Starting phenix.real_space_refine on Thu Mar 6 01:50:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7un5_26613/03_2025/7un5_26613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7un5_26613/03_2025/7un5_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/cci-nas-00/data/ceres_data/7un5_26613/03_2025/7un5_26613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7un5_26613/03_2025/7un5_26613.map" model { file = "/net/cci-nas-00/data/ceres_data/7un5_26613/03_2025/7un5_26613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7un5_26613/03_2025/7un5_26613.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.72, per 1000 atoms: 0.85 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 604.1 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: 0.77 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: 1.03 Time building geometry restraints manager: 1.26 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: 0.00 - 1.53: 5803 1.53 - 3.05: 253 3.05 - 4.58: 38 4.58 - 6.10: 13 6.10 - 7.63: 3 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 3.120 nonbonded pdb=" NE2 HIS B 85 " pdb=" OG SER B 132 " model vdw 2.405 3.120 nonbonded pdb=" NE2 HIS C 85 " pdb=" OG SER C 132 " model vdw 2.405 3.120 nonbonded pdb=" OG SER A 97 " pdb=" NE1 TRP A 99 " model vdw 2.429 3.120 nonbonded pdb=" NE2 HIS A 85 " pdb=" OG SER A 132 " model vdw 2.453 3.120 ... (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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 1.820 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.606 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: 0.1751 time to fit residues: 22.2739 Evaluate side-chains 96 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** ** D 91 GLN ** 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 I 111 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.101106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.091963 restraints weight = 9597.359| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.34 r_work: 0.3696 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4530 Z= 0.530 Angle : 0.771 5.317 6110 Z= 0.394 Chirality : 0.046 0.139 560 Planarity : 0.005 0.031 800 Dihedral : 5.586 25.940 631 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.67 % Favored : 86.33 % Rotamer: Outliers : 2.05 % Allowed : 21.28 % Favored : 76.67 % 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: -3.93 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS D 96 PHE 0.006 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 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.498 Fit side-chains REVERT: C 109 MET cc_start: 0.8342 (mtm) cc_final: 0.8069 (mtm) REVERT: F 100 ASN cc_start: 0.8845 (t0) cc_final: 0.8121 (t0) REVERT: F 136 ARG cc_start: 0.8172 (ttm170) cc_final: 0.6152 (tpp-160) REVERT: I 134 MET cc_start: 0.8367 (mtp) cc_final: 0.8060 (mtp) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.1621 time to fit residues: 20.6786 Evaluate side-chains 93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain I residue 91 GLN 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 44 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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 ** D 91 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.103063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.093736 restraints weight = 9441.500| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.37 r_work: 0.3737 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1076 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= 0.327 Angle : 0.670 5.263 6110 Z= 0.331 Chirality : 0.044 0.117 560 Planarity : 0.004 0.032 800 Dihedral : 5.215 19.658 630 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.31 % Allowed : 20.26 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.011 0.001 TRP B 99 HIS 0.003 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 107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.499 Fit side-chains REVERT: D 134 MET cc_start: 0.7893 (ttt) cc_final: 0.7688 (ttt) REVERT: H 125 LEU cc_start: 0.9240 (tt) cc_final: 0.9015 (tt) REVERT: F 136 ARG cc_start: 0.8239 (ttm170) cc_final: 0.6201 (tpp-160) REVERT: I 83 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8735 (pt0) REVERT: I 134 MET cc_start: 0.8339 (mtp) cc_final: 0.7930 (mtp) outliers start: 9 outliers final: 3 residues processed: 103 average time/residue: 0.1710 time to fit residues: 22.1166 Evaluate side-chains 100 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 132 SER 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 27 optimal weight: 0.5980 chunk 34 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 2 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 overall best weight: 2.9364 ------------------------------------------------------------------------------- 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** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.104821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.095366 restraints weight = 9397.833| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.41 r_work: 0.3770 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4530 Z= 0.231 Angle : 0.624 5.551 6110 Z= 0.302 Chirality : 0.043 0.118 560 Planarity : 0.004 0.028 800 Dihedral : 4.996 19.833 630 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.82 % Allowed : 20.77 % Favored : 76.41 % 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: -3.82 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 99 HIS 0.002 0.001 HIS D 111 PHE 0.006 0.001 PHE C 141 TYR 0.009 0.002 TYR I 128 ARG 0.002 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 110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.466 Fit side-chains REVERT: E 109 MET cc_start: 0.8434 (mtm) cc_final: 0.8128 (mtm) REVERT: B 109 MET cc_start: 0.8395 (mtm) cc_final: 0.8046 (mtp) REVERT: H 99 TRP cc_start: 0.8463 (m-90) cc_final: 0.7857 (m-90) REVERT: H 108 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7376 (p0) REVERT: F 136 ARG cc_start: 0.8192 (ttm170) cc_final: 0.6148 (tpp-160) outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 0.1624 time to fit residues: 22.0527 Evaluate side-chains 100 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 132 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 24 optimal weight: 0.0370 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 0.0060 chunk 58 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 overall best weight: 3.5878 ------------------------------------------------------------------------------- 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** ** D 91 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.104080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.094434 restraints weight = 9610.114| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 3.43 r_work: 0.3766 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1249 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= 0.270 Angle : 0.645 7.070 6110 Z= 0.310 Chirality : 0.043 0.118 560 Planarity : 0.004 0.029 800 Dihedral : 4.982 19.796 630 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.85 % Allowed : 20.00 % Favored : 76.15 % 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: -3.79 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.002 0.001 HIS D 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 106 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.490 Fit side-chains REVERT: B 109 MET cc_start: 0.8417 (mtm) cc_final: 0.8163 (mtp) REVERT: F 136 ARG cc_start: 0.8216 (ttm170) cc_final: 0.6126 (tpp-160) REVERT: I 83 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8665 (pt0) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 0.1613 time to fit residues: 20.7965 Evaluate side-chains 101 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 132 SER 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 26 optimal weight: 8.9990 chunk 40 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 7.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.103639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.094162 restraints weight = 10358.959| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.57 r_work: 0.3688 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 4530 Z= 0.528 Angle : 0.762 6.014 6110 Z= 0.380 Chirality : 0.045 0.121 560 Planarity : 0.005 0.033 800 Dihedral : 5.341 19.656 630 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 3.33 % Allowed : 21.28 % Favored : 75.38 % 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: -3.84 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 99 HIS 0.004 0.001 HIS G 111 PHE 0.006 0.002 PHE H 141 TYR 0.011 0.002 TYR I 128 ARG 0.004 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 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.496 Fit side-chains REVERT: F 136 ARG cc_start: 0.8236 (ttm170) cc_final: 0.6211 (tpp-160) REVERT: G 108 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6397 (p0) REVERT: J 99 TRP cc_start: 0.8318 (m-90) cc_final: 0.8040 (m-90) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.1605 time to fit residues: 19.8480 Evaluate side-chains 95 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 MET 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 I residue 130 LEU 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 24 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.104367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 19)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094940 restraints weight = 10226.508| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 3.51 r_work: 0.3696 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4530 Z= 0.436 Angle : 0.737 6.323 6110 Z= 0.363 Chirality : 0.045 0.120 560 Planarity : 0.005 0.033 800 Dihedral : 5.337 19.935 630 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 3.85 % Allowed : 21.03 % Favored : 75.13 % 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: -3.88 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (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 F 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 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.469 Fit side-chains REVERT: B 91 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8310 (tt0) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.1513 time to fit residues: 19.2409 Evaluate side-chains 96 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 109 MET 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 I residue 130 LEU 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 44 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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** I 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.104584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.095148 restraints weight = 9367.552| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.36 r_work: 0.3740 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1465 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= 0.278 Angle : 0.686 6.593 6110 Z= 0.330 Chirality : 0.044 0.119 560 Planarity : 0.004 0.029 800 Dihedral : 5.134 20.217 630 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.33 % Allowed : 22.82 % Favored : 73.85 % 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: -3.83 (0.25), 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 0.020 0.001 TRP F 99 HIS 0.002 0.001 HIS D 111 PHE 0.004 0.001 PHE C 141 TYR 0.011 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 105 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.463 Fit side-chains REVERT: E 109 MET cc_start: 0.8577 (mtm) cc_final: 0.8307 (mtm) REVERT: D 83 GLN cc_start: 0.9028 (pt0) cc_final: 0.8796 (pt0) REVERT: H 109 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8579 (mtp) outliers start: 13 outliers final: 10 residues processed: 101 average time/residue: 0.1497 time to fit residues: 19.2714 Evaluate side-chains 99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 109 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 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** I 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.106728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.097036 restraints weight = 9984.945| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 3.53 r_work: 0.3744 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1477 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= 0.274 Angle : 0.685 7.213 6110 Z= 0.328 Chirality : 0.044 0.119 560 Planarity : 0.004 0.034 800 Dihedral : 5.098 20.416 630 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.59 % Allowed : 22.82 % 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: -3.82 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 99 HIS 0.002 0.001 HIS D 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 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 102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.552 Fit side-chains REVERT: D 83 GLN cc_start: 0.9034 (pt0) cc_final: 0.8813 (pt0) REVERT: H 109 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (mtp) REVERT: F 83 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8669 (pt0) REVERT: G 100 ASN cc_start: 0.9222 (t0) cc_final: 0.8958 (t0) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.1524 time to fit residues: 19.2304 Evaluate side-chains 100 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 MET 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 109 MET 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 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 29 optimal weight: 0.9990 chunk 30 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 32 optimal weight: 0.0070 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.105464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.095919 restraints weight = 10031.366| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 3.50 r_work: 0.3714 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 4530 Z= 0.379 Angle : 0.727 7.597 6110 Z= 0.353 Chirality : 0.045 0.120 560 Planarity : 0.004 0.032 800 Dihedral : 5.229 20.159 630 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 3.33 % Allowed : 22.56 % 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: -3.83 (0.25), 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 0.017 0.001 TRP B 99 HIS 0.003 0.001 HIS G 111 PHE 0.004 0.001 PHE H 141 TYR 0.011 0.002 TYR I 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 104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 1.033 Fit side-chains REVERT: B 91 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8342 (tt0) REVERT: D 83 GLN cc_start: 0.9061 (pt0) cc_final: 0.8715 (pt0) REVERT: H 109 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: I 83 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8832 (pt0) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.2364 time to fit residues: 31.0161 Evaluate side-chains 102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 91 GLN 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 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 58 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.103122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.093770 restraints weight = 9585.860| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 3.41 r_work: 0.3715 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 4530 Z= 0.514 Angle : 1.251 59.199 6110 Z= 0.757 Chirality : 0.047 0.260 560 Planarity : 0.007 0.140 800 Dihedral : 5.269 20.187 630 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 3.08 % Allowed : 23.08 % Favored : 73.85 % 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: -3.87 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 81 HIS 0.003 0.001 HIS G 111 PHE 0.004 0.001 PHE F 141 TYR 0.011 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: 2631.31 seconds wall clock time: 47 minutes 37.06 seconds (2857.06 seconds total)