Starting phenix.real_space_refine on Sun Mar 10 19:32:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/03_2024/7un5_26613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/03_2024/7un5_26613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/03_2024/7un5_26613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/03_2024/7un5_26613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/03_2024/7un5_26613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/03_2024/7un5_26613.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2760 2.51 5 N 850 2.21 5 O 740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4380 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "B" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "H" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "F" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "I" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 438 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Time building chain proxies: 2.67, per 1000 atoms: 0.61 Number of scatterers: 4380 At special positions: 0 Unit cell: (91.63, 118.58, 53.9, 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 30 16.00 O 740 8.00 N 850 7.00 C 2760 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: 1.67 Conformation dependent library (CDL) restraints added in 848.6 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 6.696A pdb=" N THR A 95 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLN B 98 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER A 97 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR E 95 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLN C 98 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER E 97 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR C 95 " --> pdb=" O HIS D 96 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLN D 98 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER C 97 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 111 removed outlier: 7.145A pdb=" N MET A 109 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS B 110 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ASN E 108 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N HIS B 111 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS E 110 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA B 113 " --> pdb=" O LYS E 110 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N MET E 112 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET E 109 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS C 110 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET C 109 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS D 110 " --> pdb=" O MET C 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122 removed outlier: 5.975A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA B 118 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY E 119 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA E 118 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL C 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA E 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA C 118 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL D 121 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 120 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 135 removed outlier: 6.315A pdb=" N VAL A 129 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N SER B 132 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 131 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N MET B 134 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 133 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL E 129 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N SER C 132 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY E 131 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N MET C 134 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA E 133 " --> pdb=" O MET C 134 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL C 129 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER D 132 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY C 131 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N MET D 134 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA C 133 " --> pdb=" O MET D 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 removed outlier: 6.257A pdb=" N ILE E 138 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 95 through 98 removed outlier: 6.490A pdb=" N HIS F 96 " --> pdb=" O SER G 97 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS G 96 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N HIS H 96 " --> pdb=" O SER J 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 109 through 110 removed outlier: 6.544A pdb=" N MET F 109 " --> pdb=" O LYS G 110 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET G 109 " --> pdb=" O LYS I 110 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET H 109 " --> pdb=" O LYS J 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 120 through 122 Processing sheet with id=AA9, first strand: chain 'F' and resid 129 through 135 removed outlier: 6.279A pdb=" N LEU G 130 " --> pdb=" O GLY I 131 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA I 133 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER G 132 " --> pdb=" O ALA I 133 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER I 135 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET G 134 " --> pdb=" O SER I 135 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL H 129 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER I 132 " --> pdb=" O VAL H 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY H 131 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N MET I 134 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA H 133 " --> pdb=" O MET I 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 138 through 140 removed outlier: 6.408A pdb=" N ILE F 138 " --> pdb=" O ILE G 139 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE G 138 " --> pdb=" O ILE I 139 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE H 138 " --> pdb=" O ILE J 139 " (cutoff:3.500A) 49 hydrogen bonds defined for protein. 147 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: 0.91 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1440 1.34 - 1.45: 847 1.45 - 1.57: 2183 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 4530 Sorted by residual: bond pdb=" N SER E 103 " pdb=" CA SER E 103 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.22e-02 6.72e+03 4.90e+00 bond pdb=" CA SER E 103 " pdb=" CB SER E 103 " ideal model delta sigma weight residual 1.533 1.511 0.022 1.46e-02 4.69e+03 2.25e+00 bond pdb=" C GLY I 88 " pdb=" O GLY I 88 " ideal model delta sigma weight residual 1.243 1.230 0.013 9.30e-03 1.16e+04 1.83e+00 bond pdb=" C SER E 103 " pdb=" O SER E 103 " ideal model delta sigma weight residual 1.235 1.245 -0.010 1.10e-02 8.26e+03 8.59e-01 bond pdb=" C GLY G 88 " pdb=" O GLY G 88 " ideal model delta sigma weight residual 1.237 1.229 0.008 9.70e-03 1.06e+04 6.99e-01 ... (remaining 4525 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.83: 257 106.83 - 113.63: 2351 113.63 - 120.44: 1407 120.44 - 127.24: 1957 127.24 - 134.05: 138 Bond angle restraints: 6110 Sorted by residual: angle pdb=" CA GLN A 83 " pdb=" CB GLN A 83 " pdb=" CG GLN A 83 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.41e+00 angle pdb=" N GLN G 83 " pdb=" CA GLN G 83 " pdb=" C GLN G 83 " ideal model delta sigma weight residual 108.76 112.07 -3.31 1.44e+00 4.82e-01 5.27e+00 angle pdb=" N GLN F 83 " pdb=" CA GLN F 83 " pdb=" C GLN F 83 " ideal model delta sigma weight residual 108.76 112.01 -3.25 1.44e+00 4.82e-01 5.10e+00 angle pdb=" N GLY H 87 " pdb=" CA GLY H 87 " pdb=" C GLY H 87 " ideal model delta sigma weight residual 113.18 118.43 -5.25 2.37e+00 1.78e-01 4.90e+00 angle pdb=" CA LEU G 125 " pdb=" CB LEU G 125 " pdb=" CG LEU G 125 " ideal model delta sigma weight residual 116.30 123.93 -7.63 3.50e+00 8.16e-02 4.75e+00 ... (remaining 6105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 2161 16.07 - 32.15: 220 32.15 - 48.22: 60 48.22 - 64.29: 15 64.29 - 80.37: 4 Dihedral angle restraints: 2460 sinusoidal: 900 harmonic: 1560 Sorted by residual: dihedral pdb=" CA ALA I 86 " pdb=" C ALA I 86 " pdb=" N GLY I 87 " pdb=" CA GLY I 87 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ALA G 86 " pdb=" C ALA G 86 " pdb=" N GLY G 87 " pdb=" CA GLY G 87 " ideal model delta harmonic sigma weight residual -180.00 -160.72 -19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ALA H 86 " pdb=" C ALA H 86 " pdb=" N GLY H 87 " pdb=" CA GLY H 87 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 306 0.028 - 0.056: 163 0.056 - 0.085: 32 0.085 - 0.113: 49 0.113 - 0.141: 10 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA MET E 134 " pdb=" N MET E 134 " pdb=" C MET E 134 " pdb=" CB MET E 134 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILE B 138 " pdb=" N ILE B 138 " pdb=" C ILE B 138 " pdb=" CB ILE B 138 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA ILE C 138 " pdb=" N ILE C 138 " pdb=" C ILE C 138 " pdb=" CB ILE C 138 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 557 not shown) Planarity restraints: 800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F 136 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C ARG F 136 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG F 136 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO F 137 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG I 136 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C ARG I 136 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG I 136 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO I 137 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 136 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO I 137 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO I 137 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO I 137 " -0.020 5.00e-02 4.00e+02 ... (remaining 797 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1576 2.89 - 3.39: 3526 3.39 - 3.89: 7085 3.89 - 4.40: 7575 4.40 - 4.90: 14230 Nonbonded interactions: 33992 Sorted by model distance: nonbonded pdb=" NE2 HIS D 85 " pdb=" OG SER D 132 " model vdw 2.387 2.520 nonbonded pdb=" NE2 HIS B 85 " pdb=" OG SER B 132 " model vdw 2.405 2.520 nonbonded pdb=" NE2 HIS C 85 " pdb=" OG SER C 132 " model vdw 2.405 2.520 nonbonded pdb=" OG SER A 97 " pdb=" NE1 TRP A 99 " model vdw 2.429 2.520 nonbonded pdb=" NE2 HIS A 85 " pdb=" OG SER A 132 " model vdw 2.453 2.520 ... (remaining 33987 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.730 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.830 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4530 Z= 0.248 Angle : 0.725 7.627 6110 Z= 0.379 Chirality : 0.045 0.141 560 Planarity : 0.004 0.036 800 Dihedral : 14.461 80.368 1520 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.51 % Allowed : 19.74 % Favored : 79.74 % 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: -3.83 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 99 HIS 0.002 0.001 HIS A 111 PHE 0.015 0.001 PHE B 141 TYR 0.009 0.002 TYR I 128 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.438 Fit side-chains REVERT: E 83 GLN cc_start: 0.9116 (pt0) cc_final: 0.8841 (pm20) REVERT: E 109 MET cc_start: 0.8206 (mtm) cc_final: 0.7944 (mtm) REVERT: A 99 TRP cc_start: 0.8336 (m100) cc_final: 0.7956 (m100) REVERT: C 134 MET cc_start: 0.7682 (mtp) cc_final: 0.7481 (mtt) outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.1660 time to fit residues: 21.1055 Evaluate side-chains 96 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS F 111 HIS ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 4530 Z= 0.558 Angle : 0.780 5.310 6110 Z= 0.400 Chirality : 0.046 0.136 560 Planarity : 0.005 0.032 800 Dihedral : 5.751 39.871 631 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 2.82 % Allowed : 19.49 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.005 0.001 HIS E 96 PHE 0.007 0.002 PHE H 141 TYR 0.014 0.002 TYR I 128 ARG 0.005 0.001 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.485 Fit side-chains REVERT: C 109 MET cc_start: 0.8231 (mtm) cc_final: 0.8006 (mtm) REVERT: H 108 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7915 (p0) REVERT: F 100 ASN cc_start: 0.9028 (t0) cc_final: 0.8432 (t0) REVERT: F 136 ARG cc_start: 0.8491 (ttm170) cc_final: 0.6611 (tpp-160) REVERT: I 134 MET cc_start: 0.8147 (mtp) cc_final: 0.7901 (mtp) REVERT: J 100 ASN cc_start: 0.8883 (t0) cc_final: 0.8657 (t0) outliers start: 11 outliers final: 6 residues processed: 99 average time/residue: 0.1641 time to fit residues: 20.4740 Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 HIS ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4530 Z= 0.276 Angle : 0.649 5.388 6110 Z= 0.318 Chirality : 0.043 0.117 560 Planarity : 0.004 0.032 800 Dihedral : 5.163 19.577 630 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.08 % Allowed : 18.97 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.001 HIS H 111 PHE 0.006 0.001 PHE C 141 TYR 0.010 0.002 TYR I 128 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.480 Fit side-chains REVERT: H 99 TRP cc_start: 0.8318 (m-90) cc_final: 0.8038 (m-90) REVERT: H 108 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7867 (p0) REVERT: F 100 ASN cc_start: 0.9016 (t0) cc_final: 0.8462 (t0) REVERT: F 136 ARG cc_start: 0.8523 (ttm170) cc_final: 0.6669 (tpp-160) REVERT: G 108 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7164 (p0) REVERT: G 112 MET cc_start: 0.8395 (mpp) cc_final: 0.8062 (mmt) REVERT: I 83 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8827 (pt0) REVERT: I 134 MET cc_start: 0.8107 (mtp) cc_final: 0.7843 (mtp) outliers start: 12 outliers final: 6 residues processed: 108 average time/residue: 0.1703 time to fit residues: 22.8474 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 108 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 111 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 4530 Z= 0.413 Angle : 0.708 7.718 6110 Z= 0.350 Chirality : 0.044 0.119 560 Planarity : 0.005 0.031 800 Dihedral : 5.268 19.467 630 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 4.10 % Allowed : 18.97 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 99 HIS 0.003 0.001 HIS G 111 PHE 0.005 0.001 PHE H 141 TYR 0.012 0.002 TYR I 128 ARG 0.003 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.475 Fit side-chains REVERT: H 108 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7928 (p0) REVERT: F 136 ARG cc_start: 0.8532 (ttm170) cc_final: 0.6679 (tpp-160) REVERT: G 108 ASN cc_start: 0.7655 (OUTLIER) cc_final: 0.7224 (p0) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1482 time to fit residues: 19.7505 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 132 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4530 Z= 0.264 Angle : 0.646 5.997 6110 Z= 0.312 Chirality : 0.043 0.119 560 Planarity : 0.004 0.030 800 Dihedral : 5.069 19.682 630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.85 % Allowed : 20.26 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.002 0.001 HIS G 111 PHE 0.005 0.001 PHE C 141 TYR 0.010 0.002 TYR I 128 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.444 Fit side-chains REVERT: E 109 MET cc_start: 0.8380 (mtm) cc_final: 0.8161 (mtm) REVERT: H 108 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7911 (p0) REVERT: F 136 ARG cc_start: 0.8542 (ttm170) cc_final: 0.6652 (tpp-160) REVERT: G 108 ASN cc_start: 0.7512 (OUTLIER) cc_final: 0.7064 (p0) REVERT: I 83 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8795 (pt0) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.1581 time to fit residues: 21.7269 Evaluate side-chains 107 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 132 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4530 Z= 0.362 Angle : 0.688 5.942 6110 Z= 0.336 Chirality : 0.044 0.120 560 Planarity : 0.004 0.031 800 Dihedral : 5.145 19.626 630 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.36 % Allowed : 19.74 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 99 HIS 0.003 0.001 HIS G 111 PHE 0.004 0.001 PHE H 141 TYR 0.010 0.002 TYR I 128 ARG 0.003 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.452 Fit side-chains REVERT: H 108 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7901 (p0) REVERT: H 109 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8248 (mtp) REVERT: F 136 ARG cc_start: 0.8541 (ttm170) cc_final: 0.6651 (tpp-160) REVERT: G 108 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7171 (p0) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.1655 time to fit residues: 21.3567 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 132 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4530 Z= 0.428 Angle : 0.728 7.214 6110 Z= 0.360 Chirality : 0.044 0.120 560 Planarity : 0.004 0.034 800 Dihedral : 5.334 19.956 630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 4.10 % Allowed : 20.26 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS G 111 PHE 0.005 0.001 PHE H 141 TYR 0.012 0.002 TYR I 128 ARG 0.003 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.478 Fit side-chains REVERT: H 108 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7925 (p0) REVERT: H 109 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8305 (mtp) REVERT: F 136 ARG cc_start: 0.8511 (ttm170) cc_final: 0.6749 (tpt170) REVERT: G 108 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7216 (p0) REVERT: G 128 TYR cc_start: 0.9019 (m-80) cc_final: 0.8724 (m-80) REVERT: I 83 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8911 (pt0) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 0.1493 time to fit residues: 18.7457 Evaluate side-chains 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 108 ASN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 132 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4530 Z= 0.257 Angle : 0.676 8.054 6110 Z= 0.324 Chirality : 0.044 0.119 560 Planarity : 0.004 0.031 800 Dihedral : 5.110 20.191 630 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.59 % Allowed : 21.54 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.002 0.001 HIS D 111 PHE 0.005 0.001 PHE C 141 TYR 0.009 0.002 TYR I 128 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.485 Fit side-chains REVERT: H 108 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7970 (p0) REVERT: F 83 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8964 (pt0) REVERT: F 136 ARG cc_start: 0.8476 (ttm170) cc_final: 0.6698 (tpt170) REVERT: G 108 ASN cc_start: 0.7535 (OUTLIER) cc_final: 0.6863 (p0) outliers start: 14 outliers final: 9 residues processed: 102 average time/residue: 0.1567 time to fit residues: 20.3393 Evaluate side-chains 104 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 91 GLN Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 132 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 47 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4530 Z= 0.229 Angle : 0.665 7.899 6110 Z= 0.315 Chirality : 0.044 0.118 560 Planarity : 0.004 0.032 800 Dihedral : 4.964 19.930 630 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.59 % Allowed : 21.79 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 99 HIS 0.003 0.001 HIS C 111 PHE 0.006 0.001 PHE C 141 TYR 0.008 0.001 TYR I 128 ARG 0.002 0.000 ARG D 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 0.494 Fit side-chains REVERT: H 108 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8000 (p0) REVERT: F 83 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.9012 (pt0) REVERT: F 136 ARG cc_start: 0.8460 (ttm170) cc_final: 0.6700 (tpt170) REVERT: G 108 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7034 (p0) REVERT: I 134 MET cc_start: 0.8148 (mtp) cc_final: 0.7845 (mtp) REVERT: J 100 ASN cc_start: 0.8803 (t0) cc_final: 0.8592 (t0) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 0.1586 time to fit residues: 20.9918 Evaluate side-chains 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 83 GLN Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4530 Z= 0.406 Angle : 0.739 8.076 6110 Z= 0.360 Chirality : 0.045 0.119 560 Planarity : 0.004 0.034 800 Dihedral : 5.258 19.629 630 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 3.85 % Allowed : 22.05 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 99 HIS 0.003 0.001 HIS D 111 PHE 0.005 0.001 PHE H 141 TYR 0.011 0.002 TYR F 128 ARG 0.003 0.000 ARG D 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.408 Fit side-chains REVERT: H 108 ASN cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (p0) REVERT: F 136 ARG cc_start: 0.8464 (ttm170) cc_final: 0.6704 (tpt170) REVERT: G 108 ASN cc_start: 0.7596 (OUTLIER) cc_final: 0.7127 (p0) REVERT: G 128 TYR cc_start: 0.8995 (m-80) cc_final: 0.8665 (m-80) REVERT: I 134 MET cc_start: 0.8216 (mtp) cc_final: 0.7745 (mtp) outliers start: 15 outliers final: 11 residues processed: 95 average time/residue: 0.1549 time to fit residues: 18.7503 Evaluate side-chains 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 SER Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 108 ASN Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 132 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0040 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.106026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.096482 restraints weight = 9977.640| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.55 r_work: 0.3749 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4530 Z= 0.309 Angle : 0.702 8.288 6110 Z= 0.336 Chirality : 0.044 0.119 560 Planarity : 0.004 0.033 800 Dihedral : 5.131 20.227 630 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.85 % Allowed : 22.56 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP G 99 HIS 0.002 0.001 HIS C 111 PHE 0.004 0.001 PHE C 141 TYR 0.009 0.002 TYR I 128 ARG 0.002 0.000 ARG D 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.06 seconds wall clock time: 22 minutes 39.05 seconds (1359.05 seconds total)