Starting phenix.real_space_refine (version: dev) on Fri Feb 17 10:05:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/02_2023/7un5_26613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/02_2023/7un5_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_26613/02_2023/7un5_26613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/02_2023/7un5_26613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/02_2023/7un5_26613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7un5_26613/02_2023/7un5_26613.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 2.83, per 1000 atoms: 0.65 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: 1.48 Conformation dependent library (CDL) restraints added in 906.9 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: 0.31 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: 0.94 Time building geometry restraints manager: 1.63 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 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. 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: 4.140 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: 7.580 Check model and map are aligned: 0.060 Process input model: 15.840 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.050 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: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 % 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 *********************** 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 : 0.479 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 102 average time/residue: 0.1746 time to fit residues: 22.3004 Evaluate side-chains 96 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0426 time to fit residues: 0.7254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8077 moved from start: 0.1067 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= 0.551 Angle : 0.776 5.330 6110 Z= 0.397 Chirality : 0.046 0.139 560 Planarity : 0.005 0.032 800 Dihedral : 5.511 19.451 630 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.33 % Favored : 85.67 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.19), residues: 600 *********************** 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 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.496 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 100 average time/residue: 0.1602 time to fit residues: 20.3799 Evaluate side-chains 95 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0523 time to fit residues: 1.1962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** C 111 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 4530 Z= 0.313 Angle : 0.656 5.319 6110 Z= 0.325 Chirality : 0.044 0.118 560 Planarity : 0.004 0.031 800 Dihedral : 5.187 19.610 630 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 1.28 % 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: -3.96 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 600 *********************** 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 105 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 100 time to evaluate : 0.477 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 101 average time/residue: 0.1690 time to fit residues: 21.3893 Evaluate side-chains 94 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0596 time to fit residues: 0.7096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN F 91 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 111 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1344 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= 0.377 Angle : 0.686 6.469 6110 Z= 0.340 Chirality : 0.044 0.124 560 Planarity : 0.004 0.030 800 Dihedral : 5.259 19.396 630 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer Outliers : 2.82 % 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 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 600 *********************** 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 106 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 0.510 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 103 average time/residue: 0.1649 time to fit residues: 21.8909 Evaluate side-chains 100 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 0.473 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0543 time to fit residues: 1.1067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.026 4530 Z= 0.315 Angle : 0.667 6.629 6110 Z= 0.325 Chirality : 0.043 0.119 560 Planarity : 0.004 0.032 800 Dihedral : 5.153 19.704 630 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer Outliers : 0.77 % 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 *********************** 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 103 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 0.453 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 100 average time/residue: 0.1707 time to fit residues: 21.3208 Evaluate side-chains 94 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0666 time to fit residues: 0.7811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.041 4530 Z= 0.513 Angle : 0.768 8.035 6110 Z= 0.385 Chirality : 0.045 0.143 560 Planarity : 0.005 0.035 800 Dihedral : 5.465 19.357 630 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % Rotamer Outliers : 2.56 % 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 *********************** 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 fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.500 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 0.1702 time to fit residues: 21.3861 Evaluate side-chains 92 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.501 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0491 time to fit residues: 1.0046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 GLN ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1685 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= 0.421 Angle : 0.741 8.470 6110 Z= 0.369 Chirality : 0.046 0.156 560 Planarity : 0.005 0.035 800 Dihedral : 5.404 19.946 630 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 1.54 % 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: -3.99 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.19), residues: 600 *********************** 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 99 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.516 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 96 average time/residue: 0.1513 time to fit residues: 18.5186 Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0538 time to fit residues: 0.7773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1660 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= 0.316 Angle : 0.697 8.279 6110 Z= 0.340 Chirality : 0.045 0.159 560 Planarity : 0.004 0.035 800 Dihedral : 5.248 20.132 630 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer Outliers : 0.77 % 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 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.19), residues: 600 *********************** 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 97 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 0.479 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 97 average time/residue: 0.1900 time to fit residues: 22.8880 Evaluate side-chains 90 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 0.448 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0692 time to fit residues: 0.6902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 83 GLN ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 4530 Z= 0.213 Angle : 0.658 7.692 6110 Z= 0.310 Chirality : 0.044 0.120 560 Planarity : 0.004 0.035 800 Dihedral : 4.997 20.246 630 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.77 % 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 *********************** 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 100 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.491 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 98 average time/residue: 0.1895 time to fit residues: 22.9235 Evaluate side-chains 93 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.505 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0741 time to fit residues: 0.7260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.0670 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1827 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= 0.359 Angle : 0.718 7.835 6110 Z= 0.347 Chirality : 0.044 0.119 560 Planarity : 0.004 0.036 800 Dihedral : 5.191 20.079 630 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer Outliers : 0.26 % 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: -3.91 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 600 ********************** 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 97 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.444 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 96 average time/residue: 0.1665 time to fit residues: 19.8265 Evaluate side-chains 91 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0508 time to fit residues: 0.6460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.105487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.095892 restraints weight = 9313.675| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 3.40 r_work: 0.3803 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.1832 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= 0.328 Angle : 0.727 7.970 6110 Z= 0.347 Chirality : 0.044 0.119 560 Planarity : 0.004 0.036 800 Dihedral : 5.220 20.499 630 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 1.03 % 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 =============================================================================== Job complete usr+sys time: 1216.27 seconds wall clock time: 22 minutes 54.37 seconds (1374.37 seconds total)