Starting phenix.real_space_refine on Mon Sep 23 19:58:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/09_2024/8ade_15361.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/09_2024/8ade_15361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/09_2024/8ade_15361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/09_2024/8ade_15361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/09_2024/8ade_15361.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/09_2024/8ade_15361.cif" } resolution = 2.78 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= 0.002 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 7 5.16 5 C 3255 2.51 5 N 826 2.21 5 O 938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5026 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 2.30, per 1000 atoms: 0.46 Number of scatterers: 5026 At special positions: 0 Unit cell: (68.64, 85.28, 50.96, 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 7 16.00 O 938 8.00 N 826 7.00 C 3255 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 672.0 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.253A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS C 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 12 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS D 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 12 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS E 15 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 12 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS F 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL E 14 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU F 12 " --> pdb=" O MET G 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS G 15 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL F 14 " --> pdb=" O LYS G 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.802A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL F 20 " --> pdb=" O ARG G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.403A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR D 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU D 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR F 59 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU G 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU F 61 " --> pdb=" O GLU G 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.474A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU B 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 72 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU D 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU E 72 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU F 72 " --> pdb=" O ILE G 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 7.031A pdb=" N TRP A 79 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP B 79 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 80 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP C 79 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS D 80 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP D 79 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS E 80 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP E 79 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS F 80 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP F 79 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS G 80 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 98 Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AB1, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.486A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 109 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 109 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA D 109 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA E 109 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA F 109 " --> pdb=" O LEU G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.857A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR F 114 " --> pdb=" O SER G 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 114 hydrogen bonds defined for protein. 342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 902 1.33 - 1.45: 1317 1.45 - 1.57: 2912 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 5145 Sorted by residual: bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" N ILE E 26 " pdb=" CA ILE E 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.37e+01 bond pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.36e+01 bond pdb=" N ILE G 26 " pdb=" CA ILE G 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.36e+01 ... (remaining 5140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 4654 1.46 - 2.91: 1910 2.91 - 4.37: 366 4.37 - 5.83: 42 5.83 - 7.28: 28 Bond angle restraints: 7000 Sorted by residual: angle pdb=" C PRO B 24 " pdb=" CA PRO B 24 " pdb=" CB PRO B 24 " ideal model delta sigma weight residual 110.95 104.89 6.06 1.31e+00 5.83e-01 2.14e+01 angle pdb=" C PRO C 24 " pdb=" CA PRO C 24 " pdb=" CB PRO C 24 " ideal model delta sigma weight residual 110.95 104.91 6.04 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C PRO E 24 " pdb=" CA PRO E 24 " pdb=" CB PRO E 24 " ideal model delta sigma weight residual 110.95 104.91 6.04 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C PRO A 24 " pdb=" CA PRO A 24 " pdb=" CB PRO A 24 " ideal model delta sigma weight residual 110.95 104.92 6.03 1.31e+00 5.83e-01 2.12e+01 angle pdb=" C PRO D 24 " pdb=" CA PRO D 24 " pdb=" CB PRO D 24 " ideal model delta sigma weight residual 110.95 104.93 6.02 1.31e+00 5.83e-01 2.11e+01 ... (remaining 6995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.52: 2737 11.52 - 23.03: 238 23.03 - 34.55: 42 34.55 - 46.07: 0 46.07 - 57.58: 14 Dihedral angle restraints: 3031 sinusoidal: 1148 harmonic: 1883 Sorted by residual: dihedral pdb=" C PRO C 24 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " pdb=" CB PRO C 24 " ideal model delta harmonic sigma weight residual -120.70 -112.66 -8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C PRO B 24 " pdb=" N PRO B 24 " pdb=" CA PRO B 24 " pdb=" CB PRO B 24 " ideal model delta harmonic sigma weight residual -120.70 -112.66 -8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C PRO E 24 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " pdb=" CB PRO E 24 " ideal model delta harmonic sigma weight residual -120.70 -112.67 -8.03 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 3028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 209 0.047 - 0.094: 249 0.094 - 0.141: 203 0.141 - 0.189: 116 0.189 - 0.236: 49 Chirality restraints: 826 Sorted by residual: chirality pdb=" CA ILE F 68 " pdb=" N ILE F 68 " pdb=" C ILE F 68 " pdb=" CB ILE F 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE E 68 " pdb=" N ILE E 68 " pdb=" C ILE E 68 " pdb=" CB ILE E 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 823 not shown) Planarity restraints: 861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 114 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C TYR C 114 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR C 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 114 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C TYR A 114 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR A 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 114 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C TYR E 114 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR E 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER E 115 " 0.015 2.00e-02 2.50e+03 ... (remaining 858 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 406 2.75 - 3.29: 5005 3.29 - 3.82: 8088 3.82 - 4.36: 11472 4.36 - 4.90: 20635 Nonbonded interactions: 45606 Sorted by model distance: nonbonded pdb=" O SER A 117 " pdb=" OG SER B 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER D 117 " pdb=" OG SER E 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER C 117 " pdb=" OG SER D 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER B 117 " pdb=" OG SER C 117 " model vdw 2.213 3.040 nonbonded pdb=" O SER F 117 " pdb=" OG SER G 117 " model vdw 2.213 3.040 ... (remaining 45601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.012 0.042 5145 Z= 0.832 Angle : 1.581 7.283 7000 Z= 1.154 Chirality : 0.107 0.236 826 Planarity : 0.005 0.026 861 Dihedral : 9.637 57.583 1813 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.12 (0.23), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP E 79 HIS 0.003 0.001 HIS B 90 PHE 0.004 0.001 PHE G 33 TYR 0.006 0.001 TYR C 116 ARG 0.002 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.8874 (m) cc_final: 0.8558 (p) REVERT: C 123 THR cc_start: 0.7245 (t) cc_final: 0.6610 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.1685 time to fit residues: 218.8238 Evaluate side-chains 132 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5145 Z= 0.338 Angle : 0.677 6.850 7000 Z= 0.353 Chirality : 0.050 0.164 826 Planarity : 0.005 0.045 861 Dihedral : 5.178 16.565 693 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.30 % Allowed : 17.95 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.22 (0.25), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.19), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 79 HIS 0.002 0.001 HIS B 88 PHE 0.013 0.002 PHE B 33 TYR 0.016 0.002 TYR E 114 ARG 0.009 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7230 (tm-30) REVERT: B 99 ASP cc_start: 0.6966 (t0) cc_final: 0.6706 (t0) REVERT: B 104 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7175 (ttm110) REVERT: C 92 GLU cc_start: 0.7889 (pt0) cc_final: 0.7527 (tm-30) REVERT: D 92 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7247 (tm-30) REVERT: E 21 ARG cc_start: 0.8342 (mmm160) cc_final: 0.7822 (tpp80) REVERT: F 34 ARG cc_start: 0.8004 (tpt-90) cc_final: 0.7674 (ttt90) REVERT: G 13 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7120 (tmt) outliers start: 18 outliers final: 4 residues processed: 147 average time/residue: 1.5613 time to fit residues: 236.5286 Evaluate side-chains 120 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 5145 Z= 0.367 Angle : 0.665 7.271 7000 Z= 0.348 Chirality : 0.051 0.162 826 Planarity : 0.005 0.048 861 Dihedral : 5.316 16.571 693 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.11 % Allowed : 20.70 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.04 (0.26), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.003 0.001 HIS D 88 PHE 0.011 0.002 PHE B 33 TYR 0.019 0.002 TYR F 114 ARG 0.007 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: B 104 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7144 (ttm110) REVERT: C 92 GLU cc_start: 0.8108 (pt0) cc_final: 0.7770 (tm-30) REVERT: D 92 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7503 (tm-30) REVERT: E 13 MET cc_start: 0.7602 (tmt) cc_final: 0.6744 (tmt) REVERT: E 21 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7879 (tpp80) REVERT: E 26 ILE cc_start: 0.8599 (pt) cc_final: 0.8398 (mt) REVERT: F 21 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7818 (tpp80) REVERT: G 13 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7291 (tmt) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 1.7274 time to fit residues: 223.9465 Evaluate side-chains 121 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5145 Z= 0.332 Angle : 0.619 6.625 7000 Z= 0.325 Chirality : 0.050 0.135 826 Planarity : 0.004 0.049 861 Dihedral : 5.243 16.868 693 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.11 % Allowed : 21.61 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.92 (0.26), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 79 HIS 0.002 0.001 HIS D 88 PHE 0.008 0.002 PHE B 33 TYR 0.016 0.002 TYR C 114 ARG 0.008 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: B 104 ARG cc_start: 0.7771 (ttp-110) cc_final: 0.7240 (ttm110) REVERT: C 92 GLU cc_start: 0.8076 (pt0) cc_final: 0.7739 (tm-30) REVERT: D 13 MET cc_start: 0.7263 (tmt) cc_final: 0.7026 (tpt) REVERT: D 21 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7658 (mmm-85) REVERT: D 92 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7569 (tm-30) REVERT: E 13 MET cc_start: 0.7514 (tmt) cc_final: 0.6734 (tmt) REVERT: E 21 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7879 (tpp80) REVERT: E 26 ILE cc_start: 0.8597 (pt) cc_final: 0.8371 (mt) REVERT: F 13 MET cc_start: 0.7498 (tmt) cc_final: 0.7261 (tmt) REVERT: F 21 ARG cc_start: 0.8153 (mmm-85) cc_final: 0.7829 (tpp80) REVERT: G 13 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7234 (tmt) REVERT: G 80 LYS cc_start: 0.8168 (tttt) cc_final: 0.7889 (tttm) outliers start: 17 outliers final: 9 residues processed: 117 average time/residue: 1.8303 time to fit residues: 219.8425 Evaluate side-chains 119 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5145 Z= 0.268 Angle : 0.597 5.830 7000 Z= 0.312 Chirality : 0.049 0.142 826 Planarity : 0.004 0.052 861 Dihedral : 5.114 16.343 693 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.93 % Allowed : 21.79 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.86 (0.27), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.002 0.000 HIS A 88 PHE 0.007 0.001 PHE C 33 TYR 0.014 0.002 TYR C 114 ARG 0.009 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: B 104 ARG cc_start: 0.7754 (ttp-110) cc_final: 0.7260 (ttm110) REVERT: C 92 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: D 21 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7645 (mmm-85) REVERT: D 92 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7502 (tm-30) REVERT: E 13 MET cc_start: 0.7537 (tmt) cc_final: 0.6747 (tmt) REVERT: E 21 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7872 (tpp80) REVERT: E 104 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7271 (ttp-110) REVERT: F 21 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7831 (tpp80) REVERT: F 76 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8000 (mptt) REVERT: G 13 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7281 (tmt) REVERT: G 34 ARG cc_start: 0.8154 (tpt-90) cc_final: 0.7893 (tpt-90) REVERT: G 80 LYS cc_start: 0.8137 (tttt) cc_final: 0.7816 (tttm) outliers start: 16 outliers final: 4 residues processed: 115 average time/residue: 1.8937 time to fit residues: 223.6104 Evaluate side-chains 111 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5145 Z= 0.324 Angle : 0.614 5.504 7000 Z= 0.320 Chirality : 0.050 0.148 826 Planarity : 0.004 0.054 861 Dihedral : 5.200 17.373 693 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.48 % Allowed : 22.16 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.69 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 79 HIS 0.002 0.001 HIS A 88 PHE 0.006 0.002 PHE E 64 TYR 0.014 0.002 TYR C 114 ARG 0.011 0.001 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 106 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7831 (tm-30) REVERT: B 92 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: D 13 MET cc_start: 0.7291 (tmt) cc_final: 0.6913 (tpt) REVERT: D 21 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7632 (mmm-85) REVERT: D 92 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7547 (tm-30) REVERT: E 13 MET cc_start: 0.7547 (tmt) cc_final: 0.6784 (tmt) REVERT: E 21 ARG cc_start: 0.8313 (mmm160) cc_final: 0.7903 (tpp80) REVERT: F 13 MET cc_start: 0.7603 (tmt) cc_final: 0.7344 (tmt) REVERT: F 21 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7825 (tpp80) REVERT: F 35 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8091 (ttmt) REVERT: G 13 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7307 (tmt) REVERT: G 34 ARG cc_start: 0.8175 (tpt-90) cc_final: 0.7920 (tpt-90) REVERT: G 80 LYS cc_start: 0.8139 (tttt) cc_final: 0.7844 (tttm) outliers start: 19 outliers final: 9 residues processed: 114 average time/residue: 1.7723 time to fit residues: 207.4645 Evaluate side-chains 113 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5145 Z= 0.375 Angle : 0.654 6.733 7000 Z= 0.342 Chirality : 0.051 0.151 826 Planarity : 0.005 0.061 861 Dihedral : 5.305 18.395 693 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.48 % Allowed : 22.71 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.61 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 79 HIS 0.005 0.001 HIS F 90 PHE 0.007 0.002 PHE A 33 TYR 0.013 0.002 TYR C 114 ARG 0.013 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7816 (tm-30) REVERT: D 13 MET cc_start: 0.7332 (tmt) cc_final: 0.6844 (tpt) REVERT: D 21 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7429 (mmm-85) REVERT: D 92 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7718 (tm-30) REVERT: E 13 MET cc_start: 0.7533 (tmt) cc_final: 0.6815 (tmt) REVERT: E 21 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7856 (tpp80) REVERT: F 21 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7828 (tpp80) REVERT: G 13 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7299 (tmt) REVERT: G 34 ARG cc_start: 0.8192 (tpt-90) cc_final: 0.7935 (tpt-90) REVERT: G 66 GLU cc_start: 0.7608 (tt0) cc_final: 0.7361 (tt0) REVERT: G 80 LYS cc_start: 0.8156 (tttt) cc_final: 0.7871 (tttm) outliers start: 19 outliers final: 12 residues processed: 117 average time/residue: 1.6819 time to fit residues: 202.4320 Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 0.0970 chunk 5 optimal weight: 0.0170 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.0970 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5145 Z= 0.254 Angle : 0.625 7.674 7000 Z= 0.321 Chirality : 0.050 0.166 826 Planarity : 0.005 0.058 861 Dihedral : 5.133 16.666 693 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.38 % Allowed : 24.54 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.62 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.002 0.000 HIS C 88 PHE 0.007 0.001 PHE E 64 TYR 0.013 0.002 TYR C 114 ARG 0.013 0.001 ARG B 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7815 (tm-30) REVERT: B 92 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: D 13 MET cc_start: 0.7324 (tmt) cc_final: 0.6860 (tpt) REVERT: D 21 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7382 (mmm-85) REVERT: D 92 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7708 (tm-30) REVERT: E 13 MET cc_start: 0.7577 (tmt) cc_final: 0.6887 (tmt) REVERT: E 21 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7839 (tpp80) REVERT: F 13 MET cc_start: 0.7571 (tmt) cc_final: 0.7328 (tmt) REVERT: F 21 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7822 (tpp80) REVERT: G 13 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7301 (tmt) REVERT: G 34 ARG cc_start: 0.8211 (tpt-90) cc_final: 0.7979 (tpt-90) REVERT: G 66 GLU cc_start: 0.7589 (tt0) cc_final: 0.7338 (tt0) REVERT: G 80 LYS cc_start: 0.8061 (tttt) cc_final: 0.7794 (tttm) outliers start: 13 outliers final: 7 residues processed: 115 average time/residue: 1.7593 time to fit residues: 207.9403 Evaluate side-chains 110 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 41 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5145 Z= 0.270 Angle : 0.645 9.834 7000 Z= 0.329 Chirality : 0.049 0.145 826 Planarity : 0.005 0.064 861 Dihedral : 5.112 16.552 693 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.38 % Allowed : 24.73 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.59 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.002 0.000 HIS A 88 PHE 0.007 0.001 PHE E 64 TYR 0.013 0.002 TYR C 114 ARG 0.020 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7821 (tm-30) REVERT: B 92 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7759 (tm-30) REVERT: B 104 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7643 (ttm110) REVERT: D 13 MET cc_start: 0.7335 (tmt) cc_final: 0.6869 (tpt) REVERT: D 21 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7430 (mmm-85) REVERT: D 92 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7716 (tm-30) REVERT: E 13 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6885 (tmt) REVERT: E 21 ARG cc_start: 0.8293 (mmm160) cc_final: 0.7881 (tpp80) REVERT: F 13 MET cc_start: 0.7625 (tmt) cc_final: 0.7345 (tmt) REVERT: F 21 ARG cc_start: 0.8191 (mmm-85) cc_final: 0.7839 (tpp80) REVERT: F 35 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8019 (ttmt) REVERT: F 104 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7641 (ttm110) REVERT: G 13 MET cc_start: 0.7585 (tmm) cc_final: 0.7295 (tmt) REVERT: G 34 ARG cc_start: 0.8203 (tpt-90) cc_final: 0.7980 (tpt-90) REVERT: G 80 LYS cc_start: 0.8065 (tttt) cc_final: 0.7781 (tttm) outliers start: 13 outliers final: 8 residues processed: 112 average time/residue: 1.9703 time to fit residues: 226.5745 Evaluate side-chains 114 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.0000 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5145 Z= 0.248 Angle : 0.626 7.093 7000 Z= 0.322 Chirality : 0.050 0.168 826 Planarity : 0.005 0.069 861 Dihedral : 5.058 16.514 693 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.20 % Allowed : 25.46 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.002 0.000 HIS A 88 PHE 0.006 0.001 PHE E 64 TYR 0.012 0.002 TYR E 114 ARG 0.020 0.001 ARG E 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7812 (tm-30) REVERT: B 92 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: D 13 MET cc_start: 0.7357 (tmt) cc_final: 0.6875 (tpt) REVERT: D 21 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7578 (mmm-85) REVERT: D 92 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7717 (tm-30) REVERT: E 13 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6873 (tmt) REVERT: E 21 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7878 (tpp80) REVERT: F 21 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7839 (tpp80) REVERT: F 35 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8012 (ttmt) REVERT: F 104 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7631 (ttm110) REVERT: G 13 MET cc_start: 0.7585 (tmm) cc_final: 0.7295 (tmt) REVERT: G 34 ARG cc_start: 0.8197 (tpt-90) cc_final: 0.7983 (tpt-90) REVERT: G 80 LYS cc_start: 0.8002 (tttt) cc_final: 0.7736 (tttm) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 1.8121 time to fit residues: 202.7887 Evaluate side-chains 113 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.146095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.121152 restraints weight = 5742.377| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.53 r_work: 0.3833 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 5145 Z= 0.444 Angle : 0.699 6.936 7000 Z= 0.368 Chirality : 0.051 0.162 826 Planarity : 0.005 0.059 861 Dihedral : 5.434 18.701 693 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.20 % Allowed : 25.46 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.45 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 79 HIS 0.003 0.001 HIS A 88 PHE 0.007 0.002 PHE A 33 TYR 0.012 0.002 TYR F 114 ARG 0.019 0.001 ARG E 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.91 seconds wall clock time: 63 minutes 50.05 seconds (3830.05 seconds total)