Starting phenix.real_space_refine on Fri Mar 15 20:00:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/03_2024/3j6j_5925.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/03_2024/3j6j_5925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/03_2024/3j6j_5925.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/03_2024/3j6j_5925.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/03_2024/3j6j_5925.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6j_5925/03_2024/3j6j_5925.pdb" } resolution = 3.64 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= 0.032 sd= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6344 atoms to isotropic. 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 48 5.16 5 C 4040 2.51 5 N 1088 2.21 5 O 1168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 5": "OE1" <-> "OE2" Residue "D GLU 26": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "I" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 793 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Time building chain proxies: 3.76, per 1000 atoms: 0.59 Number of scatterers: 6344 At special positions: 0 Unit cell: (99, 96.8, 80.3, 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 48 16.00 O 1168 8.00 N 1088 7.00 C 4040 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 - 3.50 Amino acid : False - 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 Processing helix chain 'A' and resid 15 through 20 removed outlier: 4.052A pdb=" N PHE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 20' Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.686A pdb=" N HIS A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.651A pdb=" N TYR A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 16 through 20 removed outlier: 3.903A pdb=" N CYS B 20 " --> pdb=" O SER B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 35 through 50 removed outlier: 4.101A pdb=" N ASP B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 41 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 removed outlier: 3.529A pdb=" N TRP B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.660A pdb=" N TYR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 3.673A pdb=" N SER B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.705A pdb=" N ASP C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 63 removed outlier: 3.660A pdb=" N HIS C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.600A pdb=" N TYR C 71 " --> pdb=" O GLY C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'D' and resid 2 through 15 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.667A pdb=" N PHE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS D 20 " --> pdb=" O PHE D 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 15 through 20' Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 35 through 50 removed outlier: 4.090A pdb=" N ASP D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 63 removed outlier: 3.502A pdb=" N TRP D 56 " --> pdb=" O ARG D 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.953A pdb=" N PHE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 15 through 20' Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 35 through 50 removed outlier: 4.123A pdb=" N ASP E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 removed outlier: 3.865A pdb=" N TRP E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.836A pdb=" N TYR E 71 " --> pdb=" O GLY E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 15 through 20 removed outlier: 3.834A pdb=" N PHE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 15 through 20' Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 35 through 50 removed outlier: 3.985A pdb=" N ASP G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.666A pdb=" N TRP G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 3.537A pdb=" N TYR G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 95 removed outlier: 3.613A pdb=" N TYR G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 15 through 20 removed outlier: 3.668A pdb=" N PHE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS I 20 " --> pdb=" O PHE I 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 15 through 20' Processing helix chain 'I' and resid 23 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 35 through 50 removed outlier: 3.889A pdb=" N ASP I 40 " --> pdb=" O ALA I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 63 removed outlier: 3.992A pdb=" N TRP I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 removed outlier: 3.655A pdb=" N TYR I 71 " --> pdb=" O GLY I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 94 Processing helix chain 'L' and resid 2 through 15 Processing helix chain 'L' and resid 15 through 20 removed outlier: 3.564A pdb=" N PHE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS L 20 " --> pdb=" O PHE L 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 15 through 20' Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 35 through 50 removed outlier: 3.997A pdb=" N ASP L 40 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 63 removed outlier: 3.570A pdb=" N TRP L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 79 removed outlier: 3.710A pdb=" N TYR L 71 " --> pdb=" O GLY L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 94 396 hydrogen bonds defined for protein. 1185 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: 1.70 Time building geometry restraints manager: 2.53 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: 2016 1.33 - 1.46: 1206 1.46 - 1.58: 3218 1.58 - 1.70: 0 1.70 - 1.82: 56 Bond restraints: 6496 Sorted by residual: bond pdb=" C LEU L 28 " pdb=" N PRO L 29 " ideal model delta sigma weight residual 1.336 1.419 -0.083 1.20e-02 6.94e+03 4.81e+01 bond pdb=" N PRO L 29 " pdb=" CD PRO L 29 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.93e+00 bond pdb=" C ILE D 12 " pdb=" O ILE D 12 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.80e+00 bond pdb=" C ILE B 12 " pdb=" O ILE B 12 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.80e+00 bond pdb=" N CYS D 20 " pdb=" CA CYS D 20 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.62e+00 ... (remaining 6491 not shown) Histogram of bond angle deviations from ideal: 97.09 - 106.88: 198 106.88 - 116.66: 4334 116.66 - 126.45: 4219 126.45 - 136.23: 88 136.23 - 146.02: 1 Bond angle restraints: 8840 Sorted by residual: angle pdb=" N ARG A 37 " pdb=" CA ARG A 37 " pdb=" C ARG A 37 " ideal model delta sigma weight residual 111.36 119.53 -8.17 1.09e+00 8.42e-01 5.61e+01 angle pdb=" C LEU D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta sigma weight residual 119.87 127.63 -7.76 1.04e+00 9.25e-01 5.57e+01 angle pdb=" N ASN A 51 " pdb=" CA ASN A 51 " pdb=" C ASN A 51 " ideal model delta sigma weight residual 111.03 118.81 -7.78 1.11e+00 8.12e-01 4.91e+01 angle pdb=" CA PRO L 29 " pdb=" N PRO L 29 " pdb=" CD PRO L 29 " ideal model delta sigma weight residual 112.00 102.49 9.51 1.40e+00 5.10e-01 4.61e+01 angle pdb=" C LEU L 28 " pdb=" N PRO L 29 " pdb=" CA PRO L 29 " ideal model delta sigma weight residual 118.85 111.48 7.37 1.09e+00 8.42e-01 4.57e+01 ... (remaining 8835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 3418 16.97 - 33.94: 279 33.94 - 50.91: 111 50.91 - 67.88: 45 67.88 - 84.85: 3 Dihedral angle restraints: 3856 sinusoidal: 1536 harmonic: 2320 Sorted by residual: dihedral pdb=" CG ARG I 64 " pdb=" CD ARG I 64 " pdb=" NE ARG I 64 " pdb=" CZ ARG I 64 " ideal model delta sinusoidal sigma weight residual -90.00 -10.80 -79.20 2 1.50e+01 4.44e-03 2.06e+01 dihedral pdb=" CG ARG G 64 " pdb=" CD ARG G 64 " pdb=" NE ARG G 64 " pdb=" CZ ARG G 64 " ideal model delta sinusoidal sigma weight residual -90.00 -12.28 -77.72 2 1.50e+01 4.44e-03 2.04e+01 dihedral pdb=" CA LEU I 48 " pdb=" C LEU I 48 " pdb=" N SER I 49 " pdb=" CA SER I 49 " ideal model delta harmonic sigma weight residual -180.00 -163.64 -16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 770 0.069 - 0.137: 170 0.137 - 0.206: 23 0.206 - 0.275: 4 0.275 - 0.343: 1 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA LEU L 28 " pdb=" N LEU L 28 " pdb=" C LEU L 28 " pdb=" CB LEU L 28 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ARG A 37 " pdb=" N ARG A 37 " pdb=" C ARG A 37 " pdb=" CB ARG A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PHE D 19 " pdb=" N PHE D 19 " pdb=" C PHE D 19 " pdb=" CB PHE D 19 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 965 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 57 " -0.013 2.00e-02 2.50e+03 1.56e-02 3.63e+00 pdb=" CG HIS G 57 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS G 57 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS G 57 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS G 57 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS G 57 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 36 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ALA G 36 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA G 36 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG G 37 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 20 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C CYS A 20 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 20 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN A 21 " 0.010 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 27 2.24 - 2.91: 2828 2.91 - 3.57: 10142 3.57 - 4.24: 15508 4.24 - 4.90: 26180 Nonbonded interactions: 54685 Sorted by model distance: nonbonded pdb=" NH2 ARG A 37 " pdb=" OE2 GLU B 26 " model vdw 1.578 2.520 nonbonded pdb=" OE1 GLN B 39 " pdb=" CZ2 TRP C 56 " model vdw 1.753 3.340 nonbonded pdb=" NH2 ARG B 43 " pdb=" CH2 TRP C 56 " model vdw 1.838 3.420 nonbonded pdb=" OE1 GLN C 39 " pdb=" CZ2 TRP G 56 " model vdw 1.889 3.340 nonbonded pdb=" NH2 ARG B 43 " pdb=" CZ3 TRP C 56 " model vdw 1.926 3.420 ... (remaining 54680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.090 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 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 0.083 6496 Z= 0.452 Angle : 1.414 21.017 8840 Z= 0.997 Chirality : 0.058 0.343 968 Planarity : 0.005 0.036 1144 Dihedral : 15.900 84.850 2352 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 33.23 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.08 % Favored : 95.00 % Rotamer: Outliers : 6.10 % Allowed : 9.16 % Favored : 84.74 % 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: -1.46 (0.26), residues: 760 helix: -0.53 (0.19), residues: 536 sheet: None (None), residues: 0 loop : -1.78 (0.33), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 56 HIS 0.019 0.003 HIS G 57 PHE 0.021 0.002 PHE I 72 TYR 0.026 0.003 TYR G 30 ARG 0.012 0.001 ARG L 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 516 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9289 (mmtt) cc_final: 0.9074 (mmtm) REVERT: A 66 PRO cc_start: 0.9215 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: A 77 ARG cc_start: 0.8669 (mtt-85) cc_final: 0.8379 (mtp85) REVERT: A 82 VAL cc_start: 0.9016 (t) cc_final: 0.8698 (p) REVERT: B 14 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8738 (mtm-85) REVERT: B 24 VAL cc_start: 0.9299 (t) cc_final: 0.8624 (t) REVERT: B 35 THR cc_start: 0.9204 (m) cc_final: 0.8680 (m) REVERT: B 38 ASP cc_start: 0.9603 (t0) cc_final: 0.9261 (m-30) REVERT: B 77 ARG cc_start: 0.8949 (mtt-85) cc_final: 0.8473 (mmt90) REVERT: B 83 ASP cc_start: 0.9129 (m-30) cc_final: 0.8784 (m-30) REVERT: B 95 TYR cc_start: 0.8993 (m-80) cc_final: 0.8391 (m-80) REVERT: B 96 GLN cc_start: 0.7958 (mt0) cc_final: 0.7754 (mm-40) REVERT: C 3 PHE cc_start: 0.7767 (t80) cc_final: 0.7242 (t80) REVERT: C 21 ASN cc_start: 0.9164 (m110) cc_final: 0.8558 (m-40) REVERT: C 31 LEU cc_start: 0.9161 (mt) cc_final: 0.8903 (mt) REVERT: C 41 ARG cc_start: 0.9284 (ttt180) cc_final: 0.8894 (tpp80) REVERT: C 53 ASP cc_start: 0.9613 (m-30) cc_final: 0.9190 (m-30) REVERT: D 3 PHE cc_start: 0.8490 (t80) cc_final: 0.7684 (t80) REVERT: D 14 ARG cc_start: 0.8780 (ttp-110) cc_final: 0.8449 (mtm-85) REVERT: D 21 ASN cc_start: 0.9174 (m110) cc_final: 0.8873 (m-40) REVERT: D 35 THR cc_start: 0.8773 (m) cc_final: 0.8411 (p) REVERT: D 40 ASP cc_start: 0.8091 (m-30) cc_final: 0.7796 (m-30) REVERT: D 54 THR cc_start: 0.9471 (m) cc_final: 0.9148 (p) REVERT: E 9 TYR cc_start: 0.9417 (t80) cc_final: 0.9077 (t80) REVERT: E 23 ASP cc_start: 0.9264 (t70) cc_final: 0.9057 (t0) REVERT: E 35 THR cc_start: 0.8651 (m) cc_final: 0.8180 (p) REVERT: E 60 ASN cc_start: 0.9546 (t0) cc_final: 0.9279 (m110) REVERT: E 87 GLU cc_start: 0.8960 (tt0) cc_final: 0.8664 (tp30) REVERT: E 90 SER cc_start: 0.9179 (t) cc_final: 0.8827 (p) REVERT: G 5 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7779 (mt-10) REVERT: G 24 VAL cc_start: 0.9330 (t) cc_final: 0.9022 (m) REVERT: G 28 LEU cc_start: 0.9350 (mt) cc_final: 0.9050 (mt) REVERT: G 35 THR cc_start: 0.8615 (m) cc_final: 0.8237 (p) REVERT: G 76 LEU cc_start: 0.9456 (mt) cc_final: 0.9015 (mt) REVERT: I 14 ARG cc_start: 0.9140 (ttp-110) cc_final: 0.8839 (mtm-85) REVERT: I 24 VAL cc_start: 0.9488 (t) cc_final: 0.9102 (m) REVERT: I 53 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.8794 (m-30) REVERT: I 60 ASN cc_start: 0.9562 (t0) cc_final: 0.9317 (m110) REVERT: I 72 PHE cc_start: 0.9444 (t80) cc_final: 0.9172 (t80) REVERT: I 90 SER cc_start: 0.8871 (t) cc_final: 0.8571 (p) REVERT: L 21 ASN cc_start: 0.8869 (m110) cc_final: 0.8508 (m-40) REVERT: L 28 LEU cc_start: 0.8607 (mt) cc_final: 0.8371 (mt) REVERT: L 31 LEU cc_start: 0.9130 (mt) cc_final: 0.8905 (mt) REVERT: L 40 ASP cc_start: 0.8676 (m-30) cc_final: 0.8423 (m-30) REVERT: L 41 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8294 (ttm170) outliers start: 42 outliers final: 3 residues processed: 524 average time/residue: 0.2192 time to fit residues: 141.4684 Evaluate side-chains 467 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 462 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain L residue 41 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 57 HIS A 63 GLN A 96 GLN B 21 ASN B 60 ASN ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 21 ASN D 96 GLN E 18 ASN E 39 GLN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 57 HIS L 21 ASN L 39 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN L 96 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6496 Z= 0.274 Angle : 0.724 7.482 8840 Z= 0.379 Chirality : 0.042 0.149 968 Planarity : 0.006 0.047 1144 Dihedral : 5.928 50.814 896 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.97 % Favored : 97.76 % Rotamer: Outliers : 8.87 % Allowed : 25.58 % Favored : 65.55 % 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: 1.47 (0.28), residues: 760 helix: 1.10 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 0.91 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 56 HIS 0.002 0.001 HIS I 57 PHE 0.032 0.003 PHE G 59 TYR 0.025 0.002 TYR L 92 ARG 0.009 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 515 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 PHE cc_start: 0.9364 (t80) cc_final: 0.9158 (t80) REVERT: A 37 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7862 (ttp80) REVERT: A 51 ASN cc_start: 0.8523 (p0) cc_final: 0.8019 (t0) REVERT: A 52 ARG cc_start: 0.8920 (ptp-110) cc_final: 0.8537 (ptp-110) REVERT: A 55 LEU cc_start: 0.9204 (mt) cc_final: 0.8854 (mt) REVERT: A 64 ARG cc_start: 0.8940 (tpp80) cc_final: 0.8679 (tpp80) REVERT: A 96 GLN cc_start: 0.7779 (mt0) cc_final: 0.7321 (mm-40) REVERT: B 51 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7484 (t0) REVERT: B 54 THR cc_start: 0.9463 (m) cc_final: 0.9203 (p) REVERT: B 55 LEU cc_start: 0.9311 (mt) cc_final: 0.9010 (mt) REVERT: C 15 ASN cc_start: 0.9442 (m110) cc_final: 0.9193 (m110) REVERT: C 19 PHE cc_start: 0.8872 (m-80) cc_final: 0.8572 (m-80) REVERT: C 35 THR cc_start: 0.8991 (m) cc_final: 0.8425 (p) REVERT: C 38 ASP cc_start: 0.9561 (m-30) cc_final: 0.9098 (m-30) REVERT: C 41 ARG cc_start: 0.9431 (ttt180) cc_final: 0.9067 (ttp-170) REVERT: C 60 ASN cc_start: 0.9458 (t0) cc_final: 0.9171 (m-40) REVERT: D 3 PHE cc_start: 0.8367 (t80) cc_final: 0.8060 (t80) REVERT: D 16 PHE cc_start: 0.8827 (t80) cc_final: 0.8515 (t80) REVERT: D 53 ASP cc_start: 0.9078 (m-30) cc_final: 0.8392 (m-30) REVERT: D 57 HIS cc_start: 0.9809 (m-70) cc_final: 0.9556 (m-70) REVERT: D 87 GLU cc_start: 0.9144 (tt0) cc_final: 0.8929 (tp30) REVERT: E 3 PHE cc_start: 0.8948 (t80) cc_final: 0.8557 (t80) REVERT: E 7 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9083 (mmtm) REVERT: E 16 PHE cc_start: 0.9320 (t80) cc_final: 0.9059 (t80) REVERT: E 23 ASP cc_start: 0.9183 (t70) cc_final: 0.8521 (t0) REVERT: E 35 THR cc_start: 0.8768 (m) cc_final: 0.8410 (p) REVERT: E 51 ASN cc_start: 0.8697 (p0) cc_final: 0.8409 (t0) REVERT: E 60 ASN cc_start: 0.9731 (t0) cc_final: 0.9439 (m110) REVERT: E 77 ARG cc_start: 0.9069 (ttm110) cc_final: 0.8682 (mmt90) REVERT: E 95 TYR cc_start: 0.9044 (m-80) cc_final: 0.8805 (m-80) REVERT: G 5 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8214 (mt-10) REVERT: G 31 LEU cc_start: 0.9191 (mt) cc_final: 0.8976 (mm) REVERT: G 59 PHE cc_start: 0.9491 (m-80) cc_final: 0.9159 (m-80) REVERT: G 60 ASN cc_start: 0.9425 (t0) cc_final: 0.9170 (m110) REVERT: G 66 PRO cc_start: 0.9374 (Cg_exo) cc_final: 0.9145 (Cg_endo) REVERT: G 76 LEU cc_start: 0.9652 (mt) cc_final: 0.9401 (mt) REVERT: G 77 ARG cc_start: 0.9343 (tpp80) cc_final: 0.8853 (mmt90) REVERT: G 95 TYR cc_start: 0.8887 (m-80) cc_final: 0.8687 (m-80) REVERT: I 14 ARG cc_start: 0.9227 (ttp-110) cc_final: 0.8721 (mtm-85) REVERT: I 38 ASP cc_start: 0.9420 (m-30) cc_final: 0.8767 (p0) REVERT: I 77 ARG cc_start: 0.9251 (ttm110) cc_final: 0.8797 (mmt90) REVERT: I 90 SER cc_start: 0.9392 (t) cc_final: 0.9128 (p) REVERT: I 96 GLN cc_start: 0.8596 (mt0) cc_final: 0.7826 (tp40) REVERT: L 14 ARG cc_start: 0.8828 (ttp-110) cc_final: 0.7786 (mtp-110) REVERT: L 26 GLU cc_start: 0.9148 (mp0) cc_final: 0.8849 (mp0) REVERT: L 41 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8329 (ttp-110) REVERT: L 54 THR cc_start: 0.9443 (m) cc_final: 0.9241 (p) REVERT: L 59 PHE cc_start: 0.9524 (m-80) cc_final: 0.8972 (m-80) REVERT: L 64 ARG cc_start: 0.9372 (mmt90) cc_final: 0.9139 (mmm-85) outliers start: 61 outliers final: 36 residues processed: 526 average time/residue: 0.2157 time to fit residues: 140.5211 Evaluate side-chains 529 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 492 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 51 ASN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain I residue 18 ASN Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 53 ASP Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 96 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN B 96 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 63 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN G 18 ASN G 39 GLN I 15 ASN ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6496 Z= 0.258 Angle : 0.694 8.360 8840 Z= 0.361 Chirality : 0.043 0.143 968 Planarity : 0.007 0.083 1144 Dihedral : 4.638 18.182 880 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.32 % Favored : 98.42 % Rotamer: Outliers : 10.32 % Allowed : 29.36 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.66 (0.29), residues: 760 helix: 1.06 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 1.79 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 56 HIS 0.002 0.001 HIS A 57 PHE 0.030 0.003 PHE G 59 TYR 0.027 0.002 TYR D 92 ARG 0.013 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 506 time to evaluate : 0.773 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 3 PHE cc_start: 0.9415 (t80) cc_final: 0.9119 (t80) REVERT: A 14 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8599 (mtm-85) REVERT: A 51 ASN cc_start: 0.8546 (p0) cc_final: 0.8271 (t0) REVERT: A 52 ARG cc_start: 0.9018 (ptp-110) cc_final: 0.8464 (ptp-110) REVERT: A 55 LEU cc_start: 0.9131 (mt) cc_final: 0.8831 (mt) REVERT: A 77 ARG cc_start: 0.8947 (mmt-90) cc_final: 0.8684 (mmt180) REVERT: A 96 GLN cc_start: 0.7575 (mt0) cc_final: 0.7346 (mm110) REVERT: B 14 ARG cc_start: 0.9232 (ttp-110) cc_final: 0.8870 (mtm-85) REVERT: B 16 PHE cc_start: 0.9161 (t80) cc_final: 0.8889 (t80) REVERT: B 53 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: B 54 THR cc_start: 0.9451 (m) cc_final: 0.9212 (p) REVERT: B 77 ARG cc_start: 0.9127 (mtt-85) cc_final: 0.8897 (mmt180) REVERT: C 9 TYR cc_start: 0.9140 (t80) cc_final: 0.8719 (t80) REVERT: C 14 ARG cc_start: 0.8887 (mtm-85) cc_final: 0.8528 (mtm-85) REVERT: C 35 THR cc_start: 0.8985 (m) cc_final: 0.8539 (p) REVERT: C 38 ASP cc_start: 0.9501 (m-30) cc_final: 0.9205 (m-30) REVERT: C 41 ARG cc_start: 0.9328 (ttt180) cc_final: 0.9060 (ttp-170) REVERT: C 86 ASP cc_start: 0.9363 (p0) cc_final: 0.9118 (p0) REVERT: D 14 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8651 (mtm-85) REVERT: D 37 ARG cc_start: 0.8703 (ttt180) cc_final: 0.8269 (tmm-80) REVERT: D 41 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8349 (ttm110) REVERT: D 57 HIS cc_start: 0.9782 (m-70) cc_final: 0.9572 (m-70) REVERT: D 77 ARG cc_start: 0.9349 (ttm110) cc_final: 0.9040 (mmt90) REVERT: E 3 PHE cc_start: 0.9069 (t80) cc_final: 0.8710 (t80) REVERT: E 7 LYS cc_start: 0.9341 (mmtt) cc_final: 0.8960 (mmtm) REVERT: E 35 THR cc_start: 0.8979 (m) cc_final: 0.8655 (p) REVERT: E 51 ASN cc_start: 0.8894 (p0) cc_final: 0.8635 (p0) REVERT: E 60 ASN cc_start: 0.9742 (t0) cc_final: 0.9525 (t0) REVERT: E 77 ARG cc_start: 0.9103 (ttm110) cc_final: 0.8742 (mmt180) REVERT: E 95 TYR cc_start: 0.9195 (m-80) cc_final: 0.8508 (m-80) REVERT: G 14 ARG cc_start: 0.8966 (mtm-85) cc_final: 0.8718 (mtm-85) REVERT: G 24 VAL cc_start: 0.9614 (m) cc_final: 0.9368 (p) REVERT: G 38 ASP cc_start: 0.9527 (m-30) cc_final: 0.9275 (m-30) REVERT: G 45 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9344 (t) REVERT: G 64 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8796 (mmm-85) REVERT: G 71 TYR cc_start: 0.9493 (m-80) cc_final: 0.9208 (m-80) REVERT: G 72 PHE cc_start: 0.9668 (t80) cc_final: 0.9332 (t80) REVERT: G 76 LEU cc_start: 0.9729 (mt) cc_final: 0.9429 (mt) REVERT: G 77 ARG cc_start: 0.9398 (tpp80) cc_final: 0.8954 (mmt90) REVERT: G 90 SER cc_start: 0.9514 (OUTLIER) cc_final: 0.9212 (p) REVERT: G 95 TYR cc_start: 0.9157 (m-80) cc_final: 0.8833 (m-80) REVERT: I 14 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8781 (mtm-85) REVERT: I 24 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9228 (p) REVERT: I 37 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8610 (ptm-80) REVERT: I 38 ASP cc_start: 0.9420 (m-30) cc_final: 0.9051 (p0) REVERT: I 41 ARG cc_start: 0.9260 (mmm-85) cc_final: 0.8743 (tpp80) REVERT: I 77 ARG cc_start: 0.9299 (ttm110) cc_final: 0.9001 (mmt90) REVERT: I 95 TYR cc_start: 0.9275 (m-80) cc_final: 0.9039 (m-80) REVERT: I 96 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: L 21 ASN cc_start: 0.9019 (m-40) cc_final: 0.8716 (m110) REVERT: L 26 GLU cc_start: 0.9335 (mp0) cc_final: 0.8955 (mp0) REVERT: L 41 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8430 (ttm110) REVERT: L 42 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9262 (mm) REVERT: L 64 ARG cc_start: 0.9393 (mmt90) cc_final: 0.9165 (mmm-85) outliers start: 71 outliers final: 44 residues processed: 513 average time/residue: 0.2300 time to fit residues: 145.6970 Evaluate side-chains 541 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 488 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 90 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 18 ASN Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.0970 chunk 49 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS C 63 GLN C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 HIS ** I 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.8228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6496 Z= 0.210 Angle : 0.674 8.056 8840 Z= 0.347 Chirality : 0.041 0.152 968 Planarity : 0.005 0.050 1144 Dihedral : 4.485 18.870 880 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.84 % Favored : 97.89 % Rotamer: Outliers : 8.28 % Allowed : 34.59 % Favored : 57.12 % 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: 1.47 (0.29), residues: 760 helix: 0.82 (0.20), residues: 600 sheet: None (None), residues: 0 loop : 2.20 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 56 HIS 0.001 0.000 HIS A 57 PHE 0.031 0.003 PHE I 16 TYR 0.023 0.002 TYR D 92 ARG 0.008 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 490 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8656 (mtm-85) REVERT: A 51 ASN cc_start: 0.8423 (p0) cc_final: 0.7892 (t0) REVERT: A 52 ARG cc_start: 0.8987 (ptp-110) cc_final: 0.8493 (ptp-110) REVERT: A 55 LEU cc_start: 0.9059 (mt) cc_final: 0.8609 (mt) REVERT: A 64 ARG cc_start: 0.9027 (tpp80) cc_final: 0.8608 (tpp80) REVERT: B 14 ARG cc_start: 0.9217 (ttp-110) cc_final: 0.8851 (mtm-85) REVERT: B 16 PHE cc_start: 0.9057 (t80) cc_final: 0.8046 (t80) REVERT: B 54 THR cc_start: 0.9440 (m) cc_final: 0.9215 (p) REVERT: B 77 ARG cc_start: 0.9359 (mtt-85) cc_final: 0.9037 (mmt180) REVERT: B 87 GLU cc_start: 0.9549 (tp30) cc_final: 0.9312 (tp30) REVERT: C 3 PHE cc_start: 0.8668 (t80) cc_final: 0.8154 (t80) REVERT: C 9 TYR cc_start: 0.9222 (t80) cc_final: 0.9004 (t80) REVERT: C 14 ARG cc_start: 0.8991 (mtm-85) cc_final: 0.8698 (mtm-85) REVERT: C 19 PHE cc_start: 0.9215 (m-80) cc_final: 0.8914 (m-80) REVERT: C 35 THR cc_start: 0.8950 (m) cc_final: 0.8249 (p) REVERT: C 38 ASP cc_start: 0.9424 (m-30) cc_final: 0.9143 (m-30) REVERT: C 40 ASP cc_start: 0.9190 (p0) cc_final: 0.8951 (p0) REVERT: C 41 ARG cc_start: 0.9334 (ttt180) cc_final: 0.9017 (ttp-170) REVERT: C 54 THR cc_start: 0.9758 (t) cc_final: 0.9382 (m) REVERT: C 63 GLN cc_start: 0.9625 (OUTLIER) cc_final: 0.9302 (pp30) REVERT: D 14 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8635 (mtm-85) REVERT: D 37 ARG cc_start: 0.8817 (ttt180) cc_final: 0.8581 (tmm-80) REVERT: D 77 ARG cc_start: 0.9273 (ttm110) cc_final: 0.8959 (mmt90) REVERT: D 87 GLU cc_start: 0.9421 (tt0) cc_final: 0.9200 (tp30) REVERT: E 3 PHE cc_start: 0.9019 (t80) cc_final: 0.8680 (t80) REVERT: E 7 LYS cc_start: 0.9354 (mmtt) cc_final: 0.8984 (mmtm) REVERT: E 71 TYR cc_start: 0.9520 (m-80) cc_final: 0.9209 (m-80) REVERT: E 95 TYR cc_start: 0.9286 (m-80) cc_final: 0.8425 (m-80) REVERT: G 1 MET cc_start: 0.7954 (ttm) cc_final: 0.7496 (ttm) REVERT: G 9 TYR cc_start: 0.9283 (t80) cc_final: 0.8945 (t80) REVERT: G 14 ARG cc_start: 0.9105 (mtm-85) cc_final: 0.8803 (mtm-85) REVERT: G 24 VAL cc_start: 0.9565 (m) cc_final: 0.9194 (p) REVERT: G 45 THR cc_start: 0.9601 (OUTLIER) cc_final: 0.9369 (t) REVERT: G 71 TYR cc_start: 0.9548 (m-80) cc_final: 0.9335 (m-80) REVERT: G 72 PHE cc_start: 0.9670 (t80) cc_final: 0.9312 (t80) REVERT: G 76 LEU cc_start: 0.9734 (mt) cc_final: 0.9387 (mt) REVERT: G 77 ARG cc_start: 0.9364 (tpp80) cc_final: 0.9026 (mmt90) REVERT: I 9 TYR cc_start: 0.9418 (t80) cc_final: 0.9119 (t80) REVERT: I 14 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8701 (mtm-85) REVERT: I 24 VAL cc_start: 0.9423 (m) cc_final: 0.8939 (p) REVERT: I 30 TYR cc_start: 0.8901 (m-10) cc_final: 0.8588 (m-10) REVERT: I 38 ASP cc_start: 0.9371 (m-30) cc_final: 0.9160 (p0) REVERT: I 96 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: L 21 ASN cc_start: 0.9053 (m-40) cc_final: 0.8771 (m-40) REVERT: L 27 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8430 (tp) REVERT: L 41 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8505 (ttm110) REVERT: L 42 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9219 (mm) REVERT: L 54 THR cc_start: 0.9764 (t) cc_final: 0.9429 (p) REVERT: L 64 ARG cc_start: 0.9420 (mmt90) cc_final: 0.9103 (mmm-85) outliers start: 57 outliers final: 31 residues processed: 499 average time/residue: 0.2156 time to fit residues: 132.9759 Evaluate side-chains 513 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 475 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 63 GLN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 46 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 57 HIS ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** L 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.8669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6496 Z= 0.254 Angle : 0.704 9.602 8840 Z= 0.367 Chirality : 0.043 0.147 968 Planarity : 0.005 0.033 1144 Dihedral : 4.609 21.011 880 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 8.28 % Allowed : 36.77 % Favored : 54.94 % 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: 1.05 (0.29), residues: 760 helix: 0.79 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 0.82 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 56 HIS 0.002 0.000 HIS B 57 PHE 0.022 0.003 PHE D 72 TYR 0.022 0.002 TYR G 95 ARG 0.008 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 474 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.9390 (mmmm) cc_final: 0.8937 (mmmm) REVERT: A 52 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8873 (ptp-110) REVERT: A 64 ARG cc_start: 0.9133 (tpp80) cc_final: 0.8858 (tpp80) REVERT: B 14 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8757 (mtm-85) REVERT: B 53 ASP cc_start: 0.9136 (m-30) cc_final: 0.8788 (m-30) REVERT: B 54 THR cc_start: 0.9615 (m) cc_final: 0.9375 (p) REVERT: B 77 ARG cc_start: 0.9375 (mtt-85) cc_final: 0.9076 (mmt180) REVERT: B 87 GLU cc_start: 0.9581 (tp30) cc_final: 0.9281 (tp30) REVERT: C 3 PHE cc_start: 0.8863 (t80) cc_final: 0.8514 (t80) REVERT: C 10 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9260 (ptmm) REVERT: C 14 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8302 (mtm110) REVERT: C 35 THR cc_start: 0.9016 (m) cc_final: 0.8365 (p) REVERT: C 38 ASP cc_start: 0.9444 (m-30) cc_final: 0.9076 (m-30) REVERT: C 41 ARG cc_start: 0.9302 (ttt180) cc_final: 0.8993 (ttp-170) REVERT: D 14 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8864 (mtp-110) REVERT: D 37 ARG cc_start: 0.8875 (ttt180) cc_final: 0.8482 (tmm-80) REVERT: D 39 GLN cc_start: 0.9366 (pt0) cc_final: 0.9137 (pt0) REVERT: D 41 ARG cc_start: 0.8955 (ttm110) cc_final: 0.8687 (ttp-110) REVERT: D 87 GLU cc_start: 0.9437 (tt0) cc_final: 0.9208 (tp30) REVERT: D 95 TYR cc_start: 0.8995 (m-10) cc_final: 0.8520 (m-10) REVERT: E 3 PHE cc_start: 0.9089 (t80) cc_final: 0.8790 (t80) REVERT: E 7 LYS cc_start: 0.9379 (mmtt) cc_final: 0.8966 (mmtm) REVERT: E 41 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8460 (tpp80) REVERT: E 95 TYR cc_start: 0.9335 (m-80) cc_final: 0.8628 (m-80) REVERT: G 1 MET cc_start: 0.8030 (ttm) cc_final: 0.7632 (ttm) REVERT: G 9 TYR cc_start: 0.9371 (t80) cc_final: 0.9090 (t80) REVERT: G 24 VAL cc_start: 0.9366 (m) cc_final: 0.9000 (p) REVERT: G 28 LEU cc_start: 0.9573 (mt) cc_final: 0.9333 (mt) REVERT: G 45 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9328 (t) REVERT: G 72 PHE cc_start: 0.9672 (t80) cc_final: 0.9443 (t80) REVERT: G 76 LEU cc_start: 0.9758 (mt) cc_final: 0.9481 (mt) REVERT: G 77 ARG cc_start: 0.9403 (tpp80) cc_final: 0.9011 (mmt90) REVERT: I 1 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7616 (ttp) REVERT: I 14 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9071 (mtm110) REVERT: I 30 TYR cc_start: 0.9187 (m-10) cc_final: 0.8929 (m-10) REVERT: I 38 ASP cc_start: 0.9398 (m-30) cc_final: 0.9119 (m-30) REVERT: I 41 ARG cc_start: 0.9375 (mmm-85) cc_final: 0.8881 (mmm-85) REVERT: I 77 ARG cc_start: 0.9201 (mmt90) cc_final: 0.8995 (mmt180) REVERT: I 96 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8159 (tp40) REVERT: L 9 TYR cc_start: 0.9471 (t80) cc_final: 0.9253 (t80) REVERT: L 14 ARG cc_start: 0.9080 (mtm-85) cc_final: 0.8858 (mtm-85) REVERT: L 21 ASN cc_start: 0.9077 (m-40) cc_final: 0.8752 (m-40) REVERT: L 27 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8416 (tp) REVERT: L 41 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8573 (ttm110) REVERT: L 42 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9214 (mm) REVERT: L 54 THR cc_start: 0.9742 (t) cc_final: 0.9353 (p) REVERT: L 64 ARG cc_start: 0.9405 (mmt90) cc_final: 0.9134 (mmm-85) outliers start: 57 outliers final: 36 residues processed: 484 average time/residue: 0.2124 time to fit residues: 127.2845 Evaluate side-chains 512 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 467 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 18 ASN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 69 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN B 57 HIS ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 57 HIS C 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.9044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6496 Z= 0.267 Angle : 0.742 9.538 8840 Z= 0.381 Chirality : 0.043 0.166 968 Planarity : 0.005 0.029 1144 Dihedral : 4.599 21.490 880 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.76 % Favored : 96.97 % Rotamer: Outliers : 7.99 % Allowed : 37.21 % Favored : 54.80 % 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: 1.01 (0.29), residues: 760 helix: 0.72 (0.20), residues: 560 sheet: None (None), residues: 0 loop : 0.95 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 56 HIS 0.001 0.000 HIS C 57 PHE 0.033 0.002 PHE I 16 TYR 0.031 0.002 TYR L 95 ARG 0.008 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 480 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.8546 (mtm-85) REVERT: A 64 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8864 (tpp80) REVERT: B 14 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8727 (mtm-85) REVERT: B 17 SER cc_start: 0.9655 (p) cc_final: 0.9413 (m) REVERT: B 77 ARG cc_start: 0.9390 (mtt-85) cc_final: 0.9081 (mmt180) REVERT: B 87 GLU cc_start: 0.9557 (tp30) cc_final: 0.9241 (tp30) REVERT: C 3 PHE cc_start: 0.8886 (t80) cc_final: 0.8097 (t80) REVERT: C 7 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8839 (mmmm) REVERT: C 9 TYR cc_start: 0.9317 (t80) cc_final: 0.8949 (t80) REVERT: C 10 LYS cc_start: 0.9606 (OUTLIER) cc_final: 0.9360 (ptmm) REVERT: C 14 ARG cc_start: 0.9109 (mtm-85) cc_final: 0.8707 (mtm-85) REVERT: C 35 THR cc_start: 0.9022 (m) cc_final: 0.8447 (p) REVERT: C 38 ASP cc_start: 0.9432 (m-30) cc_final: 0.9025 (m-30) REVERT: C 41 ARG cc_start: 0.9296 (ttt180) cc_final: 0.8952 (ttp-170) REVERT: C 54 THR cc_start: 0.9784 (t) cc_final: 0.9468 (m) REVERT: C 91 VAL cc_start: 0.9254 (t) cc_final: 0.9013 (p) REVERT: D 10 LYS cc_start: 0.9552 (ptpt) cc_final: 0.9265 (ttpp) REVERT: D 14 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8692 (mtp-110) REVERT: D 37 ARG cc_start: 0.8872 (ttt180) cc_final: 0.8584 (tmm-80) REVERT: D 39 GLN cc_start: 0.9344 (pt0) cc_final: 0.9105 (pt0) REVERT: D 87 GLU cc_start: 0.9436 (tt0) cc_final: 0.9221 (tp30) REVERT: D 95 TYR cc_start: 0.9016 (m-10) cc_final: 0.8656 (m-10) REVERT: E 3 PHE cc_start: 0.9082 (t80) cc_final: 0.8837 (t80) REVERT: E 9 TYR cc_start: 0.9337 (t80) cc_final: 0.9118 (t80) REVERT: E 41 ARG cc_start: 0.9323 (tpp80) cc_final: 0.8508 (tpp80) REVERT: E 52 ARG cc_start: 0.9379 (ttm-80) cc_final: 0.9148 (tpp80) REVERT: G 1 MET cc_start: 0.8048 (ttm) cc_final: 0.7630 (ttm) REVERT: G 9 TYR cc_start: 0.9364 (t80) cc_final: 0.9072 (t80) REVERT: G 24 VAL cc_start: 0.9264 (m) cc_final: 0.9014 (p) REVERT: G 45 THR cc_start: 0.9625 (OUTLIER) cc_final: 0.9414 (p) REVERT: G 53 ASP cc_start: 0.8995 (m-30) cc_final: 0.7825 (m-30) REVERT: G 54 THR cc_start: 0.9674 (OUTLIER) cc_final: 0.9405 (p) REVERT: G 72 PHE cc_start: 0.9671 (t80) cc_final: 0.9437 (t80) REVERT: G 76 LEU cc_start: 0.9770 (mt) cc_final: 0.9485 (mt) REVERT: G 77 ARG cc_start: 0.9386 (tpp80) cc_final: 0.9037 (mmt90) REVERT: I 1 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7543 (ttp) REVERT: I 24 VAL cc_start: 0.9418 (m) cc_final: 0.8732 (p) REVERT: I 30 TYR cc_start: 0.9314 (m-10) cc_final: 0.9082 (m-10) REVERT: I 38 ASP cc_start: 0.9350 (m-30) cc_final: 0.9126 (m-30) REVERT: I 46 CYS cc_start: 0.9713 (t) cc_final: 0.9406 (t) REVERT: I 96 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8093 (tp40) REVERT: L 9 TYR cc_start: 0.9471 (t80) cc_final: 0.9232 (t80) REVERT: L 14 ARG cc_start: 0.9071 (mtm-85) cc_final: 0.8831 (mtm110) REVERT: L 21 ASN cc_start: 0.9133 (m-40) cc_final: 0.8789 (m-40) REVERT: L 42 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9245 (mm) REVERT: L 54 THR cc_start: 0.9760 (t) cc_final: 0.9374 (p) REVERT: L 64 ARG cc_start: 0.9394 (mmt90) cc_final: 0.9142 (mmm-85) REVERT: L 91 VAL cc_start: 0.9202 (t) cc_final: 0.8989 (p) outliers start: 55 outliers final: 33 residues processed: 489 average time/residue: 0.2102 time to fit residues: 128.0135 Evaluate side-chains 515 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 474 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 63 GLN C 21 ASN C 39 GLN C 51 ASN ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.9327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6496 Z= 0.328 Angle : 0.776 9.818 8840 Z= 0.404 Chirality : 0.046 0.167 968 Planarity : 0.005 0.027 1144 Dihedral : 4.745 22.146 880 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 22.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.16 % Favored : 96.58 % Rotamer: Outliers : 8.28 % Allowed : 39.83 % Favored : 51.89 % 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: 0.98 (0.30), residues: 760 helix: 0.42 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.38 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 56 HIS 0.001 0.000 HIS C 57 PHE 0.027 0.002 PHE D 16 TYR 0.030 0.002 TYR L 95 ARG 0.009 0.001 ARG D 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 480 time to evaluate : 0.768 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 14 ARG cc_start: 0.9050 (mtm-85) cc_final: 0.8569 (mtm-85) REVERT: A 77 ARG cc_start: 0.9268 (mmt90) cc_final: 0.9005 (mmt180) REVERT: B 14 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8667 (mtm-85) REVERT: B 41 ARG cc_start: 0.8655 (ttm110) cc_final: 0.8379 (ttm110) REVERT: B 77 ARG cc_start: 0.9370 (mtt-85) cc_final: 0.8972 (mmt180) REVERT: B 87 GLU cc_start: 0.9577 (tp30) cc_final: 0.9248 (tp30) REVERT: C 10 LYS cc_start: 0.9634 (OUTLIER) cc_final: 0.9380 (ptmm) REVERT: C 14 ARG cc_start: 0.9168 (mtm-85) cc_final: 0.8820 (mtm-85) REVERT: C 35 THR cc_start: 0.9077 (m) cc_final: 0.8511 (p) REVERT: C 38 ASP cc_start: 0.9465 (m-30) cc_final: 0.9065 (m-30) REVERT: C 40 ASP cc_start: 0.9307 (p0) cc_final: 0.9054 (p0) REVERT: C 41 ARG cc_start: 0.9306 (ttt180) cc_final: 0.8958 (ttp-170) REVERT: C 45 THR cc_start: 0.9610 (m) cc_final: 0.9398 (p) REVERT: D 14 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8604 (mtm-85) REVERT: D 37 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8558 (tmm-80) REVERT: D 39 GLN cc_start: 0.9320 (pt0) cc_final: 0.9068 (pt0) REVERT: D 41 ARG cc_start: 0.9150 (ttp-170) cc_final: 0.8846 (ttp-170) REVERT: D 63 GLN cc_start: 0.9628 (OUTLIER) cc_final: 0.9394 (pp30) REVERT: D 87 GLU cc_start: 0.9458 (tt0) cc_final: 0.9231 (tp30) REVERT: E 3 PHE cc_start: 0.9094 (t80) cc_final: 0.8839 (t80) REVERT: E 9 TYR cc_start: 0.9364 (t80) cc_final: 0.9005 (t80) REVERT: E 41 ARG cc_start: 0.9342 (tpp80) cc_final: 0.8505 (tpp80) REVERT: E 52 ARG cc_start: 0.9465 (ttm-80) cc_final: 0.9069 (tpp80) REVERT: E 87 GLU cc_start: 0.9409 (tt0) cc_final: 0.9159 (tp30) REVERT: G 1 MET cc_start: 0.8133 (ttm) cc_final: 0.7724 (ttm) REVERT: G 14 ARG cc_start: 0.9294 (mtp-110) cc_final: 0.8965 (mtm-85) REVERT: G 45 THR cc_start: 0.9627 (OUTLIER) cc_final: 0.9395 (p) REVERT: G 53 ASP cc_start: 0.9028 (m-30) cc_final: 0.7887 (m-30) REVERT: G 54 THR cc_start: 0.9695 (OUTLIER) cc_final: 0.9428 (p) REVERT: G 72 PHE cc_start: 0.9701 (t80) cc_final: 0.9433 (t80) REVERT: G 76 LEU cc_start: 0.9744 (mt) cc_final: 0.9460 (mt) REVERT: G 77 ARG cc_start: 0.9415 (tpp80) cc_final: 0.9036 (mmt90) REVERT: I 10 LYS cc_start: 0.9674 (ttmt) cc_final: 0.9415 (mppt) REVERT: I 14 ARG cc_start: 0.9177 (mtm110) cc_final: 0.8923 (mtm-85) REVERT: I 46 CYS cc_start: 0.9694 (t) cc_final: 0.9486 (t) REVERT: I 77 ARG cc_start: 0.9336 (mmt90) cc_final: 0.8960 (mmt-90) REVERT: I 87 GLU cc_start: 0.9359 (tt0) cc_final: 0.9097 (tp30) REVERT: L 9 TYR cc_start: 0.9512 (t80) cc_final: 0.9123 (t80) REVERT: L 21 ASN cc_start: 0.9192 (m-40) cc_final: 0.8863 (m-40) REVERT: L 54 THR cc_start: 0.9765 (t) cc_final: 0.9407 (p) REVERT: L 64 ARG cc_start: 0.9381 (mmt90) cc_final: 0.9139 (mmm-85) outliers start: 57 outliers final: 39 residues processed: 491 average time/residue: 0.2061 time to fit residues: 126.1211 Evaluate side-chains 513 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 468 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 18 ASN Chi-restraints excluded: chain A residue 33 CYS Chi-restraints excluded: chain A residue 51 ASN Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 6 ASP Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 0.0980 chunk 64 optimal weight: 9.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 51 ASN C 57 HIS C 96 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.9627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6496 Z= 0.266 Angle : 0.812 10.727 8840 Z= 0.412 Chirality : 0.044 0.172 968 Planarity : 0.005 0.028 1144 Dihedral : 4.767 22.622 880 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.03 % Favored : 96.71 % Rotamer: Outliers : 6.54 % Allowed : 43.46 % Favored : 50.00 % 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: 0.84 (0.30), residues: 760 helix: 0.36 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.16 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.001 0.000 HIS A 57 PHE 0.028 0.002 PHE C 59 TYR 0.033 0.003 TYR C 9 ARG 0.008 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 485 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.9288 (mmt90) cc_final: 0.9047 (mmt180) REVERT: A 95 TYR cc_start: 0.9109 (m-80) cc_final: 0.8837 (m-80) REVERT: B 14 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8700 (mtm-85) REVERT: B 71 TYR cc_start: 0.9413 (m-80) cc_final: 0.9050 (m-80) REVERT: B 77 ARG cc_start: 0.9386 (mtt-85) cc_final: 0.9073 (mmt180) REVERT: B 87 GLU cc_start: 0.9542 (tp30) cc_final: 0.9226 (tp30) REVERT: C 7 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8913 (mmmm) REVERT: C 9 TYR cc_start: 0.9327 (t80) cc_final: 0.9082 (t80) REVERT: C 35 THR cc_start: 0.9001 (m) cc_final: 0.8538 (p) REVERT: C 38 ASP cc_start: 0.9446 (m-30) cc_final: 0.8949 (m-30) REVERT: C 40 ASP cc_start: 0.9288 (p0) cc_final: 0.9019 (p0) REVERT: C 41 ARG cc_start: 0.9285 (ttt180) cc_final: 0.8942 (ttp-110) REVERT: C 60 ASN cc_start: 0.9704 (t0) cc_final: 0.9488 (m110) REVERT: C 96 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7654 (tp-100) REVERT: D 14 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8663 (mtm-85) REVERT: D 20 CYS cc_start: 0.9634 (p) cc_final: 0.9177 (t) REVERT: D 37 ARG cc_start: 0.8944 (ttt180) cc_final: 0.8692 (tmm-80) REVERT: D 39 GLN cc_start: 0.9290 (pt0) cc_final: 0.9000 (pt0) REVERT: D 40 ASP cc_start: 0.9008 (t0) cc_final: 0.8772 (t0) REVERT: D 52 ARG cc_start: 0.9529 (mtp-110) cc_final: 0.9322 (mmm-85) REVERT: D 87 GLU cc_start: 0.9468 (tt0) cc_final: 0.9189 (tp30) REVERT: E 3 PHE cc_start: 0.9043 (t80) cc_final: 0.8760 (t80) REVERT: E 52 ARG cc_start: 0.9441 (ttm-80) cc_final: 0.9038 (tpp80) REVERT: E 87 GLU cc_start: 0.9402 (tt0) cc_final: 0.9160 (tp30) REVERT: G 1 MET cc_start: 0.8111 (ttm) cc_final: 0.7697 (ttm) REVERT: G 45 THR cc_start: 0.9633 (OUTLIER) cc_final: 0.9429 (p) REVERT: G 54 THR cc_start: 0.9688 (OUTLIER) cc_final: 0.9450 (p) REVERT: G 71 TYR cc_start: 0.9558 (m-80) cc_final: 0.9317 (m-80) REVERT: G 72 PHE cc_start: 0.9696 (t80) cc_final: 0.9310 (t80) REVERT: G 76 LEU cc_start: 0.9704 (mt) cc_final: 0.9397 (mt) REVERT: G 77 ARG cc_start: 0.9389 (tpp80) cc_final: 0.9072 (mmt90) REVERT: I 1 MET cc_start: 0.8033 (tpp) cc_final: 0.7663 (mmp) REVERT: I 3 PHE cc_start: 0.8695 (t80) cc_final: 0.8365 (t80) REVERT: I 10 LYS cc_start: 0.9649 (ttmt) cc_final: 0.9383 (mppt) REVERT: I 14 ARG cc_start: 0.9149 (mtm110) cc_final: 0.8878 (mtm-85) REVERT: I 38 ASP cc_start: 0.9289 (m-30) cc_final: 0.8881 (p0) REVERT: I 46 CYS cc_start: 0.9691 (t) cc_final: 0.9453 (t) REVERT: I 77 ARG cc_start: 0.9356 (mmt90) cc_final: 0.8970 (mmt-90) REVERT: I 87 GLU cc_start: 0.9371 (tt0) cc_final: 0.9127 (tp30) REVERT: I 91 VAL cc_start: 0.9173 (t) cc_final: 0.8885 (p) REVERT: L 9 TYR cc_start: 0.9443 (t80) cc_final: 0.9085 (t80) REVERT: L 14 ARG cc_start: 0.9087 (mtp-110) cc_final: 0.8768 (mtm110) REVERT: L 21 ASN cc_start: 0.9210 (m-40) cc_final: 0.8998 (m-40) REVERT: L 54 THR cc_start: 0.9746 (t) cc_final: 0.9395 (p) REVERT: L 64 ARG cc_start: 0.9399 (mmt90) cc_final: 0.9164 (mmm-85) outliers start: 45 outliers final: 32 residues processed: 494 average time/residue: 0.2079 time to fit residues: 127.5628 Evaluate side-chains 504 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 467 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 84 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.2980 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 57 HIS E 60 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN I 60 ASN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.9780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6496 Z= 0.243 Angle : 0.842 10.647 8840 Z= 0.419 Chirality : 0.044 0.173 968 Planarity : 0.005 0.033 1144 Dihedral : 4.744 22.949 880 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.03 % Favored : 96.71 % Rotamer: Outliers : 5.52 % Allowed : 44.62 % Favored : 49.85 % 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: 0.66 (0.30), residues: 760 helix: 0.24 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.09 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 56 HIS 0.001 0.000 HIS G 57 PHE 0.033 0.003 PHE C 59 TYR 0.028 0.003 TYR C 9 ARG 0.009 0.001 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 473 time to evaluate : 0.758 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 14 ARG cc_start: 0.9047 (mtp-110) cc_final: 0.8818 (mtm110) REVERT: A 39 GLN cc_start: 0.9115 (pt0) cc_final: 0.8684 (pp30) REVERT: A 77 ARG cc_start: 0.9312 (mmt90) cc_final: 0.9061 (mmt180) REVERT: A 95 TYR cc_start: 0.9124 (m-80) cc_final: 0.8822 (m-80) REVERT: B 14 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8856 (mtp-110) REVERT: B 37 ARG cc_start: 0.8329 (ppt170) cc_final: 0.6364 (mmm-85) REVERT: B 41 ARG cc_start: 0.8585 (ttm110) cc_final: 0.7960 (ptp-170) REVERT: B 77 ARG cc_start: 0.9428 (mtt-85) cc_final: 0.9138 (mmt-90) REVERT: B 87 GLU cc_start: 0.9534 (tp30) cc_final: 0.9246 (tp30) REVERT: C 9 TYR cc_start: 0.9356 (t80) cc_final: 0.9064 (t80) REVERT: C 19 PHE cc_start: 0.9271 (m-80) cc_final: 0.8983 (m-80) REVERT: C 40 ASP cc_start: 0.9225 (p0) cc_final: 0.8994 (p0) REVERT: C 41 ARG cc_start: 0.9264 (ttt180) cc_final: 0.8938 (ttp-110) REVERT: D 3 PHE cc_start: 0.8896 (t80) cc_final: 0.8589 (t80) REVERT: D 7 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8837 (mtpp) REVERT: D 14 ARG cc_start: 0.9114 (ttp-110) cc_final: 0.8764 (mtm110) REVERT: D 37 ARG cc_start: 0.8959 (ttt180) cc_final: 0.8717 (tmm-80) REVERT: D 40 ASP cc_start: 0.9043 (t0) cc_final: 0.8831 (t0) REVERT: D 77 ARG cc_start: 0.9329 (mmt90) cc_final: 0.9120 (mmt90) REVERT: D 87 GLU cc_start: 0.9470 (tt0) cc_final: 0.9149 (tp30) REVERT: D 91 VAL cc_start: 0.9319 (t) cc_final: 0.8912 (p) REVERT: E 9 TYR cc_start: 0.9337 (t80) cc_final: 0.9111 (t80) REVERT: E 52 ARG cc_start: 0.9440 (ttm-80) cc_final: 0.9059 (tpp80) REVERT: E 87 GLU cc_start: 0.9397 (tt0) cc_final: 0.9161 (tp30) REVERT: G 9 TYR cc_start: 0.9221 (t80) cc_final: 0.8985 (t80) REVERT: G 14 ARG cc_start: 0.9295 (mtp-110) cc_final: 0.8827 (mtm-85) REVERT: G 45 THR cc_start: 0.9628 (m) cc_final: 0.9405 (p) REVERT: G 54 THR cc_start: 0.9669 (OUTLIER) cc_final: 0.9469 (p) REVERT: G 59 PHE cc_start: 0.9536 (m-80) cc_final: 0.9263 (m-80) REVERT: G 71 TYR cc_start: 0.9550 (m-80) cc_final: 0.9319 (m-80) REVERT: G 72 PHE cc_start: 0.9669 (t80) cc_final: 0.9350 (t80) REVERT: G 76 LEU cc_start: 0.9681 (mt) cc_final: 0.9425 (mt) REVERT: G 77 ARG cc_start: 0.9363 (tpp80) cc_final: 0.9009 (mmt90) REVERT: G 91 VAL cc_start: 0.9378 (t) cc_final: 0.9126 (p) REVERT: I 1 MET cc_start: 0.7883 (tpp) cc_final: 0.7508 (mmp) REVERT: I 3 PHE cc_start: 0.8487 (t80) cc_final: 0.8218 (t80) REVERT: I 10 LYS cc_start: 0.9643 (ttmt) cc_final: 0.9418 (mppt) REVERT: I 46 CYS cc_start: 0.9682 (t) cc_final: 0.9464 (t) REVERT: I 87 GLU cc_start: 0.9400 (tt0) cc_final: 0.9127 (tp30) REVERT: I 91 VAL cc_start: 0.9150 (t) cc_final: 0.8874 (p) REVERT: L 9 TYR cc_start: 0.9407 (t80) cc_final: 0.9081 (t80) REVERT: L 14 ARG cc_start: 0.9060 (mtp-110) cc_final: 0.8823 (mtm110) REVERT: L 21 ASN cc_start: 0.9174 (m-40) cc_final: 0.8823 (m-40) REVERT: L 54 THR cc_start: 0.9733 (t) cc_final: 0.9410 (p) REVERT: L 64 ARG cc_start: 0.9389 (mmt90) cc_final: 0.9140 (mmm-85) outliers start: 38 outliers final: 27 residues processed: 479 average time/residue: 0.2142 time to fit residues: 127.5530 Evaluate side-chains 492 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 463 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 0.0030 chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 overall best weight: 3.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN C 39 GLN ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 ASN D 63 GLN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 ASN I 63 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.9981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6496 Z= 0.268 Angle : 0.878 11.833 8840 Z= 0.439 Chirality : 0.045 0.175 968 Planarity : 0.006 0.057 1144 Dihedral : 4.831 23.091 880 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.16 % Favored : 96.58 % Rotamer: Outliers : 4.65 % Allowed : 46.80 % Favored : 48.55 % 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: 0.63 (0.30), residues: 760 helix: 0.22 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 2.07 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 56 HIS 0.003 0.001 HIS I 57 PHE 0.028 0.002 PHE L 59 TYR 0.027 0.002 TYR C 9 ARG 0.015 0.001 ARG E 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 472 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 GLN cc_start: 0.9134 (pt0) cc_final: 0.8469 (pp30) REVERT: A 77 ARG cc_start: 0.9314 (mmt90) cc_final: 0.9062 (mmt180) REVERT: A 95 TYR cc_start: 0.9083 (m-80) cc_final: 0.8805 (m-80) REVERT: B 14 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8806 (mtp-110) REVERT: B 41 ARG cc_start: 0.8587 (ttm110) cc_final: 0.7687 (ptp-170) REVERT: B 77 ARG cc_start: 0.9433 (mtt-85) cc_final: 0.9121 (mmt180) REVERT: B 87 GLU cc_start: 0.9550 (tp30) cc_final: 0.9225 (tp30) REVERT: C 9 TYR cc_start: 0.9321 (t80) cc_final: 0.8964 (t80) REVERT: C 19 PHE cc_start: 0.9286 (m-80) cc_final: 0.8956 (m-80) REVERT: C 35 THR cc_start: 0.9247 (m) cc_final: 0.9045 (p) REVERT: C 38 ASP cc_start: 0.9446 (m-30) cc_final: 0.9165 (m-30) REVERT: C 40 ASP cc_start: 0.9254 (p0) cc_final: 0.8998 (p0) REVERT: C 41 ARG cc_start: 0.9280 (ttt180) cc_final: 0.8877 (ttp-170) REVERT: C 77 ARG cc_start: 0.9244 (mmt90) cc_final: 0.9040 (mmt-90) REVERT: D 3 PHE cc_start: 0.8849 (t80) cc_final: 0.8606 (t80) REVERT: D 14 ARG cc_start: 0.9140 (ttp-110) cc_final: 0.8820 (mtm110) REVERT: D 37 ARG cc_start: 0.8962 (ttt180) cc_final: 0.8724 (tmm-80) REVERT: D 40 ASP cc_start: 0.9081 (t0) cc_final: 0.8848 (t0) REVERT: D 87 GLU cc_start: 0.9467 (tt0) cc_final: 0.9147 (tp30) REVERT: D 91 VAL cc_start: 0.9347 (t) cc_final: 0.9019 (p) REVERT: E 52 ARG cc_start: 0.9405 (ttm-80) cc_final: 0.9004 (tpp80) REVERT: E 56 TRP cc_start: 0.9023 (t60) cc_final: 0.7960 (t60) REVERT: E 77 ARG cc_start: 0.9360 (mmt90) cc_final: 0.8940 (mmt180) REVERT: E 87 GLU cc_start: 0.9407 (tt0) cc_final: 0.9185 (tp30) REVERT: G 3 PHE cc_start: 0.8971 (t80) cc_final: 0.8704 (t80) REVERT: G 9 TYR cc_start: 0.9237 (t80) cc_final: 0.9029 (t80) REVERT: G 14 ARG cc_start: 0.9329 (mtp-110) cc_final: 0.8872 (mtm-85) REVERT: G 45 THR cc_start: 0.9625 (m) cc_final: 0.9412 (t) REVERT: G 54 THR cc_start: 0.9676 (OUTLIER) cc_final: 0.9377 (p) REVERT: G 71 TYR cc_start: 0.9550 (m-80) cc_final: 0.9328 (m-80) REVERT: G 72 PHE cc_start: 0.9675 (t80) cc_final: 0.9454 (t80) REVERT: G 77 ARG cc_start: 0.9375 (tpp80) cc_final: 0.9005 (mmt90) REVERT: G 91 VAL cc_start: 0.9382 (t) cc_final: 0.9129 (p) REVERT: I 1 MET cc_start: 0.8031 (tpp) cc_final: 0.7682 (mmp) REVERT: I 3 PHE cc_start: 0.8517 (t80) cc_final: 0.8261 (t80) REVERT: I 46 CYS cc_start: 0.9691 (t) cc_final: 0.9463 (t) REVERT: I 71 TYR cc_start: 0.9453 (m-10) cc_final: 0.9240 (m-80) REVERT: I 77 ARG cc_start: 0.9395 (mmt90) cc_final: 0.9092 (mmt180) REVERT: I 87 GLU cc_start: 0.9368 (tt0) cc_final: 0.9085 (tp30) REVERT: I 91 VAL cc_start: 0.9198 (t) cc_final: 0.8768 (p) REVERT: L 9 TYR cc_start: 0.9421 (t80) cc_final: 0.9091 (t80) REVERT: L 14 ARG cc_start: 0.9079 (mtp-110) cc_final: 0.8803 (mtm110) REVERT: L 21 ASN cc_start: 0.9224 (m-40) cc_final: 0.8828 (m-40) REVERT: L 54 THR cc_start: 0.9718 (t) cc_final: 0.9372 (p) REVERT: L 64 ARG cc_start: 0.9371 (mmt90) cc_final: 0.9124 (mmm-85) outliers start: 32 outliers final: 25 residues processed: 480 average time/residue: 0.2191 time to fit residues: 130.2024 Evaluate side-chains 488 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 461 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain B residue 14 ARG Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain L residue 6 ASP Chi-restraints excluded: chain L residue 27 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain L residue 62 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.0170 chunk 8 optimal weight: 0.0070 chunk 15 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 63 GLN C 21 ASN ** G 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.063062 restraints weight = 22555.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.065141 restraints weight = 11874.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.066516 restraints weight = 7458.713| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 1.0114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6496 Z= 0.260 Angle : 0.884 11.359 8840 Z= 0.442 Chirality : 0.045 0.175 968 Planarity : 0.005 0.053 1144 Dihedral : 4.833 23.685 880 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.29 % Favored : 96.45 % Rotamer: Outliers : 5.09 % Allowed : 46.37 % Favored : 48.55 % 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: 0.50 (0.30), residues: 760 helix: 0.13 (0.20), residues: 608 sheet: None (None), residues: 0 loop : 1.99 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 56 HIS 0.001 0.000 HIS A 57 PHE 0.043 0.003 PHE D 59 TYR 0.026 0.002 TYR D 9 ARG 0.015 0.001 ARG A 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.20 seconds wall clock time: 40 minutes 35.34 seconds (2435.34 seconds total)