Starting phenix.real_space_refine on Mon Jul 28 00:39:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xqj_33398/07_2025/7xqj_33398.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xqj_33398/07_2025/7xqj_33398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xqj_33398/07_2025/7xqj_33398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xqj_33398/07_2025/7xqj_33398.map" model { file = "/net/cci-nas-00/data/ceres_data/7xqj_33398/07_2025/7xqj_33398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xqj_33398/07_2025/7xqj_33398.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 54 5.16 5 C 6642 2.51 5 N 1590 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9960 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1660 Classifications: {'peptide': 204} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.98, per 1000 atoms: 0.40 Number of scatterers: 9960 At special positions: 0 Unit cell: (102.608, 104.304, 101.76, 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 54 16.00 O 1674 8.00 N 1590 7.00 C 6642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.04 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 73.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS A 13 " --> pdb=" O LYS A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 removed outlier: 3.738A pdb=" N ARG A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.943A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 85 removed outlier: 3.523A pdb=" N PHE A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 Processing helix chain 'A' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 removed outlier: 3.739A pdb=" N ARG B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.944A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 177 Processing helix chain 'B' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS C 13 " --> pdb=" O LYS C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.739A pdb=" N ARG C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.545A pdb=" N GLY C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.943A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 177 Processing helix chain 'C' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.738A pdb=" N ARG D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.944A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 85 removed outlier: 3.523A pdb=" N PHE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 177 Processing helix chain 'D' and resid 202 through 238 removed outlier: 3.718A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.738A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 40 removed outlier: 3.544A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.943A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 177 Processing helix chain 'E' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 removed outlier: 4.903A pdb=" N LYS F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 removed outlier: 3.739A pdb=" N ARG F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 40 removed outlier: 3.545A pdb=" N GLY F 38 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.944A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.874A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 85 removed outlier: 3.522A pdb=" N PHE F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 89 through 107 removed outlier: 3.714A pdb=" N LEU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 177 Processing helix chain 'F' and resid 202 through 238 removed outlier: 3.717A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.503A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.503A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.503A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.503A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.503A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.502A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1890 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: 2.68 Time building geometry restraints manager: 3.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2934 1.34 - 1.46: 2224 1.46 - 1.57: 4988 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 10218 Sorted by residual: bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.31e+00 bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.21e+00 bond pdb=" C VAL A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 ... (remaining 10213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 13172 1.65 - 3.30: 508 3.30 - 4.95: 108 4.95 - 6.61: 24 6.61 - 8.26: 12 Bond angle restraints: 13824 Sorted by residual: angle pdb=" N GLU B 42 " pdb=" CA GLU B 42 " pdb=" C GLU B 42 " ideal model delta sigma weight residual 112.90 107.89 5.01 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N GLU A 42 " pdb=" CA GLU A 42 " pdb=" C GLU A 42 " ideal model delta sigma weight residual 112.90 107.90 5.00 1.31e+00 5.83e-01 1.46e+01 angle pdb=" N GLU D 42 " pdb=" CA GLU D 42 " pdb=" C GLU D 42 " ideal model delta sigma weight residual 112.90 107.91 4.99 1.31e+00 5.83e-01 1.45e+01 angle pdb=" N GLU C 42 " pdb=" CA GLU C 42 " pdb=" C GLU C 42 " ideal model delta sigma weight residual 112.90 107.93 4.97 1.31e+00 5.83e-01 1.44e+01 angle pdb=" N GLU F 42 " pdb=" CA GLU F 42 " pdb=" C GLU F 42 " ideal model delta sigma weight residual 112.90 107.93 4.97 1.31e+00 5.83e-01 1.44e+01 ... (remaining 13819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 5149 13.83 - 27.65: 479 27.65 - 41.48: 210 41.48 - 55.30: 120 55.30 - 69.13: 54 Dihedral angle restraints: 6012 sinusoidal: 2430 harmonic: 3582 Sorted by residual: dihedral pdb=" CA PRO B 193 " pdb=" C PRO B 193 " pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PRO F 193 " pdb=" C PRO F 193 " pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA PRO A 193 " pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta harmonic sigma weight residual 180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 998 0.035 - 0.071: 373 0.071 - 0.106: 157 0.106 - 0.141: 32 0.141 - 0.177: 12 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA ALA E 6 " pdb=" N ALA E 6 " pdb=" C ALA E 6 " pdb=" CB ALA E 6 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ALA C 6 " pdb=" N ALA C 6 " pdb=" C ALA C 6 " pdb=" CB ALA C 6 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ALA F 6 " pdb=" N ALA F 6 " pdb=" C ALA F 6 " pdb=" CB ALA F 6 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.17 2.00e-01 2.50e+01 7.60e-01 ... (remaining 1569 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 87 " 0.035 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO A 88 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 87 " 0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO F 88 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 88 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 87 " 0.035 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO E 88 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 88 " 0.030 5.00e-02 4.00e+02 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3939 2.90 - 3.40: 9991 3.40 - 3.90: 16156 3.90 - 4.40: 15725 4.40 - 4.90: 27759 Nonbonded interactions: 73570 Sorted by model distance: nonbonded pdb=" O ALA C 40 " pdb=" OG SER C 43 " model vdw 2.401 3.040 nonbonded pdb=" O ALA D 40 " pdb=" OG SER D 43 " model vdw 2.402 3.040 nonbonded pdb=" O ALA A 40 " pdb=" OG SER A 43 " model vdw 2.402 3.040 nonbonded pdb=" O ALA F 40 " pdb=" OG SER F 43 " model vdw 2.402 3.040 nonbonded pdb=" O ALA E 40 " pdb=" OG SER E 43 " model vdw 2.402 3.040 ... (remaining 73565 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.200 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:3.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.007 0.049 10236 Z= 0.316 Angle : 0.838 8.257 13860 Z= 0.488 Chirality : 0.045 0.177 1572 Planarity : 0.007 0.052 1662 Dihedral : 15.982 69.127 3642 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 6.01 % Allowed : 11.48 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.20), residues: 1200 helix: -1.68 (0.14), residues: 822 sheet: 2.82 (0.55), residues: 60 loop : -2.92 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 25 HIS 0.003 0.001 HIS E 74 PHE 0.011 0.002 PHE C 97 TYR 0.008 0.001 TYR D 92 ARG 0.004 0.001 ARG F 148 Details of bonding type rmsd hydrogen bonds : bond 0.12044 ( 636) hydrogen bonds : angle 4.80179 ( 1890) SS BOND : bond 0.00378 ( 18) SS BOND : angle 0.60095 ( 36) covalent geometry : bond 0.00665 (10218) covalent geometry : angle 0.83804 (13824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 259 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7359 (p90) REVERT: A 47 ASP cc_start: 0.8821 (p0) cc_final: 0.8566 (p0) REVERT: A 100 MET cc_start: 0.9574 (ttp) cc_final: 0.8899 (tmm) REVERT: A 101 ARG cc_start: 0.9461 (ttm170) cc_final: 0.9100 (ttp-110) REVERT: A 213 MET cc_start: 0.9231 (mmm) cc_final: 0.8886 (mmp) REVERT: A 224 ASN cc_start: 0.8962 (m110) cc_final: 0.8571 (m110) REVERT: A 227 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9124 (tm-30) REVERT: B 17 TYR cc_start: 0.8703 (OUTLIER) cc_final: 0.7252 (p90) REVERT: B 100 MET cc_start: 0.9586 (ttp) cc_final: 0.9010 (ppp) REVERT: B 101 ARG cc_start: 0.9385 (ttm170) cc_final: 0.9025 (ttp-110) REVERT: B 104 GLU cc_start: 0.9417 (tp30) cc_final: 0.9077 (mm-30) REVERT: B 224 ASN cc_start: 0.8974 (m110) cc_final: 0.8561 (m110) REVERT: B 227 GLU cc_start: 0.9443 (tm-30) cc_final: 0.9010 (tm-30) REVERT: C 17 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7324 (p90) REVERT: C 100 MET cc_start: 0.9549 (ttp) cc_final: 0.9031 (ppp) REVERT: C 101 ARG cc_start: 0.9407 (ttm170) cc_final: 0.9029 (ttp-110) REVERT: C 227 GLU cc_start: 0.9469 (tm-30) cc_final: 0.9242 (tm-30) REVERT: D 17 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7089 (p90) REVERT: D 47 ASP cc_start: 0.8790 (p0) cc_final: 0.8497 (p0) REVERT: D 81 GLN cc_start: 0.9439 (tt0) cc_final: 0.9198 (tt0) REVERT: D 100 MET cc_start: 0.9557 (ttp) cc_final: 0.9050 (tmm) REVERT: D 101 ARG cc_start: 0.9439 (ttm170) cc_final: 0.9220 (ttp-110) REVERT: D 104 GLU cc_start: 0.9472 (tp30) cc_final: 0.9245 (mm-30) REVERT: D 213 MET cc_start: 0.9251 (mmm) cc_final: 0.8935 (mmp) REVERT: D 224 ASN cc_start: 0.9021 (m110) cc_final: 0.8658 (m110) REVERT: D 227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9191 (tm-30) REVERT: E 17 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7235 (p90) REVERT: E 100 MET cc_start: 0.9585 (ttp) cc_final: 0.9013 (ppp) REVERT: E 101 ARG cc_start: 0.9386 (ttm170) cc_final: 0.9019 (ttp-110) REVERT: E 104 GLU cc_start: 0.9413 (tp30) cc_final: 0.9076 (mm-30) REVERT: E 224 ASN cc_start: 0.8972 (m110) cc_final: 0.8559 (m110) REVERT: E 227 GLU cc_start: 0.9438 (tm-30) cc_final: 0.9021 (tm-30) REVERT: F 17 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7395 (p90) REVERT: F 100 MET cc_start: 0.9553 (ttp) cc_final: 0.9040 (ppp) REVERT: F 101 ARG cc_start: 0.9408 (ttm170) cc_final: 0.9036 (ttp-110) REVERT: F 227 GLU cc_start: 0.9468 (tm-30) cc_final: 0.9238 (tm-30) outliers start: 66 outliers final: 13 residues processed: 307 average time/residue: 0.2437 time to fit residues: 105.9831 Evaluate side-chains 204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 74 HIS A 224 ASN B 74 HIS B 81 GLN B 224 ASN C 74 HIS D 15 GLN D 74 HIS D 224 ASN E 74 HIS E 81 GLN E 224 ASN F 74 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.069446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053155 restraints weight = 41936.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.054895 restraints weight = 20896.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.056002 restraints weight = 13698.992| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10236 Z= 0.200 Angle : 0.756 8.445 13860 Z= 0.389 Chirality : 0.040 0.151 1572 Planarity : 0.005 0.035 1662 Dihedral : 7.748 53.973 1352 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 7.29 % Allowed : 19.22 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1200 helix: 0.46 (0.18), residues: 846 sheet: 2.87 (0.58), residues: 60 loop : -2.88 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 25 HIS 0.003 0.001 HIS C 74 PHE 0.014 0.001 PHE C 30 TYR 0.010 0.001 TYR E 92 ARG 0.005 0.001 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 636) hydrogen bonds : angle 3.61189 ( 1890) SS BOND : bond 0.00542 ( 18) SS BOND : angle 3.57271 ( 36) covalent geometry : bond 0.00432 (10218) covalent geometry : angle 0.73497 (13824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 183 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7568 (p90) REVERT: A 100 MET cc_start: 0.9404 (ttp) cc_final: 0.9133 (ppp) REVERT: A 101 ARG cc_start: 0.9397 (ttm170) cc_final: 0.9065 (ttp80) REVERT: A 213 MET cc_start: 0.9212 (mmm) cc_final: 0.8897 (mmp) REVERT: A 224 ASN cc_start: 0.8861 (m-40) cc_final: 0.8488 (m110) REVERT: A 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9102 (tm-30) REVERT: B 17 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7451 (p90) REVERT: B 48 GLU cc_start: 0.9070 (tp30) cc_final: 0.8435 (tm-30) REVERT: B 100 MET cc_start: 0.9405 (ttp) cc_final: 0.9185 (ppp) REVERT: B 101 ARG cc_start: 0.9328 (ttm170) cc_final: 0.9038 (ttp-110) REVERT: B 224 ASN cc_start: 0.8930 (m-40) cc_final: 0.8497 (m110) REVERT: B 227 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9036 (tm-30) REVERT: C 17 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7439 (p90) REVERT: C 48 GLU cc_start: 0.9061 (tp30) cc_final: 0.8379 (tm-30) REVERT: C 100 MET cc_start: 0.9369 (ttp) cc_final: 0.9056 (ppp) REVERT: C 101 ARG cc_start: 0.9346 (ttm170) cc_final: 0.9129 (ttp80) REVERT: C 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9195 (tm-30) REVERT: D 17 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7284 (p90) REVERT: D 35 LEU cc_start: 0.9454 (tp) cc_final: 0.9248 (tp) REVERT: D 47 ASP cc_start: 0.8782 (p0) cc_final: 0.8558 (p0) REVERT: D 48 GLU cc_start: 0.9056 (tp30) cc_final: 0.8545 (tm-30) REVERT: D 100 MET cc_start: 0.9415 (ttp) cc_final: 0.9189 (ppp) REVERT: D 101 ARG cc_start: 0.9376 (ttm170) cc_final: 0.9149 (ttp80) REVERT: D 213 MET cc_start: 0.9249 (mmm) cc_final: 0.8971 (mmp) REVERT: D 224 ASN cc_start: 0.8903 (m-40) cc_final: 0.8542 (m110) REVERT: D 227 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9150 (tm-30) REVERT: E 17 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7447 (p90) REVERT: E 48 GLU cc_start: 0.9083 (tp30) cc_final: 0.8436 (tm-30) REVERT: E 100 MET cc_start: 0.9407 (ttp) cc_final: 0.9186 (ppp) REVERT: E 101 ARG cc_start: 0.9336 (ttm170) cc_final: 0.9121 (ttp80) REVERT: E 224 ASN cc_start: 0.8937 (m-40) cc_final: 0.8504 (m110) REVERT: E 227 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9034 (tm-30) REVERT: F 17 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.7445 (p90) REVERT: F 35 LEU cc_start: 0.9341 (tp) cc_final: 0.9137 (tp) REVERT: F 48 GLU cc_start: 0.9054 (tp30) cc_final: 0.8345 (tm-30) REVERT: F 100 MET cc_start: 0.9364 (ttp) cc_final: 0.9056 (ppp) REVERT: F 101 ARG cc_start: 0.9347 (ttm170) cc_final: 0.9127 (ttp80) REVERT: F 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9199 (tm-30) outliers start: 80 outliers final: 35 residues processed: 241 average time/residue: 0.2337 time to fit residues: 83.5451 Evaluate side-chains 210 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 61 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain F residue 228 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 100 optimal weight: 0.0970 chunk 74 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN E 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054108 restraints weight = 42104.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055895 restraints weight = 20913.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.057067 restraints weight = 13598.192| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10236 Z= 0.136 Angle : 0.712 8.301 13860 Z= 0.364 Chirality : 0.040 0.170 1572 Planarity : 0.004 0.035 1662 Dihedral : 7.535 54.182 1352 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 6.92 % Allowed : 19.76 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1200 helix: 0.97 (0.18), residues: 852 sheet: 2.68 (0.59), residues: 60 loop : -2.73 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 25 HIS 0.002 0.001 HIS D 194 PHE 0.014 0.001 PHE B 30 TYR 0.015 0.001 TYR D 92 ARG 0.003 0.000 ARG E 53 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 636) hydrogen bonds : angle 3.53016 ( 1890) SS BOND : bond 0.00196 ( 18) SS BOND : angle 3.81427 ( 36) covalent geometry : bond 0.00305 (10218) covalent geometry : angle 0.68626 (13824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 188 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7455 (p90) REVERT: A 48 GLU cc_start: 0.9084 (tp30) cc_final: 0.8314 (tm-30) REVERT: A 49 GLN cc_start: 0.8774 (tt0) cc_final: 0.8555 (tp40) REVERT: A 100 MET cc_start: 0.9400 (ttp) cc_final: 0.9150 (ppp) REVERT: A 101 ARG cc_start: 0.9394 (ttm170) cc_final: 0.9072 (ttp-110) REVERT: A 213 MET cc_start: 0.9182 (mmm) cc_final: 0.8845 (mmp) REVERT: A 224 ASN cc_start: 0.8832 (m-40) cc_final: 0.8457 (m110) REVERT: A 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9077 (tm-30) REVERT: B 17 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.7435 (p90) REVERT: B 48 GLU cc_start: 0.9024 (tp30) cc_final: 0.8469 (tm-30) REVERT: B 101 ARG cc_start: 0.9312 (ttm170) cc_final: 0.8909 (ttp-110) REVERT: B 224 ASN cc_start: 0.8873 (m-40) cc_final: 0.8464 (m110) REVERT: B 227 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9017 (tm-30) REVERT: C 17 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7473 (p90) REVERT: C 42 GLU cc_start: 0.8933 (tp30) cc_final: 0.8649 (tp30) REVERT: C 48 GLU cc_start: 0.9029 (tp30) cc_final: 0.8426 (tm-30) REVERT: C 100 MET cc_start: 0.9304 (ttp) cc_final: 0.9071 (ppp) REVERT: C 101 ARG cc_start: 0.9360 (ttm170) cc_final: 0.9036 (ttp-110) REVERT: C 227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9186 (tm-30) REVERT: D 17 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.7134 (p90) REVERT: D 48 GLU cc_start: 0.9073 (tp30) cc_final: 0.8418 (tm-30) REVERT: D 49 GLN cc_start: 0.8779 (tt0) cc_final: 0.8393 (tp40) REVERT: D 100 MET cc_start: 0.9398 (ttp) cc_final: 0.9182 (ppp) REVERT: D 213 MET cc_start: 0.9208 (mmm) cc_final: 0.8912 (mmp) REVERT: D 224 ASN cc_start: 0.8889 (m-40) cc_final: 0.8519 (m110) REVERT: D 227 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9145 (tm-30) REVERT: E 17 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7501 (p90) REVERT: E 48 GLU cc_start: 0.9018 (tp30) cc_final: 0.8463 (tm-30) REVERT: E 101 ARG cc_start: 0.9326 (ttm170) cc_final: 0.8910 (ttp-110) REVERT: E 224 ASN cc_start: 0.8893 (m-40) cc_final: 0.8472 (m110) REVERT: E 227 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9001 (tm-30) REVERT: F 17 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7458 (p90) REVERT: F 48 GLU cc_start: 0.9038 (tp30) cc_final: 0.8416 (tm-30) REVERT: F 100 MET cc_start: 0.9300 (ttp) cc_final: 0.9067 (ppp) REVERT: F 101 ARG cc_start: 0.9361 (ttm170) cc_final: 0.9033 (ttp-110) REVERT: F 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9197 (tm-30) outliers start: 76 outliers final: 40 residues processed: 240 average time/residue: 0.2273 time to fit residues: 80.8796 Evaluate side-chains 218 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 194 HIS Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 194 HIS Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 194 HIS Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 194 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN E 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054348 restraints weight = 42084.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056142 restraints weight = 20738.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057331 restraints weight = 13488.800| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10236 Z= 0.133 Angle : 0.710 8.183 13860 Z= 0.362 Chirality : 0.039 0.177 1572 Planarity : 0.004 0.030 1662 Dihedral : 7.386 54.887 1350 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.19 % Allowed : 20.04 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1200 helix: 1.39 (0.19), residues: 822 sheet: 1.68 (0.63), residues: 66 loop : -2.26 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 25 HIS 0.003 0.001 HIS A 74 PHE 0.013 0.001 PHE B 30 TYR 0.016 0.001 TYR D 92 ARG 0.002 0.000 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03044 ( 636) hydrogen bonds : angle 3.49895 ( 1890) SS BOND : bond 0.00123 ( 18) SS BOND : angle 3.64425 ( 36) covalent geometry : bond 0.00304 (10218) covalent geometry : angle 0.68602 (13824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.7122 (p90) REVERT: A 47 ASP cc_start: 0.8802 (p0) cc_final: 0.8524 (p0) REVERT: A 48 GLU cc_start: 0.9116 (tp30) cc_final: 0.8595 (tm-30) REVERT: A 100 MET cc_start: 0.9402 (ttp) cc_final: 0.9154 (ppp) REVERT: A 101 ARG cc_start: 0.9412 (ttm170) cc_final: 0.9072 (ttp-110) REVERT: A 213 MET cc_start: 0.9133 (mmm) cc_final: 0.8819 (mmp) REVERT: A 224 ASN cc_start: 0.8807 (m-40) cc_final: 0.8418 (m110) REVERT: A 227 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9097 (tm-30) REVERT: B 17 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.7564 (p90) REVERT: B 48 GLU cc_start: 0.9050 (tp30) cc_final: 0.8509 (tm-30) REVERT: B 101 ARG cc_start: 0.9354 (ttm170) cc_final: 0.8940 (ttp-110) REVERT: B 224 ASN cc_start: 0.8853 (m-40) cc_final: 0.8617 (m110) REVERT: B 227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9030 (tm-30) REVERT: C 17 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.7511 (p90) REVERT: C 48 GLU cc_start: 0.9065 (tp30) cc_final: 0.8521 (tm-30) REVERT: C 62 GLU cc_start: 0.8483 (pp20) cc_final: 0.8246 (pp20) REVERT: C 100 MET cc_start: 0.9326 (ttp) cc_final: 0.9084 (ppp) REVERT: C 101 ARG cc_start: 0.9387 (ttm170) cc_final: 0.9034 (ttp-110) REVERT: C 227 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9207 (tm-30) REVERT: D 17 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.6737 (p90) REVERT: D 48 GLU cc_start: 0.9097 (tp30) cc_final: 0.8618 (tm-30) REVERT: D 49 GLN cc_start: 0.8814 (tt0) cc_final: 0.8600 (tt0) REVERT: D 100 MET cc_start: 0.9407 (ttp) cc_final: 0.9054 (tmm) REVERT: D 213 MET cc_start: 0.9199 (mmm) cc_final: 0.8915 (mmp) REVERT: D 224 ASN cc_start: 0.8860 (m-40) cc_final: 0.8476 (m110) REVERT: D 227 GLU cc_start: 0.9429 (tm-30) cc_final: 0.9152 (tm-30) REVERT: E 17 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7555 (p90) REVERT: E 48 GLU cc_start: 0.9075 (tp30) cc_final: 0.8513 (tm-30) REVERT: E 101 ARG cc_start: 0.9357 (ttm170) cc_final: 0.8935 (ttp-110) REVERT: E 224 ASN cc_start: 0.8860 (m-40) cc_final: 0.8628 (m110) REVERT: E 227 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9030 (tm-30) REVERT: F 17 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.7510 (p90) REVERT: F 48 GLU cc_start: 0.9079 (tp30) cc_final: 0.8503 (tm-30) REVERT: F 62 GLU cc_start: 0.8483 (pp20) cc_final: 0.8251 (pp20) REVERT: F 100 MET cc_start: 0.9321 (ttp) cc_final: 0.9082 (ppp) REVERT: F 101 ARG cc_start: 0.9382 (ttm170) cc_final: 0.9031 (ttp-110) REVERT: F 227 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9188 (tm-30) outliers start: 68 outliers final: 36 residues processed: 230 average time/residue: 0.1865 time to fit residues: 62.6444 Evaluate side-chains 212 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 224 ASN Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 224 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 9.9990 chunk 20 optimal weight: 0.0570 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.055668 restraints weight = 41889.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.057399 restraints weight = 20804.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058587 restraints weight = 13681.892| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10236 Z= 0.125 Angle : 0.702 8.220 13860 Z= 0.355 Chirality : 0.040 0.180 1572 Planarity : 0.004 0.031 1662 Dihedral : 6.696 54.175 1338 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.64 % Allowed : 21.86 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1200 helix: 1.52 (0.19), residues: 822 sheet: 1.87 (0.65), residues: 66 loop : -2.15 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 25 HIS 0.002 0.001 HIS A 74 PHE 0.016 0.001 PHE E 30 TYR 0.015 0.001 TYR D 92 ARG 0.003 0.000 ARG F 148 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 636) hydrogen bonds : angle 3.50484 ( 1890) SS BOND : bond 0.00051 ( 18) SS BOND : angle 3.54016 ( 36) covalent geometry : bond 0.00274 (10218) covalent geometry : angle 0.67887 (13824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.7361 (p90) REVERT: A 48 GLU cc_start: 0.9029 (tp30) cc_final: 0.8585 (tm-30) REVERT: A 100 MET cc_start: 0.9379 (ttp) cc_final: 0.9156 (ppp) REVERT: A 101 ARG cc_start: 0.9384 (ttm170) cc_final: 0.9069 (ttp-110) REVERT: A 213 MET cc_start: 0.9144 (mmm) cc_final: 0.8830 (mmp) REVERT: A 224 ASN cc_start: 0.8816 (m-40) cc_final: 0.8408 (m110) REVERT: A 227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9063 (tm-30) REVERT: B 17 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.7487 (p90) REVERT: B 48 GLU cc_start: 0.9003 (tp30) cc_final: 0.8554 (tm-30) REVERT: B 101 ARG cc_start: 0.9315 (ttm170) cc_final: 0.8988 (ttp-110) REVERT: B 224 ASN cc_start: 0.9070 (m-40) cc_final: 0.8637 (m110) REVERT: B 227 GLU cc_start: 0.9397 (tm-30) cc_final: 0.9006 (tm-30) REVERT: C 17 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7422 (p90) REVERT: C 62 GLU cc_start: 0.8479 (pp20) cc_final: 0.8231 (pp20) REVERT: C 100 MET cc_start: 0.9343 (ttp) cc_final: 0.9115 (ppp) REVERT: C 101 ARG cc_start: 0.9350 (ttm170) cc_final: 0.9033 (ttp-110) REVERT: C 227 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9184 (tm-30) REVERT: D 17 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.6929 (p90) REVERT: D 48 GLU cc_start: 0.9029 (tp30) cc_final: 0.8663 (tm-30) REVERT: D 100 MET cc_start: 0.9395 (ttp) cc_final: 0.8923 (ppp) REVERT: D 213 MET cc_start: 0.9221 (mmm) cc_final: 0.8943 (mmp) REVERT: D 224 ASN cc_start: 0.8880 (m-40) cc_final: 0.8474 (m110) REVERT: D 227 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9116 (tm-30) REVERT: E 17 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7492 (p90) REVERT: E 48 GLU cc_start: 0.8999 (tp30) cc_final: 0.8550 (tm-30) REVERT: E 101 ARG cc_start: 0.9318 (ttm170) cc_final: 0.8984 (ttp-110) REVERT: E 224 ASN cc_start: 0.9090 (m-40) cc_final: 0.8634 (m110) REVERT: E 227 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9009 (tm-30) REVERT: E 228 LEU cc_start: 0.9560 (tt) cc_final: 0.9274 (pp) REVERT: F 17 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7423 (p90) REVERT: F 62 GLU cc_start: 0.8471 (pp20) cc_final: 0.8226 (pp20) REVERT: F 100 MET cc_start: 0.9340 (ttp) cc_final: 0.9109 (ppp) REVERT: F 101 ARG cc_start: 0.9353 (ttm170) cc_final: 0.9032 (ttp-110) REVERT: F 227 GLU cc_start: 0.9407 (tm-30) cc_final: 0.9182 (tm-30) outliers start: 51 outliers final: 25 residues processed: 223 average time/residue: 0.1844 time to fit residues: 61.2016 Evaluate side-chains 203 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 67 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 41 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.0570 chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 106 optimal weight: 0.7980 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.072417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056506 restraints weight = 42114.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.058233 restraints weight = 20949.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.059414 restraints weight = 13831.962| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10236 Z= 0.121 Angle : 0.705 9.035 13860 Z= 0.358 Chirality : 0.041 0.180 1572 Planarity : 0.004 0.033 1662 Dihedral : 6.511 54.259 1336 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.10 % Allowed : 25.23 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1200 helix: 1.54 (0.19), residues: 822 sheet: 2.07 (0.68), residues: 66 loop : -2.09 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 25 HIS 0.002 0.001 HIS B 74 PHE 0.016 0.001 PHE E 30 TYR 0.017 0.001 TYR D 66 ARG 0.002 0.000 ARG D 148 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 636) hydrogen bonds : angle 3.51093 ( 1890) SS BOND : bond 0.00098 ( 18) SS BOND : angle 3.68569 ( 36) covalent geometry : bond 0.00257 (10218) covalent geometry : angle 0.68053 (13824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7209 (p90) REVERT: A 48 GLU cc_start: 0.8986 (tp30) cc_final: 0.8392 (tm-30) REVERT: A 49 GLN cc_start: 0.8789 (tt0) cc_final: 0.8448 (tp40) REVERT: A 100 MET cc_start: 0.9372 (ttp) cc_final: 0.9148 (ppp) REVERT: A 101 ARG cc_start: 0.9373 (ttm170) cc_final: 0.9101 (ptm-80) REVERT: A 213 MET cc_start: 0.9148 (mmm) cc_final: 0.8841 (mmp) REVERT: A 224 ASN cc_start: 0.8818 (m-40) cc_final: 0.8593 (m110) REVERT: A 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9071 (tm-30) REVERT: B 17 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7341 (p90) REVERT: B 101 ARG cc_start: 0.9341 (ttm170) cc_final: 0.9005 (ptm-80) REVERT: B 224 ASN cc_start: 0.9061 (m-40) cc_final: 0.8630 (m110) REVERT: B 227 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9003 (tm-30) REVERT: C 17 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.7318 (p90) REVERT: C 62 GLU cc_start: 0.8486 (pp20) cc_final: 0.8239 (pp20) REVERT: C 100 MET cc_start: 0.9348 (ttp) cc_final: 0.9115 (ppp) REVERT: C 101 ARG cc_start: 0.9353 (ttm170) cc_final: 0.9041 (ttp-110) REVERT: C 227 GLU cc_start: 0.9430 (tm-30) cc_final: 0.9199 (tm-30) REVERT: D 17 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.6685 (p90) REVERT: D 42 GLU cc_start: 0.8079 (pp20) cc_final: 0.7583 (pm20) REVERT: D 100 MET cc_start: 0.9123 (ttp) cc_final: 0.8657 (tmm) REVERT: D 104 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8378 (mm-30) REVERT: D 213 MET cc_start: 0.9194 (mmm) cc_final: 0.8934 (mmp) REVERT: D 224 ASN cc_start: 0.8854 (m-40) cc_final: 0.8457 (m110) REVERT: D 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9130 (tm-30) REVERT: E 17 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7333 (p90) REVERT: E 101 ARG cc_start: 0.9351 (ttm170) cc_final: 0.9003 (ptm-80) REVERT: E 227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9002 (tm-30) REVERT: E 228 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9204 (pp) REVERT: F 17 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7319 (p90) REVERT: F 62 GLU cc_start: 0.8476 (pp20) cc_final: 0.8237 (pp20) REVERT: F 100 MET cc_start: 0.9345 (ttp) cc_final: 0.9110 (ppp) REVERT: F 101 ARG cc_start: 0.9360 (ttm170) cc_final: 0.9039 (ttp-110) REVERT: F 227 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9196 (tm-30) outliers start: 45 outliers final: 31 residues processed: 222 average time/residue: 0.1786 time to fit residues: 58.3536 Evaluate side-chains 204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 0.0670 chunk 58 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.071273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055151 restraints weight = 42920.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.056888 restraints weight = 22226.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.058065 restraints weight = 14579.865| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10236 Z= 0.150 Angle : 0.709 11.127 13860 Z= 0.365 Chirality : 0.040 0.174 1572 Planarity : 0.004 0.033 1662 Dihedral : 6.317 55.127 1334 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 5.74 % Allowed : 26.32 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1200 helix: 1.56 (0.19), residues: 822 sheet: 2.07 (0.67), residues: 66 loop : -1.96 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP E 25 HIS 0.002 0.001 HIS A 194 PHE 0.025 0.001 PHE B 30 TYR 0.017 0.001 TYR D 92 ARG 0.002 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 636) hydrogen bonds : angle 3.54444 ( 1890) SS BOND : bond 0.00188 ( 18) SS BOND : angle 4.01164 ( 36) covalent geometry : bond 0.00339 (10218) covalent geometry : angle 0.67983 (13824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7341 (p90) REVERT: A 48 GLU cc_start: 0.9010 (tp30) cc_final: 0.8393 (tm-30) REVERT: A 49 GLN cc_start: 0.8902 (tt0) cc_final: 0.8415 (tp40) REVERT: A 100 MET cc_start: 0.9355 (ttp) cc_final: 0.9151 (ppp) REVERT: A 101 ARG cc_start: 0.9366 (ttm170) cc_final: 0.9071 (ttp-110) REVERT: A 213 MET cc_start: 0.9200 (mmm) cc_final: 0.8902 (mmp) REVERT: A 224 ASN cc_start: 0.9057 (m-40) cc_final: 0.8675 (m110) REVERT: A 227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9095 (tm-30) REVERT: B 17 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7412 (p90) REVERT: B 48 GLU cc_start: 0.8998 (tp30) cc_final: 0.8647 (tm-30) REVERT: B 101 ARG cc_start: 0.9477 (ttm170) cc_final: 0.9026 (ttp-110) REVERT: B 224 ASN cc_start: 0.9086 (m-40) cc_final: 0.8653 (m110) REVERT: B 227 GLU cc_start: 0.9405 (tm-30) cc_final: 0.9006 (tm-30) REVERT: C 17 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7443 (p90) REVERT: C 100 MET cc_start: 0.9351 (ttp) cc_final: 0.9127 (ppp) REVERT: C 101 ARG cc_start: 0.9363 (ttm170) cc_final: 0.9049 (ttp-110) REVERT: C 227 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9191 (tm-30) REVERT: D 17 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.6863 (p90) REVERT: D 100 MET cc_start: 0.9157 (ttp) cc_final: 0.8636 (tmm) REVERT: D 104 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8517 (mm-30) REVERT: D 213 MET cc_start: 0.9238 (mmm) cc_final: 0.8997 (mmp) REVERT: D 224 ASN cc_start: 0.8900 (m-40) cc_final: 0.8490 (m110) REVERT: D 227 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9131 (tm-30) REVERT: E 17 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7418 (p90) REVERT: E 48 GLU cc_start: 0.8991 (tp30) cc_final: 0.8612 (tm-30) REVERT: E 101 ARG cc_start: 0.9487 (ttm170) cc_final: 0.9023 (ttp-110) REVERT: E 227 GLU cc_start: 0.9410 (tm-30) cc_final: 0.9024 (tm-30) REVERT: E 228 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9256 (pp) REVERT: F 17 TYR cc_start: 0.8659 (OUTLIER) cc_final: 0.7451 (p90) REVERT: F 100 MET cc_start: 0.9341 (ttp) cc_final: 0.9132 (ppp) REVERT: F 101 ARG cc_start: 0.9342 (ttm170) cc_final: 0.9037 (ttp-110) REVERT: F 227 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9196 (tm-30) outliers start: 63 outliers final: 37 residues processed: 214 average time/residue: 0.1904 time to fit residues: 59.5297 Evaluate side-chains 209 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 30 PHE Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.2980 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.055652 restraints weight = 42230.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057375 restraints weight = 21201.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.058536 restraints weight = 13921.523| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10236 Z= 0.138 Angle : 0.760 11.881 13860 Z= 0.388 Chirality : 0.040 0.172 1572 Planarity : 0.004 0.034 1662 Dihedral : 6.229 55.682 1332 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.83 % Allowed : 26.68 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1200 helix: 1.58 (0.19), residues: 822 sheet: 2.10 (0.67), residues: 66 loop : -1.95 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 25 HIS 0.002 0.001 HIS E 74 PHE 0.025 0.001 PHE B 30 TYR 0.017 0.001 TYR B 92 ARG 0.003 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 636) hydrogen bonds : angle 3.59504 ( 1890) SS BOND : bond 0.00140 ( 18) SS BOND : angle 4.46034 ( 36) covalent geometry : bond 0.00312 (10218) covalent geometry : angle 0.72572 (13824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 172 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.6900 (p90) REVERT: A 48 GLU cc_start: 0.9001 (tp30) cc_final: 0.8621 (tm-30) REVERT: A 100 MET cc_start: 0.9355 (ttp) cc_final: 0.9149 (ppp) REVERT: A 101 ARG cc_start: 0.9363 (ttm170) cc_final: 0.9059 (ttp-110) REVERT: A 213 MET cc_start: 0.9189 (mmm) cc_final: 0.8892 (mmp) REVERT: A 227 GLU cc_start: 0.9437 (tm-30) cc_final: 0.9087 (tm-30) REVERT: B 17 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.7420 (p90) REVERT: B 48 GLU cc_start: 0.8993 (tp30) cc_final: 0.8674 (tm-30) REVERT: B 101 ARG cc_start: 0.9478 (ttm170) cc_final: 0.9015 (ttp-110) REVERT: B 224 ASN cc_start: 0.9092 (m-40) cc_final: 0.8650 (m110) REVERT: B 227 GLU cc_start: 0.9402 (tm-30) cc_final: 0.9002 (tm-30) REVERT: C 17 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7465 (p90) REVERT: C 62 GLU cc_start: 0.8585 (pp20) cc_final: 0.8328 (pp20) REVERT: C 100 MET cc_start: 0.9349 (ttp) cc_final: 0.9130 (ppp) REVERT: C 101 ARG cc_start: 0.9352 (ttm170) cc_final: 0.9029 (ttp-110) REVERT: C 227 GLU cc_start: 0.9427 (tm-30) cc_final: 0.9198 (tm-30) REVERT: D 42 GLU cc_start: 0.7920 (pm20) cc_final: 0.7478 (pm20) REVERT: D 47 ASP cc_start: 0.8697 (p0) cc_final: 0.8445 (p0) REVERT: D 100 MET cc_start: 0.9186 (ttp) cc_final: 0.8858 (tmm) REVERT: D 213 MET cc_start: 0.9229 (mmm) cc_final: 0.8979 (mmp) REVERT: D 227 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9117 (tm-30) REVERT: E 17 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7425 (p90) REVERT: E 48 GLU cc_start: 0.9010 (tp30) cc_final: 0.8693 (tm-30) REVERT: E 101 ARG cc_start: 0.9493 (ttm170) cc_final: 0.9014 (ttp-110) REVERT: E 227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9026 (tm-30) REVERT: E 228 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9236 (pp) REVERT: F 17 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7473 (p90) REVERT: F 62 GLU cc_start: 0.8571 (pp20) cc_final: 0.8325 (pp20) REVERT: F 100 MET cc_start: 0.9348 (ttp) cc_final: 0.9132 (ppp) REVERT: F 101 ARG cc_start: 0.9350 (ttm170) cc_final: 0.9024 (ttp-110) REVERT: F 227 GLU cc_start: 0.9432 (tm-30) cc_final: 0.9203 (tm-30) outliers start: 53 outliers final: 33 residues processed: 206 average time/residue: 0.1915 time to fit residues: 57.8085 Evaluate side-chains 205 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 65 CYS Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 65 CYS Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 81 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056780 restraints weight = 41947.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058539 restraints weight = 21033.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059715 restraints weight = 13797.478| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10236 Z= 0.131 Angle : 0.782 11.174 13860 Z= 0.397 Chirality : 0.041 0.170 1572 Planarity : 0.004 0.033 1662 Dihedral : 6.138 54.193 1332 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.19 % Allowed : 27.78 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1200 helix: 1.48 (0.19), residues: 822 sheet: 2.22 (0.67), residues: 66 loop : -1.93 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 25 HIS 0.002 0.001 HIS B 74 PHE 0.030 0.001 PHE E 30 TYR 0.017 0.001 TYR B 92 ARG 0.001 0.000 ARG D 101 Details of bonding type rmsd hydrogen bonds : bond 0.03207 ( 636) hydrogen bonds : angle 3.62616 ( 1890) SS BOND : bond 0.00178 ( 18) SS BOND : angle 4.44891 ( 36) covalent geometry : bond 0.00288 (10218) covalent geometry : angle 0.74989 (13824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 175 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.6800 (p90) REVERT: A 101 ARG cc_start: 0.9340 (ttm170) cc_final: 0.9091 (ptm-80) REVERT: A 213 MET cc_start: 0.9187 (mmm) cc_final: 0.8884 (mmp) REVERT: A 227 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9113 (tm-30) REVERT: B 17 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7298 (p90) REVERT: B 101 ARG cc_start: 0.9469 (ttm170) cc_final: 0.9025 (ttp80) REVERT: B 224 ASN cc_start: 0.9072 (m-40) cc_final: 0.8637 (m110) REVERT: B 227 GLU cc_start: 0.9386 (tm-30) cc_final: 0.8983 (tm-30) REVERT: C 17 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7247 (p90) REVERT: C 62 GLU cc_start: 0.8525 (pp20) cc_final: 0.8276 (pp20) REVERT: C 100 MET cc_start: 0.9343 (ttp) cc_final: 0.9135 (ppp) REVERT: C 101 ARG cc_start: 0.9345 (ttm170) cc_final: 0.9022 (ttp-110) REVERT: C 227 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9207 (tm-30) REVERT: D 47 ASP cc_start: 0.8666 (p0) cc_final: 0.8368 (p0) REVERT: D 81 GLN cc_start: 0.9425 (tt0) cc_final: 0.9211 (tt0) REVERT: D 100 MET cc_start: 0.9191 (ttp) cc_final: 0.8844 (tmm) REVERT: D 213 MET cc_start: 0.9215 (mmm) cc_final: 0.8952 (mmp) REVERT: D 227 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9111 (tm-30) REVERT: E 17 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7232 (p90) REVERT: E 48 GLU cc_start: 0.8947 (tp30) cc_final: 0.8654 (tm-30) REVERT: E 101 ARG cc_start: 0.9478 (ttm170) cc_final: 0.9013 (ttp-110) REVERT: E 227 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9017 (tm-30) REVERT: E 228 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9253 (pp) REVERT: F 17 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7269 (p90) REVERT: F 62 GLU cc_start: 0.8508 (pp20) cc_final: 0.8267 (pp20) REVERT: F 100 MET cc_start: 0.9335 (ttp) cc_final: 0.9134 (ppp) REVERT: F 101 ARG cc_start: 0.9331 (ttm170) cc_final: 0.9015 (ttp-110) REVERT: F 227 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9194 (tm-30) outliers start: 46 outliers final: 32 residues processed: 204 average time/residue: 0.1895 time to fit residues: 56.7272 Evaluate side-chains 207 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 87 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.072550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.056495 restraints weight = 42430.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058259 restraints weight = 21575.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059513 restraints weight = 14150.505| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10236 Z= 0.134 Angle : 0.791 11.081 13860 Z= 0.404 Chirality : 0.040 0.172 1572 Planarity : 0.004 0.035 1662 Dihedral : 6.147 54.476 1332 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.10 % Allowed : 27.50 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1200 helix: 1.46 (0.19), residues: 822 sheet: 2.29 (0.67), residues: 66 loop : -1.91 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP D 25 HIS 0.002 0.001 HIS A 95 PHE 0.030 0.001 PHE E 30 TYR 0.017 0.001 TYR B 92 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 636) hydrogen bonds : angle 3.67141 ( 1890) SS BOND : bond 0.00150 ( 18) SS BOND : angle 4.84236 ( 36) covalent geometry : bond 0.00297 (10218) covalent geometry : angle 0.75253 (13824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ARG cc_start: 0.9531 (ttm170) cc_final: 0.9160 (ttp80) REVERT: A 213 MET cc_start: 0.9181 (mmm) cc_final: 0.8911 (mmp) REVERT: A 227 GLU cc_start: 0.9459 (tm-30) cc_final: 0.9127 (tm-30) REVERT: B 17 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.7280 (p90) REVERT: B 48 GLU cc_start: 0.8986 (tp30) cc_final: 0.8718 (tm-30) REVERT: B 101 ARG cc_start: 0.9484 (ttm170) cc_final: 0.9032 (ttp80) REVERT: B 224 ASN cc_start: 0.9077 (m-40) cc_final: 0.8638 (m110) REVERT: B 227 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9003 (tm-30) REVERT: C 17 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7317 (p90) REVERT: C 100 MET cc_start: 0.9344 (ttp) cc_final: 0.9132 (ppp) REVERT: C 101 ARG cc_start: 0.9376 (ttm170) cc_final: 0.9026 (ttp-110) REVERT: C 227 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9211 (tm-30) REVERT: D 47 ASP cc_start: 0.8664 (p0) cc_final: 0.8369 (p0) REVERT: D 81 GLN cc_start: 0.9439 (tt0) cc_final: 0.9167 (tt0) REVERT: D 100 MET cc_start: 0.9213 (ttp) cc_final: 0.8865 (tmm) REVERT: D 213 MET cc_start: 0.9213 (mmm) cc_final: 0.8959 (mmp) REVERT: D 227 GLU cc_start: 0.9412 (tm-30) cc_final: 0.9117 (tm-30) REVERT: E 17 TYR cc_start: 0.8566 (OUTLIER) cc_final: 0.7289 (p90) REVERT: E 48 GLU cc_start: 0.8986 (tp30) cc_final: 0.8686 (tm-30) REVERT: E 101 ARG cc_start: 0.9490 (ttm170) cc_final: 0.9036 (ttp80) REVERT: E 227 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9045 (tm-30) REVERT: E 228 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9249 (pp) REVERT: F 17 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7318 (p90) REVERT: F 101 ARG cc_start: 0.9351 (ttm170) cc_final: 0.9022 (ttp-110) REVERT: F 227 GLU cc_start: 0.9440 (tm-30) cc_final: 0.9202 (tm-30) outliers start: 45 outliers final: 36 residues processed: 200 average time/residue: 0.2046 time to fit residues: 60.3865 Evaluate side-chains 213 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 30 PHE Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 192 CYS Chi-restraints excluded: chain D residue 194 HIS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 17 TYR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 67 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 4 optimal weight: 0.0040 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.072939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.057043 restraints weight = 41652.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058769 restraints weight = 20683.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.059989 restraints weight = 13552.104| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10236 Z= 0.133 Angle : 0.805 11.756 13860 Z= 0.409 Chirality : 0.040 0.169 1572 Planarity : 0.004 0.036 1662 Dihedral : 6.112 54.581 1332 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.19 % Allowed : 27.69 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1200 helix: 1.44 (0.19), residues: 822 sheet: 2.38 (0.67), residues: 66 loop : -1.90 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.001 TRP D 25 HIS 0.002 0.001 HIS F 95 PHE 0.030 0.001 PHE E 30 TYR 0.017 0.001 TYR B 92 ARG 0.005 0.000 ARG F 101 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 636) hydrogen bonds : angle 3.65990 ( 1890) SS BOND : bond 0.00107 ( 18) SS BOND : angle 4.69140 ( 36) covalent geometry : bond 0.00295 (10218) covalent geometry : angle 0.76936 (13824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3131.93 seconds wall clock time: 58 minutes 12.37 seconds (3492.37 seconds total)