Starting phenix.real_space_refine on Thu Jul 2 12:57:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pik_71670/07_2026/9pik_71670_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pik_71670/07_2026/9pik_71670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pik_71670/07_2026/9pik_71670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pik_71670/07_2026/9pik_71670.map" model { file = "/net/cci-nas-00/data/ceres_data/9pik_71670/07_2026/9pik_71670_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pik_71670/07_2026/9pik_71670_neut.cif" } resolution = 2.62 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= 0.005 sd= 0.047 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 K 3 8.98 5 S 48 5.16 5 C 5722 2.51 5 N 1276 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8435 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3998 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3998 Classifications: {'peptide': 505} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 484} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 218 Ad-hoc single atom residues: {' K': 3} Unusual residues: {'LMT': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Chain breaks: 3 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 1254 Unresolved non-hydrogen chiralities: 230 Chain: "B" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 218 Unusual residues: {'LMT': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 909 Unresolved non-hydrogen dihedrals: 1254 Unresolved non-hydrogen chiralities: 230 Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8435 At special positions: 0 Unit cell: (92.624, 101.721, 124.05, 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) K 3 19.00 S 48 16.00 O 1386 8.00 N 1276 7.00 C 5722 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 369.6 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 80.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.786A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 121 through 143 Proline residue: A 131 - end of helix removed outlier: 3.590A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 139 " --> pdb=" O MET A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 184 Processing helix chain 'A' and resid 188 through 216 removed outlier: 3.627A pdb=" N ARG A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 257 removed outlier: 3.530A pdb=" N TYR A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 272 through 295 Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 323 through 351 Processing helix chain 'A' and resid 356 through 380 Processing helix chain 'A' and resid 384 through 431 removed outlier: 3.814A pdb=" N GLY A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 457 through 500 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 622 through 651 removed outlier: 4.124A pdb=" N GLN A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 642 " --> pdb=" O LEU A 638 " (cutoff:3.500A) Proline residue: A 643 - end of helix Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 681 through 705 removed outlier: 4.328A pdb=" N GLU A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 96 through 103 removed outlier: 3.786A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 Processing helix chain 'B' and resid 121 through 143 Proline residue: B 131 - end of helix removed outlier: 3.590A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 184 Processing helix chain 'B' and resid 188 through 216 removed outlier: 3.627A pdb=" N ARG B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 257 removed outlier: 3.530A pdb=" N TYR B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 Processing helix chain 'B' and resid 272 through 295 Processing helix chain 'B' and resid 299 through 312 Processing helix chain 'B' and resid 323 through 351 Processing helix chain 'B' and resid 356 through 380 Processing helix chain 'B' and resid 384 through 431 removed outlier: 3.814A pdb=" N GLY B 422 " --> pdb=" O PHE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 457 through 500 Proline residue: B 473 - end of helix Processing helix chain 'B' and resid 622 through 651 removed outlier: 4.124A pdb=" N GLN B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Proline residue: B 643 - end of helix Processing helix chain 'B' and resid 657 through 662 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 681 through 705 removed outlier: 4.329A pdb=" N GLU B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 154 through 155 removed outlier: 4.532A pdb=" N LYS A 146 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 154 through 155 removed outlier: 4.532A pdb=" N LYS B 146 " --> pdb=" O VAL B 155 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2406 1.34 - 1.46: 1316 1.46 - 1.57: 4780 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8586 Sorted by residual: bond pdb=" CA SER A 228 " pdb=" CB SER A 228 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.61e-02 3.86e+03 1.53e+01 bond pdb=" CA SER B 228 " pdb=" CB SER B 228 " ideal model delta sigma weight residual 1.530 1.467 0.063 1.61e-02 3.86e+03 1.53e+01 bond pdb=" CA SER B 192 " pdb=" CB SER B 192 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.56e-02 4.11e+03 1.19e+01 bond pdb=" CA SER B 194 " pdb=" CB SER B 194 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.57e-02 4.06e+03 1.15e+01 bond pdb=" CA SER A 194 " pdb=" CB SER A 194 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.57e-02 4.06e+03 1.15e+01 ... (remaining 8581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 11116 1.06 - 2.12: 226 2.12 - 3.18: 92 3.18 - 4.25: 20 4.25 - 5.31: 16 Bond angle restraints: 11470 Sorted by residual: angle pdb=" N GLU A 229 " pdb=" CA GLU A 229 " pdb=" C GLU A 229 " ideal model delta sigma weight residual 112.54 107.94 4.60 1.22e+00 6.72e-01 1.42e+01 angle pdb=" N GLU B 229 " pdb=" CA GLU B 229 " pdb=" C GLU B 229 " ideal model delta sigma weight residual 112.54 107.98 4.56 1.22e+00 6.72e-01 1.40e+01 angle pdb=" N GLY A 230 " pdb=" CA GLY A 230 " pdb=" C GLY A 230 " ideal model delta sigma weight residual 112.77 108.94 3.83 1.28e+00 6.10e-01 8.96e+00 angle pdb=" N GLY B 230 " pdb=" CA GLY B 230 " pdb=" C GLY B 230 " ideal model delta sigma weight residual 112.77 108.95 3.82 1.28e+00 6.10e-01 8.92e+00 angle pdb=" CA VAL A 142 " pdb=" C VAL A 142 " pdb=" O VAL A 142 " ideal model delta sigma weight residual 121.05 117.96 3.09 1.11e+00 8.12e-01 7.74e+00 ... (remaining 11465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.73: 4647 11.73 - 23.46: 349 23.46 - 35.18: 100 35.18 - 46.91: 32 46.91 - 58.64: 10 Dihedral angle restraints: 5138 sinusoidal: 2184 harmonic: 2954 Sorted by residual: dihedral pdb=" CA LEU A 680 " pdb=" C LEU A 680 " pdb=" N LYS A 681 " pdb=" CA LYS A 681 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU B 680 " pdb=" C LEU B 680 " pdb=" N LYS B 681 " pdb=" CA LYS B 681 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" N MET B 475 " pdb=" CA MET B 475 " pdb=" CB MET B 475 " pdb=" CG MET B 475 " ideal model delta sinusoidal sigma weight residual -60.00 -105.62 45.62 3 1.50e+01 4.44e-03 8.20e+00 ... (remaining 5135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1029 0.050 - 0.099: 230 0.099 - 0.149: 31 0.149 - 0.199: 0 0.199 - 0.248: 2 Chirality restraints: 1292 Sorted by residual: chirality pdb=" CA VAL A 162 " pdb=" N VAL A 162 " pdb=" C VAL A 162 " pdb=" CB VAL A 162 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA VAL B 162 " pdb=" N VAL B 162 " pdb=" C VAL B 162 " pdb=" CB VAL B 162 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLU B 143 " pdb=" N GLU B 143 " pdb=" C GLU B 143 " pdb=" CB GLU B 143 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1289 not shown) Planarity restraints: 1350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 190 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C LEU B 190 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 190 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 191 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 190 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C LEU A 190 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU A 190 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 191 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 222 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO B 223 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 223 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 223 " 0.018 5.00e-02 4.00e+02 ... (remaining 1347 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 2135 2.80 - 3.39: 9518 3.39 - 3.97: 15548 3.97 - 4.56: 22762 4.56 - 5.14: 33036 Nonbonded interactions: 82999 Sorted by model distance: nonbonded pdb=" NH2 ARG A 96 " pdb=" CB SER A 99 " model vdw 2.219 3.520 nonbonded pdb=" NH2 ARG B 96 " pdb=" CB SER B 99 " model vdw 2.219 3.520 nonbonded pdb=" OE1 GLU B 229 " pdb=" N SER B 302 " model vdw 2.497 3.120 nonbonded pdb=" OE1 GLU A 229 " pdb=" N SER A 302 " model vdw 2.497 3.120 nonbonded pdb=" C SER A 228 " pdb=" OG SER A 228 " model vdw 2.548 2.616 ... (remaining 82994 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 82 through 706 or (resid 904 and (name C1 or name C2 or na \ me C3 or name C4 or name C5 or name C6 )) or (resid 905 and (name C2 or name C3 \ or name C4 or name C5 or name C6 )) or (resid 906 and (name C4 or name C5 or nam \ e C6 )) or (resid 907 and (name C3 or name C4 or name C5 or name C6 )) or (resid \ 908 and (name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 909 th \ rough 912 or (resid 913 and (name C10 or name C11 or name C12 or name C2 or name \ C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (res \ id 914 and (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 or na \ me C7 )) or (resid 915 through 916 and (name C2 or name C3 or name C4 or name C5 \ or name C6 or name C7 )) or resid 917 or (resid 918 and (name C4 or name C5 or \ name C6 or name C7 or name C8 or name C9 )) or (resid 919 and (name C10 or name \ C11 or name C12 or name C2 or name C3 or name C4 or name C5 or name C6 or name C \ 7 or name C8 or name C9 )) or resid 920 or (resid 921 through 923 and (name C3 o \ r name C4 or name C5 or name C6 or name C7 or name C8 )))) selection = (chain 'B' and (resid 82 through 706 or resid 804 through 805 or (resid 806 and \ (name C4 or name C5 or name C6 )) or (resid 807 and (name C3 or name C4 or name \ C5 or name C6 )) or (resid 808 and (name C4 or name C5 or name C6 or name C7 or \ name C8 )) or (resid 809 and (name C10 or name C11 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 )) or (resid 810 and (name C2 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name C8 )) or resid 811 \ through 814 or (resid 815 through 816 and (name C2 or name C3 or name C4 or name \ C5 or name C6 or name C7 )) or (resid 817 and (name C1 or name C2 or name C3 or \ name C4 or name C5 or name C6 or name C7 )) or resid 818 through 819 or (resid \ 820 and (name C4 or name C5 or name C6 or name C7 or name C8 or name C9 )) or (r \ esid 821 through 823 and (name C3 or name C4 or name C5 or name C6 or name C7 or \ name C8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.570 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 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:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.004 0.063 8586 Z= 0.223 Angle : 0.485 5.307 11470 Z= 0.275 Chirality : 0.040 0.248 1292 Planarity : 0.004 0.032 1350 Dihedral : 9.789 58.638 3230 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.24), residues: 1002 helix: 0.64 (0.17), residues: 782 sheet: None (None), residues: 0 loop : 0.00 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.012 0.001 TYR B 189 PHE 0.007 0.001 PHE B 122 TRP 0.005 0.001 TRP A 661 HIS 0.001 0.001 HIS B 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.22 ( 8586) covalent geometry : angle 0.48544 / 0.27 (11470) hydrogen bonds : bond 0.20030 / 13.51 ( 626) hydrogen bonds : angle 6.12334 / 4.40 ( 1866) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.9030 (t0) cc_final: 0.8818 (t0) REVERT: A 268 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 402 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7183 (ttm170) REVERT: A 475 MET cc_start: 0.8641 (mmm) cc_final: 0.8426 (tpt) REVERT: A 487 TYR cc_start: 0.7835 (t80) cc_final: 0.7478 (t80) REVERT: A 488 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8047 (pt0) REVERT: A 492 ASP cc_start: 0.6802 (t70) cc_final: 0.6401 (m-30) REVERT: B 176 ASN cc_start: 0.9042 (t0) cc_final: 0.8835 (t0) REVERT: B 268 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 402 ARG cc_start: 0.7563 (ttt180) cc_final: 0.7201 (ttm170) REVERT: B 475 MET cc_start: 0.8657 (mmm) cc_final: 0.8405 (tpt) REVERT: B 487 TYR cc_start: 0.7824 (t80) cc_final: 0.7467 (t80) REVERT: B 488 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8063 (pt0) REVERT: B 492 ASP cc_start: 0.6831 (t70) cc_final: 0.6427 (m-30) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.5797 time to fit residues: 59.3950 Evaluate side-chains 64 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 270 GLN B 222 ASN B 270 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.091124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.069126 restraints weight = 17274.952| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.47 r_work: 0.2861 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8586 Z= 0.132 Angle : 0.496 5.419 11470 Z= 0.263 Chirality : 0.039 0.136 1292 Planarity : 0.004 0.029 1350 Dihedral : 7.695 56.832 1380 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.74 % Allowed : 4.45 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.26), residues: 1002 helix: 2.56 (0.17), residues: 784 sheet: None (None), residues: 0 loop : 0.74 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.017 0.001 TYR B 487 PHE 0.007 0.001 PHE A 463 TRP 0.007 0.001 TRP A 115 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 8586) covalent geometry : angle 0.49604 / 0.26 (11470) hydrogen bonds : bond 0.05148 / 3.48 ( 626) hydrogen bonds : angle 3.79997 / 2.76 ( 1866) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.233 Fit side-chains REVERT: A 222 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8164 (p0) REVERT: A 274 MET cc_start: 0.8118 (tpt) cc_final: 0.7718 (tpt) REVERT: A 492 ASP cc_start: 0.7140 (t70) cc_final: 0.6798 (m-30) REVERT: B 222 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8128 (p0) REVERT: B 492 ASP cc_start: 0.7153 (t70) cc_final: 0.6851 (m-30) outliers start: 24 outliers final: 7 residues processed: 86 average time/residue: 0.4841 time to fit residues: 44.2967 Evaluate side-chains 66 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 697 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.091364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.069036 restraints weight = 17059.830| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.47 r_work: 0.2858 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8586 Z= 0.123 Angle : 0.465 5.327 11470 Z= 0.244 Chirality : 0.038 0.133 1292 Planarity : 0.004 0.032 1350 Dihedral : 6.994 58.789 1380 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.20 % Allowed : 5.14 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.82 (0.26), residues: 1002 helix: 3.01 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.70 (0.47), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.016 0.001 TYR B 439 PHE 0.007 0.001 PHE A 463 TRP 0.005 0.001 TRP A 661 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8586) covalent geometry : angle 0.46493 / 0.24 (11470) hydrogen bonds : bond 0.04494 / 3.05 ( 626) hydrogen bonds : angle 3.58236 / 2.59 ( 1866) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.248 Fit side-chains REVERT: A 222 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8298 (p0) REVERT: A 229 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: A 492 ASP cc_start: 0.7188 (t70) cc_final: 0.6805 (m-30) REVERT: A 696 MET cc_start: 0.8628 (pp-130) cc_final: 0.8244 (mtt) REVERT: A 697 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: A 704 MET cc_start: 0.9261 (ttm) cc_final: 0.8807 (tmm) REVERT: B 222 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8296 (p0) REVERT: B 229 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: B 492 ASP cc_start: 0.7215 (t70) cc_final: 0.6816 (m-30) REVERT: B 696 MET cc_start: 0.8603 (pp-130) cc_final: 0.8216 (mtt) REVERT: B 704 MET cc_start: 0.9277 (ttm) cc_final: 0.8726 (tmm) outliers start: 28 outliers final: 7 residues processed: 84 average time/residue: 0.4464 time to fit residues: 40.0602 Evaluate side-chains 78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 408 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 95 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069780 restraints weight = 17284.508| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.32 r_work: 0.2938 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 8586 Z= 0.190 Angle : 0.508 6.669 11470 Z= 0.264 Chirality : 0.040 0.135 1292 Planarity : 0.004 0.033 1350 Dihedral : 7.324 57.385 1380 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.88 % Allowed : 5.48 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.26), residues: 1002 helix: 3.07 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.56 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 269 TYR 0.016 0.002 TYR A 439 PHE 0.010 0.001 PHE B 112 TRP 0.007 0.001 TRP A 661 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.19 ( 8586) covalent geometry : angle 0.50816 / 0.26 (11470) hydrogen bonds : bond 0.04614 / 3.13 ( 626) hydrogen bonds : angle 3.59915 / 2.61 ( 1866) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.215 Fit side-chains REVERT: A 222 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8307 (p0) REVERT: A 229 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: A 492 ASP cc_start: 0.7273 (t70) cc_final: 0.6934 (m-30) REVERT: A 696 MET cc_start: 0.8937 (pp-130) cc_final: 0.8585 (mtt) REVERT: A 704 MET cc_start: 0.9121 (ttm) cc_final: 0.8774 (tmm) REVERT: B 222 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 229 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: B 492 ASP cc_start: 0.7252 (t70) cc_final: 0.6890 (m-30) REVERT: B 696 MET cc_start: 0.8901 (pp-130) cc_final: 0.8570 (mtt) REVERT: B 704 MET cc_start: 0.9121 (ttm) cc_final: 0.8738 (tmm) outliers start: 34 outliers final: 11 residues processed: 81 average time/residue: 0.4516 time to fit residues: 39.1061 Evaluate side-chains 75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 408 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.0470 overall best weight: 1.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070647 restraints weight = 17163.878| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.31 r_work: 0.2910 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8586 Z= 0.130 Angle : 0.473 5.612 11470 Z= 0.247 Chirality : 0.039 0.136 1292 Planarity : 0.004 0.033 1350 Dihedral : 7.032 54.506 1380 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.31 % Allowed : 6.62 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.92 (0.26), residues: 1002 helix: 3.13 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.48 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 96 TYR 0.016 0.001 TYR B 439 PHE 0.008 0.001 PHE A 463 TRP 0.006 0.001 TRP B 467 HIS 0.002 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8586) covalent geometry : angle 0.47339 / 0.25 (11470) hydrogen bonds : bond 0.04211 / 2.85 ( 626) hydrogen bonds : angle 3.54525 / 2.56 ( 1866) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 0.240 Fit side-chains REVERT: A 222 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8314 (p0) REVERT: A 229 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 492 ASP cc_start: 0.7262 (t70) cc_final: 0.6909 (m-30) REVERT: A 696 MET cc_start: 0.8912 (pp-130) cc_final: 0.8523 (mtt) REVERT: A 704 MET cc_start: 0.9215 (ttm) cc_final: 0.8782 (tmm) REVERT: B 222 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8280 (p0) REVERT: B 229 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: B 492 ASP cc_start: 0.7275 (t70) cc_final: 0.6912 (m-30) REVERT: B 696 MET cc_start: 0.8892 (pp-130) cc_final: 0.8512 (mtt) REVERT: B 704 MET cc_start: 0.9212 (ttm) cc_final: 0.8752 (tmm) outliers start: 29 outliers final: 14 residues processed: 78 average time/residue: 0.4791 time to fit residues: 40.0767 Evaluate side-chains 72 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 641 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071561 restraints weight = 17089.462| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.31 r_work: 0.2948 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8586 Z= 0.117 Angle : 0.465 6.093 11470 Z= 0.243 Chirality : 0.038 0.136 1292 Planarity : 0.004 0.029 1350 Dihedral : 6.766 51.515 1380 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.85 % Allowed : 7.31 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.26), residues: 1002 helix: 3.24 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.48 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.016 0.001 TYR B 439 PHE 0.008 0.001 PHE A 463 TRP 0.006 0.001 TRP A 467 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8586) covalent geometry : angle 0.46508 / 0.24 (11470) hydrogen bonds : bond 0.03968 / 2.69 ( 626) hydrogen bonds : angle 3.48331 / 2.52 ( 1866) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.209 Fit side-chains REVERT: A 222 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8285 (p0) REVERT: A 492 ASP cc_start: 0.7226 (t70) cc_final: 0.6903 (m-30) REVERT: A 696 MET cc_start: 0.8898 (pp-130) cc_final: 0.8542 (mtt) REVERT: A 704 MET cc_start: 0.9197 (ttm) cc_final: 0.8870 (tmm) REVERT: B 222 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8281 (p0) REVERT: B 492 ASP cc_start: 0.7256 (t70) cc_final: 0.6918 (m-30) REVERT: B 696 MET cc_start: 0.8898 (pp-130) cc_final: 0.8546 (mtt) REVERT: B 704 MET cc_start: 0.9169 (ttm) cc_final: 0.8829 (tmm) outliers start: 25 outliers final: 16 residues processed: 74 average time/residue: 0.4501 time to fit residues: 35.6934 Evaluate side-chains 75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 641 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071777 restraints weight = 17180.885| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.33 r_work: 0.2950 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8586 Z= 0.115 Angle : 0.465 6.691 11470 Z= 0.243 Chirality : 0.038 0.136 1292 Planarity : 0.004 0.029 1350 Dihedral : 6.611 50.960 1380 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.08 % Allowed : 7.42 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.26), residues: 1002 helix: 3.27 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.49 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.015 0.001 TYR B 439 PHE 0.008 0.001 PHE A 463 TRP 0.006 0.001 TRP A 467 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8586) covalent geometry : angle 0.46464 / 0.24 (11470) hydrogen bonds : bond 0.03867 / 2.61 ( 626) hydrogen bonds : angle 3.46839 / 2.50 ( 1866) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.191 Fit side-chains REVERT: A 222 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8327 (p0) REVERT: A 492 ASP cc_start: 0.7318 (t70) cc_final: 0.6986 (m-30) REVERT: A 696 MET cc_start: 0.8922 (pp-130) cc_final: 0.8559 (mtt) REVERT: A 704 MET cc_start: 0.9199 (ttm) cc_final: 0.8842 (tmm) REVERT: B 222 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8307 (p0) REVERT: B 492 ASP cc_start: 0.7323 (t70) cc_final: 0.6991 (m-30) REVERT: B 696 MET cc_start: 0.8896 (pp-130) cc_final: 0.8557 (mtt) REVERT: B 704 MET cc_start: 0.9179 (ttm) cc_final: 0.8804 (tmm) outliers start: 27 outliers final: 13 residues processed: 76 average time/residue: 0.4170 time to fit residues: 33.9748 Evaluate side-chains 75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 641 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 0.0980 chunk 91 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.092348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072209 restraints weight = 17140.444| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.30 r_work: 0.2957 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8586 Z= 0.114 Angle : 0.480 7.079 11470 Z= 0.250 Chirality : 0.038 0.136 1292 Planarity : 0.004 0.028 1350 Dihedral : 6.464 51.236 1380 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.85 % Allowed : 8.11 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.11 (0.27), residues: 1002 helix: 3.28 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.50 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.015 0.001 TYR B 439 PHE 0.008 0.001 PHE A 463 TRP 0.006 0.001 TRP A 467 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8586) covalent geometry : angle 0.48047 / 0.25 (11470) hydrogen bonds : bond 0.03773 / 2.56 ( 626) hydrogen bonds : angle 3.46058 / 2.50 ( 1866) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.192 Fit side-chains REVERT: A 222 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8360 (p0) REVERT: A 492 ASP cc_start: 0.7398 (t70) cc_final: 0.6987 (m-30) REVERT: A 696 MET cc_start: 0.8931 (pp-130) cc_final: 0.8517 (mtt) REVERT: A 704 MET cc_start: 0.9200 (ttm) cc_final: 0.8854 (tmm) REVERT: B 222 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8356 (p0) REVERT: B 492 ASP cc_start: 0.7378 (t70) cc_final: 0.6998 (m-30) REVERT: B 696 MET cc_start: 0.8914 (pp-130) cc_final: 0.8544 (mtt) REVERT: B 704 MET cc_start: 0.9165 (ttm) cc_final: 0.8809 (tmm) outliers start: 25 outliers final: 15 residues processed: 78 average time/residue: 0.4318 time to fit residues: 36.3664 Evaluate side-chains 75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 641 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 22 optimal weight: 3.9990 chunk 73 optimal weight: 0.0020 chunk 12 optimal weight: 3.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN A 270 GLN B 176 ASN B 222 ASN B 270 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071496 restraints weight = 17134.871| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.38 r_work: 0.2964 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8586 Z= 0.108 Angle : 0.486 7.581 11470 Z= 0.252 Chirality : 0.038 0.136 1292 Planarity : 0.004 0.028 1350 Dihedral : 6.324 51.558 1380 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.28 % Allowed : 8.90 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.10 (0.27), residues: 1002 helix: 3.27 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.51 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.015 0.001 TYR B 439 PHE 0.008 0.001 PHE B 463 TRP 0.006 0.001 TRP A 467 HIS 0.001 0.000 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8586) covalent geometry : angle 0.48603 / 0.25 (11470) hydrogen bonds : bond 0.03669 / 2.48 ( 626) hydrogen bonds : angle 3.45282 / 2.49 ( 1866) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.327 Fit side-chains REVERT: A 222 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8328 (p0) REVERT: A 351 VAL cc_start: 0.9057 (t) cc_final: 0.8839 (p) REVERT: A 492 ASP cc_start: 0.7394 (t70) cc_final: 0.6988 (m-30) REVERT: A 696 MET cc_start: 0.8919 (pp-130) cc_final: 0.8491 (mtt) REVERT: A 704 MET cc_start: 0.9195 (ttm) cc_final: 0.8853 (tmm) REVERT: B 222 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8312 (p0) REVERT: B 351 VAL cc_start: 0.9058 (t) cc_final: 0.8841 (p) REVERT: B 492 ASP cc_start: 0.7393 (t70) cc_final: 0.7001 (m-30) REVERT: B 696 MET cc_start: 0.8921 (pp-130) cc_final: 0.8473 (mtt) REVERT: B 704 MET cc_start: 0.9186 (ttm) cc_final: 0.8822 (tmm) outliers start: 20 outliers final: 12 residues processed: 72 average time/residue: 0.4749 time to fit residues: 36.8364 Evaluate side-chains 71 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 641 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN B 176 ASN B 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.091026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070510 restraints weight = 17214.506| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.32 r_work: 0.2931 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 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 0.039 8586 Z= 0.164 Angle : 0.522 7.724 11470 Z= 0.270 Chirality : 0.040 0.136 1292 Planarity : 0.004 0.028 1350 Dihedral : 6.590 50.900 1380 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.83 % Allowed : 9.25 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.26), residues: 1002 helix: 3.20 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.53 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.016 0.001 TYR A 439 PHE 0.009 0.001 PHE B 112 TRP 0.006 0.001 TRP A 467 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 ( 8586) covalent geometry : angle 0.52242 / 0.27 (11470) hydrogen bonds : bond 0.04018 / 2.71 ( 626) hydrogen bonds : angle 3.50590 / 2.53 ( 1866) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.247 Fit side-chains REVERT: A 222 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8384 (p0) REVERT: A 351 VAL cc_start: 0.9088 (t) cc_final: 0.8886 (p) REVERT: A 492 ASP cc_start: 0.7420 (t70) cc_final: 0.7019 (m-30) REVERT: A 696 MET cc_start: 0.8946 (pp-130) cc_final: 0.8549 (mtt) REVERT: A 704 MET cc_start: 0.9199 (ttm) cc_final: 0.8876 (tmm) REVERT: B 222 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8358 (p0) REVERT: B 492 ASP cc_start: 0.7455 (t70) cc_final: 0.7042 (m-30) REVERT: B 696 MET cc_start: 0.8944 (pp-130) cc_final: 0.8543 (mtt) REVERT: B 704 MET cc_start: 0.9174 (ttm) cc_final: 0.8832 (tmm) outliers start: 16 outliers final: 10 residues processed: 67 average time/residue: 0.4810 time to fit residues: 34.4635 Evaluate side-chains 67 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 222 ASN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 641 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.7980 chunk 7 optimal weight: 0.0010 chunk 56 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN A 222 ASN B 176 ASN B 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071926 restraints weight = 17108.184| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.30 r_work: 0.2958 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8586 Z= 0.114 Angle : 0.497 7.895 11470 Z= 0.257 Chirality : 0.038 0.136 1292 Planarity : 0.004 0.028 1350 Dihedral : 6.392 51.427 1380 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.05 % Allowed : 9.13 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.09 (0.27), residues: 1002 helix: 3.26 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.51 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 96 TYR 0.015 0.001 TYR B 439 PHE 0.009 0.001 PHE B 463 TRP 0.006 0.001 TRP A 467 HIS 0.001 0.000 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 8586) covalent geometry : angle 0.49739 / 0.26 (11470) hydrogen bonds : bond 0.03745 / 2.53 ( 626) hydrogen bonds : angle 3.47600 / 2.51 ( 1866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2398.49 seconds wall clock time: 41 minutes 30.88 seconds (2490.88 seconds total)