 0.00267 ( 1) SS BOND : angle 5.02288 ( 2) hydrogen bonds : bond 0.05103 ( 783) hydrogen bonds : angle 4.61647 ( 2313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7324 (t80) cc_final: 0.6974 (t80) REVERT: A 148 GLN cc_start: 0.7736 (mt0) cc_final: 0.7460 (mt0) REVERT: A 435 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8616 (tm-30) REVERT: A 459 MET cc_start: 0.6452 (ttp) cc_final: 0.6232 (ttp) REVERT: A 508 MET cc_start: 0.7856 (ttp) cc_final: 0.7441 (mtp) REVERT: A 525 LYS cc_start: 0.7914 (tttm) cc_final: 0.7549 (pttt) REVERT: A 598 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7126 (mtt-85) REVERT: B 24 THR cc_start: 0.6802 (t) cc_final: 0.6485 (t) REVERT: B 140 VAL cc_start: 0.8817 (t) cc_final: 0.8489 (t) REVERT: B 158 GLU cc_start: 0.8238 (tt0) cc_final: 0.7575 (tm-30) REVERT: B 162 ASN cc_start: 0.8269 (m110) cc_final: 0.7931 (m110) REVERT: B 175 TYR cc_start: 0.6295 (m-80) cc_final: 0.5545 (m-80) REVERT: C 1033 CYS cc_start: 0.7622 (m) cc_final: 0.7400 (m) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2622 time to fit residues: 65.6290 Evaluate side-chains 163 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN D 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.173541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.151415 restraints weight = 80261.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.154312 restraints weight = 43340.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.157217 restraints weight = 31210.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.157635 restraints weight = 21155.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.157781 restraints weight = 18310.408| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10420 Z= 0.170 Angle : 0.556 6.949 14043 Z= 0.308 Chirality : 0.036 0.345 1606 Planarity : 0.004 0.050 1790 Dihedral : 4.928 28.611 1372 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % Rotamer: Outliers : 0.09 % Allowed : 0.79 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.53 (0.24), residues: 1262 helix: 1.95 (0.17), residues: 873 sheet: -2.06 (0.84), residues: 32 loop : -1.04 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 505 TYR 0.016 0.002 TYR B 175 PHE 0.027 0.002 PHE B 171 TRP 0.014 0.002 TRP B 516 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00365 (10419) covalent geometry : angle 0.55360 (14041) SS BOND : bond 0.00254 ( 1) SS BOND : angle 4.32200 ( 2) hydrogen bonds : bond 0.05077 ( 783) hydrogen bonds : angle 4.60562 ( 2313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7370 (t80) cc_final: 0.7014 (t80) REVERT: A 148 GLN cc_start: 0.7731 (mt0) cc_final: 0.7408 (mt0) REVERT: A 435 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8594 (tm-30) REVERT: A 459 MET cc_start: 0.6538 (ttp) cc_final: 0.6231 (ttp) REVERT: A 508 MET cc_start: 0.7834 (ttp) cc_final: 0.7414 (mtp) REVERT: B 24 THR cc_start: 0.6899 (t) cc_final: 0.6567 (t) REVERT: B 140 VAL cc_start: 0.8804 (t) cc_final: 0.8383 (t) REVERT: B 158 GLU cc_start: 0.8304 (tt0) cc_final: 0.7666 (tm-30) REVERT: B 162 ASN cc_start: 0.8376 (m110) cc_final: 0.8014 (m110) REVERT: B 175 TYR cc_start: 0.6297 (m-80) cc_final: 0.5742 (m-80) REVERT: B 432 ASP cc_start: 0.8142 (m-30) cc_final: 0.7936 (m-30) REVERT: C 1023 ASP cc_start: 0.7570 (t70) cc_final: 0.7328 (t0) REVERT: C 1033 CYS cc_start: 0.7695 (m) cc_final: 0.7364 (m) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.2661 time to fit residues: 65.3482 Evaluate side-chains 161 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.173453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.151804 restraints weight = 80273.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.154546 restraints weight = 41832.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.158003 restraints weight = 28914.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.158172 restraints weight = 18419.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158243 restraints weight = 16531.594| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10420 Z= 0.168 Angle : 0.555 10.204 14043 Z= 0.307 Chirality : 0.036 0.345 1606 Planarity : 0.004 0.064 1790 Dihedral : 4.878 25.866 1372 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.72 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.55 (0.24), residues: 1262 helix: 1.98 (0.17), residues: 867 sheet: -2.05 (0.85), residues: 32 loop : -1.03 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 598 TYR 0.016 0.002 TYR B 175 PHE 0.022 0.002 PHE B 171 TRP 0.013 0.002 TRP B 516 HIS 0.007 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00356 (10419) covalent geometry : angle 0.54954 (14041) SS BOND : bond 0.00381 ( 1) SS BOND : angle 6.50142 ( 2) hydrogen bonds : bond 0.04995 ( 783) hydrogen bonds : angle 4.53663 ( 2313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7413 (t80) cc_final: 0.7069 (t80) REVERT: A 148 GLN cc_start: 0.7701 (mt0) cc_final: 0.7380 (mt0) REVERT: A 435 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 459 MET cc_start: 0.6559 (ttp) cc_final: 0.6294 (ttp) REVERT: A 508 MET cc_start: 0.7773 (ttp) cc_final: 0.7360 (mtp) REVERT: B 24 THR cc_start: 0.6877 (t) cc_final: 0.6558 (t) REVERT: B 140 VAL cc_start: 0.8805 (t) cc_final: 0.8401 (t) REVERT: B 158 GLU cc_start: 0.8285 (tt0) cc_final: 0.7656 (tm-30) REVERT: B 162 ASN cc_start: 0.8331 (m110) cc_final: 0.7981 (m110) REVERT: B 175 TYR cc_start: 0.6132 (m-80) cc_final: 0.5704 (m-80) REVERT: C 1023 ASP cc_start: 0.7643 (t70) cc_final: 0.7278 (t0) REVERT: C 1026 ASP cc_start: 0.6768 (m-30) cc_final: 0.6514 (m-30) REVERT: C 1033 CYS cc_start: 0.7647 (m) cc_final: 0.7344 (m) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.2571 time to fit residues: 64.3103 Evaluate side-chains 163 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 56 optimal weight: 0.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.175460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.153740 restraints weight = 80305.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.156977 restraints weight = 42730.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159802 restraints weight = 30037.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.160230 restraints weight = 19012.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.160332 restraints weight = 16510.711| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10420 Z= 0.127 Angle : 0.519 7.423 14043 Z= 0.284 Chirality : 0.035 0.336 1606 Planarity : 0.004 0.046 1790 Dihedral : 4.730 23.461 1372 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.81 (0.24), residues: 1262 helix: 2.15 (0.17), residues: 867 sheet: -1.86 (0.85), residues: 32 loop : -0.89 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 598 TYR 0.020 0.002 TYR A 36 PHE 0.020 0.001 PHE B 171 TRP 0.011 0.001 TRP B 516 HIS 0.007 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00260 (10419) covalent geometry : angle 0.51414 (14041) SS BOND : bond 0.00105 ( 1) SS BOND : angle 6.00905 ( 2) hydrogen bonds : bond 0.04792 ( 783) hydrogen bonds : angle 4.39733 ( 2313) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7572 (t80) cc_final: 0.7228 (t80) REVERT: A 148 GLN cc_start: 0.7678 (mt0) cc_final: 0.7473 (mt0) REVERT: A 435 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 459 MET cc_start: 0.6497 (ttp) cc_final: 0.6250 (ttp) REVERT: A 508 MET cc_start: 0.7760 (ttp) cc_final: 0.7406 (mtp) REVERT: B 24 THR cc_start: 0.6824 (t) cc_final: 0.6472 (t) REVERT: B 98 MET cc_start: 0.6400 (tmm) cc_final: 0.4781 (tpt) REVERT: B 140 VAL cc_start: 0.8759 (t) cc_final: 0.8286 (t) REVERT: B 158 GLU cc_start: 0.8262 (tt0) cc_final: 0.7586 (tm-30) REVERT: B 162 ASN cc_start: 0.8298 (m110) cc_final: 0.7935 (m110) REVERT: B 175 TYR cc_start: 0.6028 (m-80) cc_final: 0.5682 (m-80) REVERT: B 459 MET cc_start: 0.0382 (ttt) cc_final: 0.0170 (ttm) REVERT: C 1023 ASP cc_start: 0.7630 (t70) cc_final: 0.7294 (t0) REVERT: C 1026 ASP cc_start: 0.6700 (m-30) cc_final: 0.6460 (m-30) REVERT: C 1033 CYS cc_start: 0.7620 (m) cc_final: 0.7344 (m) outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.2618 time to fit residues: 64.6161 Evaluate side-chains 165 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.0270 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.173940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.152012 restraints weight = 80468.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.155453 restraints weight = 42847.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.158027 restraints weight = 29171.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158577 restraints weight = 19624.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158632 restraints weight = 16415.986| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10420 Z= 0.167 Angle : 0.542 7.815 14043 Z= 0.302 Chirality : 0.036 0.346 1606 Planarity : 0.004 0.050 1790 Dihedral : 4.749 24.095 1372 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.96 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.76 (0.24), residues: 1262 helix: 2.12 (0.17), residues: 868 sheet: -1.95 (0.84), residues: 32 loop : -0.94 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 543 TYR 0.017 0.002 TYR A 36 PHE 0.019 0.002 PHE B 171 TRP 0.012 0.001 TRP B 516 HIS 0.007 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00359 (10419) covalent geometry : angle 0.53818 (14041) SS BOND : bond 0.00247 ( 1) SS BOND : angle 5.69233 ( 2) hydrogen bonds : bond 0.04863 ( 783) hydrogen bonds : angle 4.44778 ( 2313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3649.61 seconds wall clock time: 63 minutes 1.02 seconds (3781.02 seconds total)