Starting phenix.real_space_refine on Wed Jun 18 05:18:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8soi_40658/06_2025/8soi_40658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8soi_40658/06_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_40658/06_2025/8soi_40658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8soi_40658/06_2025/8soi_40658.map" model { file = "/net/cci-nas-00/data/ceres_data/8soi_40658/06_2025/8soi_40658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8soi_40658/06_2025/8soi_40658.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.77, per 1000 atoms: 0.52 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: 6.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.32 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: 7.86 Time building geometry restraints manager: 7.17 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 47.930 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.580 ------------------------------------------------------------------------------- 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 : 9.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.002 TRP B 150 HIS 0.004 0.001 HIS B 211 PHE 0.017 0.002 PHE B 74 TYR 0.025 0.002 TYR C1007 ARG 0.003 0.000 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.10222 ( 783) hydrogen bonds : angle 5.15774 ( 2313) SS BOND : bond 0.00464 ( 1) SS BOND : angle 4.26258 ( 2) covalent geometry : bond 0.00316 (10419) covalent geometry : angle 0.59857 (14041) *********************** 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 : 1.803 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: 0.5577 time to fit residues: 118.1032 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 : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.174610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152865 restraints weight = 80955.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.156127 restraints weight = 47580.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.158910 restraints weight = 31083.502| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10420 Z= 0.178 Angle : 0.587 6.992 14043 Z= 0.326 Chirality : 0.037 0.342 1606 Planarity : 0.004 0.086 1790 Dihedral : 5.062 26.453 1372 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 0.09 % Allowed : 1.67 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1262 helix: 1.73 (0.17), residues: 878 sheet: -1.29 (0.97), residues: 24 loop : -0.92 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 516 HIS 0.013 0.001 HIS B 42 PHE 0.020 0.002 PHE A 393 TYR 0.018 0.002 TYR D 467 ARG 0.012 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05491 ( 783) hydrogen bonds : angle 4.74154 ( 2313) SS BOND : bond 0.02212 ( 1) SS BOND : angle 4.99501 ( 2) covalent geometry : bond 0.00378 (10419) covalent geometry : angle 0.58433 (14041) *********************** 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 : 1.799 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 4 TYR cc_start: 0.6330 (m-80) cc_final: 0.5883 (m-10) REVERT: A 435 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 459 MET cc_start: 0.6101 (ttp) cc_final: 0.5810 (ttp) REVERT: A 508 MET cc_start: 0.7921 (ttp) cc_final: 0.7649 (mtp) REVERT: B 140 VAL cc_start: 0.8705 (t) cc_final: 0.8342 (t) REVERT: B 154 MET cc_start: 0.7437 (mtt) cc_final: 0.7040 (mtt) REVERT: B 175 TYR cc_start: 0.6129 (m-80) cc_final: 0.5781 (m-80) REVERT: C 1033 CYS cc_start: 0.7874 (m) cc_final: 0.7620 (m) outliers start: 1 outliers final: 1 residues processed: 187 average time/residue: 0.5184 time to fit residues: 136.1455 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 : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4323 r_free = 0.4323 target = 0.173119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151688 restraints weight = 80001.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.154206 restraints weight = 43762.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.155994 restraints weight = 30668.736| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10420 Z= 0.201 Angle : 0.594 9.556 14043 Z= 0.331 Chirality : 0.037 0.349 1606 Planarity : 0.004 0.055 1790 Dihedral : 5.049 27.452 1372 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1262 helix: 1.75 (0.17), residues: 874 sheet: 1.12 (1.52), residues: 15 loop : -1.09 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 516 HIS 0.006 0.001 HIS A 147 PHE 0.021 0.002 PHE A 393 TYR 0.015 0.002 TYR B 370 ARG 0.006 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.05401 ( 783) hydrogen bonds : angle 4.70577 ( 2313) SS BOND : bond 0.00529 ( 1) SS BOND : angle 5.22916 ( 2) covalent geometry : bond 0.00429 (10419) covalent geometry : angle 0.59098 (14041) *********************** 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 179 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.616 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: A 4 TYR cc_start: 0.6425 (m-80) cc_final: 0.6100 (m-10) REVERT: A 6 PHE cc_start: 0.7543 (t80) cc_final: 0.7120 (t80) REVERT: A 148 GLN cc_start: 0.7727 (mt0) cc_final: 0.7454 (mt0) REVERT: A 435 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8565 (tm-30) REVERT: A 459 MET cc_start: 0.6230 (ttp) cc_final: 0.5978 (ttp) REVERT: A 508 MET cc_start: 0.7931 (ttp) cc_final: 0.7592 (mtp) REVERT: B 24 THR cc_start: 0.6285 (t) cc_final: 0.5924 (t) REVERT: B 140 VAL cc_start: 0.8817 (t) cc_final: 0.8457 (t) REVERT: B 175 TYR cc_start: 0.6364 (m-80) cc_final: 0.6126 (m-80) REVERT: C 1033 CYS cc_start: 0.8066 (m) cc_final: 0.7684 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.5171 time to fit residues: 129.4075 Evaluate side-chains 156 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.173585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.151538 restraints weight = 80538.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.155177 restraints weight = 42345.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156608 restraints weight = 28159.620| |-----------------------------------------------------------------------------| r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10420 Z= 0.182 Angle : 0.571 9.003 14043 Z= 0.319 Chirality : 0.036 0.347 1606 Planarity : 0.004 0.047 1790 Dihedral : 5.002 27.006 1372 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1262 helix: 1.85 (0.17), residues: 876 sheet: 0.71 (1.53), residues: 15 loop : -1.14 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 516 HIS 0.005 0.001 HIS A 147 PHE 0.018 0.002 PHE D 466 TYR 0.015 0.002 TYR B 175 ARG 0.004 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 783) hydrogen bonds : angle 4.61455 ( 2313) SS BOND : bond 0.00792 ( 1) SS BOND : angle 3.70468 ( 2) covalent geometry : bond 0.00387 (10419) covalent geometry : angle 0.56935 (14041) *********************** 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: 1 poor density : 179 time to evaluate : 1.736 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: symmetry clash REVERT: A 4 TYR cc_start: 0.6400 (m-80) cc_final: 0.6113 (m-10) REVERT: A 6 PHE cc_start: 0.7418 (t80) cc_final: 0.7028 (t80) REVERT: A 148 GLN cc_start: 0.7697 (mt0) cc_final: 0.7416 (mt0) REVERT: A 435 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 459 MET cc_start: 0.6375 (ttp) cc_final: 0.6107 (ttp) REVERT: A 508 MET cc_start: 0.7974 (ttp) cc_final: 0.7609 (mtp) REVERT: B 140 VAL cc_start: 0.8820 (t) cc_final: 0.8477 (t) REVERT: C 1033 CYS cc_start: 0.7748 (m) cc_final: 0.7421 (m) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.5506 time to fit residues: 140.2393 Evaluate side-chains 158 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 113 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.173779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.151580 restraints weight = 80318.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.155020 restraints weight = 44743.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.157469 restraints weight = 30311.893| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10420 Z= 0.167 Angle : 0.553 9.361 14043 Z= 0.308 Chirality : 0.035 0.345 1606 Planarity : 0.004 0.061 1790 Dihedral : 4.957 26.381 1372 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.80 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.24), residues: 1262 helix: 1.97 (0.17), residues: 876 sheet: -0.99 (1.25), residues: 20 loop : -1.16 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 516 HIS 0.013 0.001 HIS B 42 PHE 0.019 0.002 PHE B 171 TYR 0.015 0.002 TYR A 36 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05121 ( 783) hydrogen bonds : angle 4.54746 ( 2313) SS BOND : bond 0.00238 ( 1) SS BOND : angle 3.69726 ( 2) covalent geometry : bond 0.00354 (10419) covalent geometry : angle 0.55160 (14041) *********************** 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 180 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.743 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: 0.7550 (t80) cc_final: 0.7044 (t80) REVERT: A 148 GLN cc_start: 0.7747 (mt0) cc_final: 0.7464 (mt0) REVERT: A 435 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8611 (tm-30) REVERT: A 459 MET cc_start: 0.6384 (ttp) cc_final: 0.6147 (ttp) REVERT: A 508 MET cc_start: 0.7970 (ttp) cc_final: 0.7588 (mtp) REVERT: B 24 THR cc_start: 0.6638 (t) cc_final: 0.6403 (t) REVERT: B 140 VAL cc_start: 0.8817 (t) cc_final: 0.8451 (t) REVERT: B 158 GLU cc_start: 0.8242 (pp20) cc_final: 0.7867 (pp20) REVERT: B 459 MET cc_start: 0.0645 (ttt) cc_final: 0.0341 (ttm) REVERT: C 1033 CYS cc_start: 0.7725 (m) cc_final: 0.7455 (m) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5229 time to fit residues: 131.2013 Evaluate side-chains 159 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 65 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: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.172912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.150673 restraints weight = 80073.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.154715 restraints weight = 41784.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.155747 restraints weight = 27099.119| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10420 Z= 0.184 Angle : 0.559 8.044 14043 Z= 0.314 Chirality : 0.036 0.348 1606 Planarity : 0.004 0.048 1790 Dihedral : 4.944 26.456 1372 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1262 helix: 1.92 (0.17), residues: 876 sheet: -2.16 (0.91), residues: 32 loop : -1.03 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 516 HIS 0.008 0.001 HIS B 42 PHE 0.020 0.002 PHE D 466 TYR 0.014 0.002 TYR B 370 ARG 0.006 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 783) hydrogen bonds : angle 4.58726 ( 2313) SS BOND : bond 0.00290 ( 1) SS BOND : angle 3.32835 ( 2) covalent geometry : bond 0.00391 (10419) covalent geometry : angle 0.55810 (14041) *********************** 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 184 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.611 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: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7546 (t80) cc_final: 0.7105 (t80) REVERT: A 148 GLN cc_start: 0.7723 (mt0) cc_final: 0.7398 (mt0) REVERT: A 435 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8612 (tm-30) REVERT: A 459 MET cc_start: 0.6413 (ttp) cc_final: 0.6131 (ttp) REVERT: A 508 MET cc_start: 0.7977 (ttp) cc_final: 0.7560 (mtp) REVERT: A 598 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7139 (mtt-85) REVERT: B 24 THR cc_start: 0.6795 (t) cc_final: 0.6526 (t) REVERT: B 140 VAL cc_start: 0.8814 (t) cc_final: 0.8482 (t) REVERT: C 1033 CYS cc_start: 0.7708 (m) cc_final: 0.7477 (m) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.5258 time to fit residues: 133.7266 Evaluate side-chains 159 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 121 optimal weight: 0.4980 chunk 91 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.172895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.150727 restraints weight = 80285.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.154460 restraints weight = 42099.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.155757 restraints weight = 28070.795| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 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 0.080 10420 Z= 0.189 Angle : 0.564 6.861 14043 Z= 0.314 Chirality : 0.036 0.348 1606 Planarity : 0.004 0.049 1790 Dihedral : 4.984 30.376 1372 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1262 helix: 1.93 (0.17), residues: 876 sheet: -2.16 (0.90), residues: 32 loop : -1.08 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 516 HIS 0.008 0.001 HIS B 42 PHE 0.015 0.002 PHE B 74 TYR 0.014 0.001 TYR B 370 ARG 0.003 0.000 ARG A 548 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 783) hydrogen bonds : angle 4.60075 ( 2313) SS BOND : bond 0.00353 ( 1) SS BOND : angle 4.23273 ( 2) covalent geometry : bond 0.00411 (10419) covalent geometry : angle 0.56209 (14041) *********************** 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 180 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.635 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: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7532 (t80) cc_final: 0.7153 (t80) REVERT: A 435 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8624 (tm-30) REVERT: A 459 MET cc_start: 0.6495 (ttp) cc_final: 0.6227 (ttp) REVERT: A 508 MET cc_start: 0.7912 (ttp) cc_final: 0.7453 (mtp) REVERT: A 598 ARG cc_start: 0.7639 (mtp85) cc_final: 0.7180 (mtt-85) REVERT: B 24 THR cc_start: 0.6816 (t) cc_final: 0.6538 (t) REVERT: B 140 VAL cc_start: 0.8861 (t) cc_final: 0.8495 (t) REVERT: C 1033 CYS cc_start: 0.7668 (m) cc_final: 0.7410 (m) REVERT: D 466 PHE cc_start: 0.6816 (t80) cc_final: 0.6537 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.5385 time to fit residues: 135.6362 Evaluate side-chains 158 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.174394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.152899 restraints weight = 79894.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155447 restraints weight = 43290.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.158112 restraints weight = 29986.617| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10420 Z= 0.140 Angle : 0.534 7.018 14043 Z= 0.293 Chirality : 0.035 0.340 1606 Planarity : 0.004 0.054 1790 Dihedral : 4.873 28.729 1372 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.41 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1262 helix: 2.06 (0.17), residues: 874 sheet: -2.04 (0.88), residues: 32 loop : -0.91 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.008 0.001 HIS A 147 PHE 0.013 0.001 PHE A 393 TYR 0.014 0.001 TYR B 370 ARG 0.004 0.000 ARG A 58 Details of bonding type rmsd hydrogen bonds : bond 0.04934 ( 783) hydrogen bonds : angle 4.47331 ( 2313) SS BOND : bond 0.01167 ( 1) SS BOND : angle 4.41175 ( 2) covalent geometry : bond 0.00294 (10419) covalent geometry : angle 0.53185 (14041) *********************** 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: 0 poor density : 179 time to evaluate : 1.576 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: symmetry clash REVERT: A 6 PHE cc_start: 0.7537 (t80) cc_final: 0.7174 (t80) REVERT: A 15 THR cc_start: 0.5495 (m) cc_final: 0.5246 (p) REVERT: A 435 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 459 MET cc_start: 0.6539 (ttp) cc_final: 0.6293 (ttp) REVERT: A 508 MET cc_start: 0.7818 (ttp) cc_final: 0.7392 (mtp) REVERT: B 24 THR cc_start: 0.6758 (t) cc_final: 0.6392 (t) REVERT: B 140 VAL cc_start: 0.8792 (t) cc_final: 0.8328 (t) REVERT: B 432 ASP cc_start: 0.8142 (m-30) cc_final: 0.7938 (m-30) REVERT: B 448 LEU cc_start: 0.7762 (tp) cc_final: 0.7554 (tp) REVERT: B 459 MET cc_start: 0.0249 (ttt) cc_final: 0.0012 (ttm) REVERT: C 1033 CYS cc_start: 0.7769 (m) cc_final: 0.7458 (m) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.5277 time to fit residues: 131.4009 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 : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 66 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 108 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 overall best weight: 0.8522 ------------------------------------------------------------------------------- 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 = 0.4332 r_free = 0.4332 target = 0.173727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.151750 restraints weight = 79887.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.155428 restraints weight = 41741.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.156902 restraints weight = 27409.266| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10420 Z= 0.153 Angle : 0.539 10.687 14043 Z= 0.296 Chirality : 0.035 0.343 1606 Planarity : 0.004 0.049 1790 Dihedral : 4.801 24.531 1372 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.24), residues: 1262 helix: 2.11 (0.17), residues: 872 sheet: -1.92 (0.88), residues: 32 loop : -0.96 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.008 0.001 HIS A 147 PHE 0.021 0.001 PHE D 466 TYR 0.013 0.001 TYR B 370 ARG 0.005 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 783) hydrogen bonds : angle 4.41703 ( 2313) SS BOND : bond 0.00012 ( 1) SS BOND : angle 6.10745 ( 2) covalent geometry : bond 0.00324 (10419) covalent geometry : angle 0.53446 (14041) *********************** 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 177 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.777 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: A 6 PHE cc_start: 0.7499 (t80) cc_final: 0.7174 (t80) REVERT: A 148 GLN cc_start: 0.7677 (mt0) cc_final: 0.7425 (mt0) REVERT: A 435 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 459 MET cc_start: 0.6578 (ttp) cc_final: 0.6307 (ttp) REVERT: A 508 MET cc_start: 0.7758 (ttp) cc_final: 0.7374 (mtp) REVERT: B 24 THR cc_start: 0.6900 (t) cc_final: 0.6550 (t) REVERT: B 140 VAL cc_start: 0.8818 (t) cc_final: 0.8388 (t) REVERT: C 1023 ASP cc_start: 0.7670 (t70) cc_final: 0.7283 (t0) REVERT: C 1026 ASP cc_start: 0.6754 (m-30) cc_final: 0.6487 (m-30) REVERT: C 1033 CYS cc_start: 0.7646 (m) cc_final: 0.7378 (m) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.5332 time to fit residues: 131.5082 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 : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 100 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.174862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.153233 restraints weight = 79817.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.156210 restraints weight = 44024.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.159111 restraints weight = 30019.978| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.2515 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= 0.136 Angle : 0.527 7.713 14043 Z= 0.288 Chirality : 0.035 0.340 1606 Planarity : 0.004 0.063 1790 Dihedral : 4.738 23.440 1372 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.57 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.24), residues: 1262 helix: 2.20 (0.17), residues: 868 sheet: -1.88 (0.86), residues: 32 loop : -0.93 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 516 HIS 0.008 0.001 HIS A 147 PHE 0.014 0.001 PHE B 74 TYR 0.013 0.001 TYR B 370 ARG 0.004 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 783) hydrogen bonds : angle 4.34865 ( 2313) SS BOND : bond 0.00041 ( 1) SS BOND : angle 6.00705 ( 2) covalent geometry : bond 0.00284 (10419) covalent geometry : angle 0.52207 (14041) ********************** 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 176 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.719 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: symmetry clash REVERT: A 6 PHE cc_start: 0.7462 (t80) cc_final: 0.7161 (t80) REVERT: A 148 GLN cc_start: 0.7657 (mt0) cc_final: 0.7409 (mt0) REVERT: A 435 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8584 (tm-30) REVERT: A 459 MET cc_start: 0.6552 (ttp) cc_final: 0.6286 (ttp) REVERT: A 508 MET cc_start: 0.7733 (ttp) cc_final: 0.7365 (mtp) REVERT: B 24 THR cc_start: 0.6698 (t) cc_final: 0.6356 (t) REVERT: B 140 VAL cc_start: 0.8799 (t) cc_final: 0.8367 (t) REVERT: C 1023 ASP cc_start: 0.7699 (t70) cc_final: 0.7355 (t0) REVERT: C 1033 CYS cc_start: 0.7701 (m) cc_final: 0.7406 (m) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.5080 time to fit residues: 125.2390 Evaluate side-chains 159 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 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 = 0.4331 r_free = 0.4331 target = 0.173818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151970 restraints weight = 79996.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.155309 restraints weight = 41638.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157245 restraints weight = 27698.935| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10420 Z= 0.162 Angle : 0.535 8.035 14043 Z= 0.297 Chirality : 0.035 0.346 1606 Planarity : 0.004 0.050 1790 Dihedral : 4.736 23.871 1372 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1262 helix: 2.17 (0.17), residues: 868 sheet: -1.93 (0.86), residues: 32 loop : -0.93 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 516 HIS 0.007 0.001 HIS A 147 PHE 0.017 0.002 PHE D 466 TYR 0.019 0.001 TYR A 36 ARG 0.004 0.000 ARG A 598 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 783) hydrogen bonds : angle 4.39532 ( 2313) SS BOND : bond 0.00210 ( 1) SS BOND : angle 5.90694 ( 2) covalent geometry : bond 0.00344 (10419) covalent geometry : angle 0.53074 (14041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6527.00 seconds wall clock time: 112 minutes 22.69 seconds (6742.69 seconds total)