Starting phenix.real_space_refine on Thu Feb 5 03:35:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lzl_63529/02_2026/9lzl_63529.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lzl_63529/02_2026/9lzl_63529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lzl_63529/02_2026/9lzl_63529.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lzl_63529/02_2026/9lzl_63529.map" model { file = "/net/cci-nas-00/data/ceres_data/9lzl_63529/02_2026/9lzl_63529.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lzl_63529/02_2026/9lzl_63529.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9311 2.51 5 N 2409 2.21 5 O 2825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14611 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2365 Classifications: {'peptide': 316} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 286} Chain breaks: 1 Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 120 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2284 Classifications: {'peptide': 305} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 278} Chain: "E" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "C" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2312 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 282} Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 130 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "G" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2364 Classifications: {'peptide': 315} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 286} Chain breaks: 1 Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 107 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "H" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2292 Classifications: {'peptide': 306} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 279} Chain: "K" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 95 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "I" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2312 Classifications: {'peptide': 309} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 282} Chain: "L" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 135 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Time building chain proxies: 3.78, per 1000 atoms: 0.26 Number of scatterers: 14611 At special positions: 0 Unit cell: (156.2, 107.8, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2825 8.00 N 2409 7.00 C 9311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 318 " distance=2.04 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 318 " distance=2.04 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 318 " distance=2.04 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 318 " distance=2.04 Simple disulfide: pdb=" SG CYS I 69 " - pdb=" SG CYS I 318 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 605.6 milliseconds 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 16.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 220 through 224 removed outlier: 4.762A pdb=" N LEU A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 224' Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 341 through 353 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 220 through 224 removed outlier: 4.860A pdb=" N LEU B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 224' Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 269 through 272 No H-bonds generated for 'chain 'B' and resid 269 through 272' Processing helix chain 'B' and resid 328 through 332 removed outlier: 5.443A pdb=" N PHE B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 332' Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 220 through 224 removed outlier: 4.761A pdb=" N LEU C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 220 through 224' Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 328 through 332 removed outlier: 4.754A pdb=" N PHE C 332 " --> pdb=" O MET C 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 332' Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.504A pdb=" N ARG C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'F' and resid 366 through 380 Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 220 through 224 removed outlier: 4.522A pdb=" N LEU G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 220 through 224' Processing helix chain 'G' and resid 235 through 237 No H-bonds generated for 'chain 'G' and resid 235 through 237' Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 329 through 332 No H-bonds generated for 'chain 'G' and resid 329 through 332' Processing helix chain 'G' and resid 341 through 353 removed outlier: 3.764A pdb=" N ARG G 348 " --> pdb=" O LEU G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 362 No H-bonds generated for 'chain 'G' and resid 360 through 362' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 148 through 152 Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.778A pdb=" N LEU H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 220 through 224' Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'H' and resid 269 through 272 No H-bonds generated for 'chain 'H' and resid 269 through 272' Processing helix chain 'H' and resid 328 through 332 removed outlier: 5.767A pdb=" N PHE H 332 " --> pdb=" O MET H 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 328 through 332' Processing helix chain 'H' and resid 341 through 353 Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 148 through 152 Processing helix chain 'I' and resid 220 through 224 removed outlier: 4.594A pdb=" N LEU I 224 " --> pdb=" O LEU I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 220 through 224' Processing helix chain 'I' and resid 235 through 237 No H-bonds generated for 'chain 'I' and resid 235 through 237' Processing helix chain 'I' and resid 328 through 332 removed outlier: 5.054A pdb=" N PHE I 332 " --> pdb=" O MET I 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 332' Processing helix chain 'I' and resid 341 through 353 Processing helix chain 'I' and resid 360 through 362 No H-bonds generated for 'chain 'I' and resid 360 through 362' Processing helix chain 'L' and resid 366 through 380 131 hydrogen bonds defined for protein. 393 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: 1.87 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4729 1.35 - 1.47: 3727 1.47 - 1.60: 6429 1.60 - 1.72: 0 1.72 - 1.84: 108 Bond restraints: 14993 Sorted by residual: bond pdb=" CB GLN I 61 " pdb=" CG GLN I 61 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 bond pdb=" CB CYS C 69 " pdb=" SG CYS C 69 " ideal model delta sigma weight residual 1.808 1.842 -0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB CYS H 69 " pdb=" SG CYS H 69 " ideal model delta sigma weight residual 1.808 1.841 -0.033 3.30e-02 9.18e+02 9.77e-01 bond pdb=" CA VAL G 25 " pdb=" CB VAL G 25 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.35e-01 bond pdb=" CB CYS G 69 " pdb=" SG CYS G 69 " ideal model delta sigma weight residual 1.808 1.838 -0.030 3.30e-02 9.18e+02 8.00e-01 ... (remaining 14988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 19958 1.26 - 2.52: 397 2.52 - 3.77: 114 3.77 - 5.03: 15 5.03 - 6.29: 8 Bond angle restraints: 20492 Sorted by residual: angle pdb=" CA GLN I 61 " pdb=" CB GLN I 61 " pdb=" CG GLN I 61 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.80e+00 angle pdb=" N SER C 317 " pdb=" CA SER C 317 " pdb=" C SER C 317 " ideal model delta sigma weight residual 107.93 112.31 -4.38 1.65e+00 3.67e-01 7.05e+00 angle pdb=" CA VAL I 128 " pdb=" C VAL I 128 " pdb=" N PRO I 129 " ideal model delta sigma weight residual 117.00 119.36 -2.36 9.50e-01 1.11e+00 6.19e+00 angle pdb=" N SER I 317 " pdb=" CA SER I 317 " pdb=" C SER I 317 " ideal model delta sigma weight residual 108.32 112.18 -3.86 1.64e+00 3.72e-01 5.55e+00 angle pdb=" CA CYS A 318 " pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " ideal model delta sigma weight residual 114.40 119.35 -4.95 2.30e+00 1.89e-01 4.63e+00 ... (remaining 20487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7846 17.92 - 35.84: 831 35.84 - 53.76: 198 53.76 - 71.68: 42 71.68 - 89.60: 14 Dihedral angle restraints: 8931 sinusoidal: 3356 harmonic: 5575 Sorted by residual: dihedral pdb=" CB CYS I 69 " pdb=" SG CYS I 69 " pdb=" SG CYS I 318 " pdb=" CB CYS I 318 " ideal model delta sinusoidal sigma weight residual 93.00 150.65 -57.65 1 1.00e+01 1.00e-02 4.46e+01 dihedral pdb=" CA PRO B 73 " pdb=" C PRO B 73 " pdb=" N PRO B 74 " pdb=" CA PRO B 74 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP I 97 " pdb=" CB ASP I 97 " pdb=" CG ASP I 97 " pdb=" OD1 ASP I 97 " ideal model delta sinusoidal sigma weight residual -30.00 -89.99 59.99 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 8928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1373 0.028 - 0.056: 552 0.056 - 0.084: 175 0.084 - 0.112: 154 0.112 - 0.140: 81 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ILE B 84 " pdb=" N ILE B 84 " pdb=" C ILE B 84 " pdb=" CB ILE B 84 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA VAL C 128 " pdb=" N VAL C 128 " pdb=" C VAL C 128 " pdb=" CB VAL C 128 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL B 143 " pdb=" N VAL B 143 " pdb=" C VAL B 143 " pdb=" CB VAL B 143 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2332 not shown) Planarity restraints: 2680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 72 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO H 73 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO H 73 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 73 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 72 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO I 73 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO I 73 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 73 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 72 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO C 73 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " -0.029 5.00e-02 4.00e+02 ... (remaining 2677 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1284 2.74 - 3.28: 13222 3.28 - 3.82: 22565 3.82 - 4.36: 27575 4.36 - 4.90: 49530 Nonbonded interactions: 114176 Sorted by model distance: nonbonded pdb=" O GLN C 260 " pdb=" OG SER C 280 " model vdw 2.205 3.040 nonbonded pdb=" O GLN B 260 " pdb=" OG SER B 280 " model vdw 2.212 3.040 nonbonded pdb=" OG SER I 160 " pdb=" OE2 GLU I 257 " model vdw 2.220 3.040 nonbonded pdb=" O PRO B 129 " pdb=" OG1 THR B 132 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR G 206 " pdb=" O PRO G 208 " model vdw 2.265 3.040 ... (remaining 114171 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 58 through 362) selection = chain 'B' selection = (chain 'C' and resid 58 through 362) selection = (chain 'G' and resid 58 through 362) selection = (chain 'H' and resid 58 through 362) selection = (chain 'I' and resid 58 through 362) } ncs_group { reference = (chain 'D' and resid 365 through 377) selection = (chain 'F' and resid 365 through 377) selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } 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: 13.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 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 0.041 14999 Z= 0.104 Angle : 0.491 6.289 20504 Z= 0.254 Chirality : 0.045 0.140 2335 Planarity : 0.005 0.053 2680 Dihedral : 15.939 89.600 5311 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.60 % Allowed : 22.13 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.31 (0.20), residues: 1917 helix: -0.27 (0.31), residues: 339 sheet: 0.10 (0.20), residues: 663 loop : -0.27 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 87 TYR 0.020 0.001 TYR C 330 PHE 0.012 0.001 PHE C 231 TRP 0.012 0.001 TRP A 191 HIS 0.001 0.000 HIS G 215 Details of bonding type rmsd covalent geometry : bond 0.00251 (14993) covalent geometry : angle 0.48675 (20492) SS BOND : bond 0.00759 ( 6) SS BOND : angle 2.63786 ( 12) hydrogen bonds : bond 0.03354 ( 131) hydrogen bonds : angle 3.39138 ( 393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: B 331 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7612 (mm-40) REVERT: C 242 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: C 260 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7292 (mp-120) REVERT: C 328 MET cc_start: 0.9018 (tmm) cc_final: 0.8671 (ttp) REVERT: J 366 MET cc_start: 0.7612 (tpt) cc_final: 0.7173 (tpt) REVERT: I 162 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7828 (mt0) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 0.1533 time to fit residues: 32.5601 Evaluate side-chains 146 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain H residue 102 SER Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 170 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0010 chunk 149 optimal weight: 9.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.090217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.076836 restraints weight = 23265.694| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 1.87 r_work: 0.2685 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14999 Z= 0.179 Angle : 0.556 6.728 20504 Z= 0.284 Chirality : 0.048 0.153 2335 Planarity : 0.006 0.052 2680 Dihedral : 6.009 87.616 2067 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.69 % Allowed : 18.80 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.48 (0.20), residues: 1917 helix: -0.25 (0.31), residues: 327 sheet: 0.13 (0.21), residues: 614 loop : -0.54 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.011 0.002 TYR G 321 PHE 0.010 0.001 PHE B 76 TRP 0.012 0.002 TRP C 191 HIS 0.002 0.001 HIS G 215 Details of bonding type rmsd covalent geometry : bond 0.00459 (14993) covalent geometry : angle 0.54853 (20492) SS BOND : bond 0.01421 ( 6) SS BOND : angle 3.81045 ( 12) hydrogen bonds : bond 0.05292 ( 131) hydrogen bonds : angle 3.51309 ( 393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 130 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: C 162 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: C 242 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8513 (pt0) REVERT: C 260 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8832 (tp40) REVERT: C 328 MET cc_start: 0.9017 (tmm) cc_final: 0.8684 (ttp) REVERT: G 95 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8370 (ttt90) REVERT: I 162 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7914 (mt0) outliers start: 76 outliers final: 55 residues processed: 198 average time/residue: 0.1408 time to fit residues: 39.7338 Evaluate side-chains 189 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 319 ILE Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain L residue 366 MET Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 49 optimal weight: 0.0270 chunk 102 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.090874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.077536 restraints weight = 23252.134| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.86 r_work: 0.2712 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14999 Z= 0.145 Angle : 0.521 6.021 20504 Z= 0.265 Chirality : 0.047 0.161 2335 Planarity : 0.006 0.055 2680 Dihedral : 5.547 82.456 2053 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.75 % Allowed : 18.37 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.47 (0.20), residues: 1917 helix: -0.21 (0.31), residues: 326 sheet: 0.13 (0.21), residues: 606 loop : -0.53 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 87 TYR 0.009 0.001 TYR G 321 PHE 0.010 0.001 PHE G 231 TRP 0.010 0.001 TRP A 191 HIS 0.002 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00370 (14993) covalent geometry : angle 0.51449 (20492) SS BOND : bond 0.01213 ( 6) SS BOND : angle 3.41259 ( 12) hydrogen bonds : bond 0.04562 ( 131) hydrogen bonds : angle 3.54969 ( 393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: C 162 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: C 242 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8512 (pt0) REVERT: C 328 MET cc_start: 0.9006 (tmm) cc_final: 0.8679 (ttp) REVERT: H 329 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8807 (pp) REVERT: H 331 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.7913 (mm-40) outliers start: 77 outliers final: 59 residues processed: 204 average time/residue: 0.1386 time to fit residues: 40.9971 Evaluate side-chains 196 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 242 GLN Chi-restraints excluded: chain I residue 255 ILE Chi-restraints excluded: chain L residue 366 MET Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 24 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.088699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.075481 restraints weight = 23420.927| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.85 r_work: 0.2669 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14999 Z= 0.234 Angle : 0.603 7.250 20504 Z= 0.311 Chirality : 0.050 0.168 2335 Planarity : 0.006 0.055 2680 Dihedral : 5.572 73.743 2049 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.99 % Allowed : 18.68 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.68 (0.20), residues: 1917 helix: -0.33 (0.31), residues: 320 sheet: 0.06 (0.22), residues: 593 loop : -0.74 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 87 TYR 0.013 0.002 TYR G 321 PHE 0.013 0.002 PHE C 231 TRP 0.013 0.002 TRP C 191 HIS 0.003 0.001 HIS G 215 Details of bonding type rmsd covalent geometry : bond 0.00604 (14993) covalent geometry : angle 0.59365 (20492) SS BOND : bond 0.01674 ( 6) SS BOND : angle 4.44126 ( 12) hydrogen bonds : bond 0.05999 ( 131) hydrogen bonds : angle 3.69144 ( 393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 136 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.7197 (ttm170) REVERT: C 162 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7909 (mm-40) REVERT: F 378 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.5955 (mp) REVERT: G 95 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8382 (ttt90) REVERT: G 109 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8520 (mt0) REVERT: H 329 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8807 (pp) outliers start: 81 outliers final: 65 residues processed: 209 average time/residue: 0.1427 time to fit residues: 42.6346 Evaluate side-chains 206 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 135 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 300 ARG Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 319 ILE Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Chi-restraints excluded: chain L residue 376 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 173 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.076537 restraints weight = 23233.639| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.85 r_work: 0.2702 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14999 Z= 0.159 Angle : 0.542 6.942 20504 Z= 0.277 Chirality : 0.047 0.162 2335 Planarity : 0.006 0.055 2680 Dihedral : 5.463 69.941 2049 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.18 % Allowed : 18.56 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.61 (0.20), residues: 1917 helix: -0.25 (0.32), residues: 320 sheet: 0.02 (0.21), residues: 607 loop : -0.65 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 87 TYR 0.009 0.001 TYR G 321 PHE 0.011 0.001 PHE G 231 TRP 0.011 0.001 TRP C 191 HIS 0.002 0.001 HIS G 215 Details of bonding type rmsd covalent geometry : bond 0.00407 (14993) covalent geometry : angle 0.53467 (20492) SS BOND : bond 0.01366 ( 6) SS BOND : angle 3.71998 ( 12) hydrogen bonds : bond 0.04932 ( 131) hydrogen bonds : angle 3.60208 ( 393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 138 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: C 162 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: G 32 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6573 (ptp-170) REVERT: G 95 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8470 (ttt90) REVERT: H 329 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8785 (pp) REVERT: H 331 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: H 362 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7462 (pt0) outliers start: 84 outliers final: 68 residues processed: 214 average time/residue: 0.1408 time to fit residues: 43.0020 Evaluate side-chains 211 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 137 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 319 ILE Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 362 GLN Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Chi-restraints excluded: chain L residue 376 SER Chi-restraints excluded: chain L residue 377 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 102 optimal weight: 0.0170 chunk 76 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 274 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.078521 restraints weight = 23195.806| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.86 r_work: 0.2730 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14999 Z= 0.100 Angle : 0.488 6.496 20504 Z= 0.246 Chirality : 0.045 0.160 2335 Planarity : 0.005 0.053 2680 Dihedral : 5.227 67.097 2049 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.45 % Allowed : 20.41 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.37 (0.20), residues: 1917 helix: -0.08 (0.31), residues: 326 sheet: 0.10 (0.21), residues: 629 loop : -0.43 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 87 TYR 0.007 0.001 TYR H 347 PHE 0.011 0.001 PHE G 231 TRP 0.011 0.001 TRP A 191 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00255 (14993) covalent geometry : angle 0.48350 (20492) SS BOND : bond 0.00857 ( 6) SS BOND : angle 2.70900 ( 12) hydrogen bonds : bond 0.03760 ( 131) hydrogen bonds : angle 3.41557 ( 393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7966 (pt0) REVERT: C 162 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7850 (mm-40) REVERT: C 260 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8834 (tp40) REVERT: C 328 MET cc_start: 0.9043 (tmm) cc_final: 0.8686 (ttp) REVERT: G 32 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6556 (ptp-170) REVERT: G 95 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8358 (ttt90) REVERT: G 109 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: H 329 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8780 (pp) REVERT: H 331 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.7895 (mm-40) outliers start: 56 outliers final: 42 residues processed: 189 average time/residue: 0.1517 time to fit residues: 40.3105 Evaluate side-chains 188 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 138 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 88 optimal weight: 0.2980 chunk 110 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 172 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.079882 restraints weight = 23031.726| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 1.87 r_work: 0.2755 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14999 Z= 0.089 Angle : 0.467 6.172 20504 Z= 0.234 Chirality : 0.044 0.155 2335 Planarity : 0.005 0.055 2680 Dihedral : 4.991 61.831 2049 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.39 % Allowed : 20.28 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.14 (0.20), residues: 1917 helix: -0.06 (0.31), residues: 338 sheet: 0.20 (0.21), residues: 659 loop : -0.18 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 87 TYR 0.007 0.001 TYR H 347 PHE 0.010 0.001 PHE G 231 TRP 0.010 0.001 TRP A 191 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00225 (14993) covalent geometry : angle 0.46359 (20492) SS BOND : bond 0.00744 ( 6) SS BOND : angle 2.50540 ( 12) hydrogen bonds : bond 0.03324 ( 131) hydrogen bonds : angle 3.16816 ( 393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 141 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: B 251 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: C 162 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: C 328 MET cc_start: 0.8962 (tmm) cc_final: 0.8589 (ttp) REVERT: G 32 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6530 (ptp-170) REVERT: G 95 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8313 (ttt90) REVERT: G 109 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8467 (mt0) REVERT: H 329 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8742 (pp) REVERT: H 331 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.7836 (mm-40) REVERT: H 362 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7366 (pt0) outliers start: 55 outliers final: 41 residues processed: 190 average time/residue: 0.1513 time to fit residues: 40.3424 Evaluate side-chains 187 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 362 GLN Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 134 optimal weight: 0.0370 chunk 158 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 overall best weight: 2.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** 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 = 0.3039 r_free = 0.3039 target = 0.092145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.079096 restraints weight = 22956.264| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.85 r_work: 0.2735 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14999 Z= 0.107 Angle : 0.483 6.086 20504 Z= 0.243 Chirality : 0.045 0.153 2335 Planarity : 0.005 0.053 2680 Dihedral : 4.755 58.130 2046 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.45 % Allowed : 19.91 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.18 (0.20), residues: 1917 helix: -0.04 (0.31), residues: 338 sheet: 0.18 (0.20), residues: 664 loop : -0.24 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.008 0.001 TYR G 321 PHE 0.009 0.001 PHE G 231 TRP 0.009 0.001 TRP C 191 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00274 (14993) covalent geometry : angle 0.47899 (20492) SS BOND : bond 0.00905 ( 6) SS BOND : angle 2.73737 ( 12) hydrogen bonds : bond 0.03732 ( 131) hydrogen bonds : angle 3.18568 ( 393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 139 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: C 162 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: C 328 MET cc_start: 0.9014 (tmm) cc_final: 0.8625 (ttp) REVERT: G 32 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6540 (ptp-170) REVERT: G 95 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8299 (ttt90) REVERT: G 109 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: H 329 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8755 (pp) REVERT: H 331 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.7850 (mm-40) REVERT: H 362 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7414 (pt0) outliers start: 56 outliers final: 46 residues processed: 189 average time/residue: 0.1404 time to fit residues: 37.8301 Evaluate side-chains 191 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 362 GLN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 10.0000 chunk 167 optimal weight: 0.3980 chunk 136 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 163 optimal weight: 0.0980 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 173 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** 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 = 0.3043 r_free = 0.3043 target = 0.092410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.079208 restraints weight = 23106.525| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.87 r_work: 0.2736 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14999 Z= 0.102 Angle : 0.480 6.066 20504 Z= 0.240 Chirality : 0.045 0.153 2335 Planarity : 0.005 0.053 2680 Dihedral : 4.664 56.001 2046 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.58 % Allowed : 19.67 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.14 (0.20), residues: 1917 helix: -0.01 (0.31), residues: 338 sheet: 0.19 (0.20), residues: 666 loop : -0.21 (0.22), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.007 0.001 TYR H 145 PHE 0.010 0.001 PHE G 231 TRP 0.009 0.001 TRP A 191 HIS 0.001 0.000 HIS G 215 Details of bonding type rmsd covalent geometry : bond 0.00264 (14993) covalent geometry : angle 0.47522 (20492) SS BOND : bond 0.00875 ( 6) SS BOND : angle 2.69323 ( 12) hydrogen bonds : bond 0.03637 ( 131) hydrogen bonds : angle 3.19209 ( 393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 141 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: C 162 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7893 (mm-40) REVERT: C 328 MET cc_start: 0.9009 (tmm) cc_final: 0.8618 (ttp) REVERT: G 32 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6380 (ptp-170) REVERT: G 95 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8369 (ttt90) REVERT: G 109 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: H 329 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8753 (pp) REVERT: H 331 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: H 362 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7399 (pt0) outliers start: 58 outliers final: 50 residues processed: 192 average time/residue: 0.1441 time to fit residues: 39.0872 Evaluate side-chains 197 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 140 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 362 GLN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Chi-restraints excluded: chain L residue 376 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 20 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 0.0020 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 144 ASN ** 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 = 0.3048 r_free = 0.3048 target = 0.092714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.079457 restraints weight = 23119.780| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.86 r_work: 0.2748 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14999 Z= 0.099 Angle : 0.480 6.052 20504 Z= 0.241 Chirality : 0.045 0.154 2335 Planarity : 0.005 0.053 2680 Dihedral : 4.553 53.660 2046 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.51 % Allowed : 19.85 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.11 (0.20), residues: 1917 helix: 0.02 (0.31), residues: 338 sheet: 0.22 (0.20), residues: 667 loop : -0.20 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 87 TYR 0.007 0.001 TYR G 321 PHE 0.010 0.001 PHE G 231 TRP 0.009 0.001 TRP A 191 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00254 (14993) covalent geometry : angle 0.47597 (20492) SS BOND : bond 0.00841 ( 6) SS BOND : angle 2.61415 ( 12) hydrogen bonds : bond 0.03549 ( 131) hydrogen bonds : angle 3.16247 ( 393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3834 Ramachandran restraints generated. 1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: C 162 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: C 328 MET cc_start: 0.8991 (tmm) cc_final: 0.8599 (ttp) REVERT: G 32 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6380 (ptp-170) REVERT: G 95 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8325 (ttt90) REVERT: G 109 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: H 329 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8754 (pp) REVERT: H 331 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: H 362 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7399 (pt0) outliers start: 57 outliers final: 50 residues processed: 191 average time/residue: 0.1484 time to fit residues: 40.3532 Evaluate side-chains 196 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain E residue 375 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 ASP Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 32 ARG Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 189 THR Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain H residue 255 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 362 GLN Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain L residue 372 SER Chi-restraints excluded: chain L residue 376 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 91 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 165 optimal weight: 0.1980 chunk 13 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN ** G 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.091987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.078807 restraints weight = 23032.134| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.85 r_work: 0.2744 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14999 Z= 0.117 Angle : 0.497 6.120 20504 Z= 0.251 Chirality : 0.046 0.154 2335 Planarity : 0.005 0.052 2680 Dihedral : 4.562 51.550 2046 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.70 % Allowed : 19.61 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.13 (0.20), residues: 1917 helix: -0.02 (0.31), residues: 338 sheet: 0.31 (0.21), residues: 622 loop : -0.27 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 87 TYR 0.008 0.001 TYR G 321 PHE 0.008 0.001 PHE G 231 TRP 0.008 0.001 TRP C 191 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd covalent geometry : bond 0.00299 (14993) covalent geometry : angle 0.49176 (20492) SS BOND : bond 0.00996 ( 6) SS BOND : angle 2.94151 ( 12) hydrogen bonds : bond 0.03950 ( 131) hydrogen bonds : angle 3.19516 ( 393) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.57 seconds wall clock time: 63 minutes 44.01 seconds (3824.01 seconds total)