Starting phenix.real_space_refine on Thu Dec 7 21:03:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/12_2023/6rtb_4996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/12_2023/6rtb_4996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/12_2023/6rtb_4996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/12_2023/6rtb_4996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/12_2023/6rtb_4996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rtb_4996/12_2023/6rtb_4996.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 2895 2.51 5 N 829 2.21 5 O 957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 35": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4681 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "I" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "D" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 460 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain breaks: 2 Chain: "J" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "E" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "G" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "B" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "F" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 469 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain breaks: 2 Time building chain proxies: 2.75, per 1000 atoms: 0.59 Number of scatterers: 4681 At special positions: 0 Unit cell: (104.24, 132.431, 41.9584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 957 8.00 N 829 7.00 C 2895 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: 1.82 Conformation dependent library (CDL) restraints added in 944.4 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1178 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'J' and resid 15 through 17 removed outlier: 6.428A pdb=" N VAL H 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 37 through 43 removed outlier: 6.129A pdb=" N GLY I 36 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR J 39 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU I 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLY J 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL I 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS J 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER I 42 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL G 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL F 40 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR G 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N SER F 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY G 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 48 through 50 removed outlier: 6.537A pdb=" N VAL H 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL G 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 65 through 66 removed outlier: 6.779A pdb=" N ASN H 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN G 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 70 through 72 removed outlier: 6.593A pdb=" N VAL G 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 75 through 79 removed outlier: 6.403A pdb=" N ALA H 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N GLN G 79 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA H 78 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA G 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN F 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 82 through 83 removed outlier: 6.722A pdb=" N VAL H 82 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.262A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.424A pdb=" N VAL C 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 15 " --> pdb=" O VAL A 16 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 37 through 43 removed outlier: 6.463A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY D 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL C 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS D 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 47 through 52 removed outlier: 6.859A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL C 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY B 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N HIS C 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 48 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLY A 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N HIS B 50 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.196A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.346A pdb=" N THR D 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR C 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA D 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 88 through 89 removed outlier: 6.494A pdb=" N SER C 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 79 hydrogen bonds defined for protein. 237 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: 1.08 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 837 1.29 - 1.35: 733 1.35 - 1.42: 127 1.42 - 1.49: 864 1.49 - 1.56: 2110 Bond restraints: 4671 Sorted by residual: bond pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.57e+00 bond pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.59e+00 bond pdb=" CA THR D 92 " pdb=" CB THR D 92 " ideal model delta sigma weight residual 1.534 1.497 0.037 1.78e-02 3.16e+03 4.32e+00 bond pdb=" N ALA B 19 " pdb=" CA ALA B 19 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.29e+00 bond pdb=" CB VAL F 16 " pdb=" CG1 VAL F 16 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 4666 not shown) Histogram of bond angle deviations from ideal: 101.49 - 107.52: 148 107.52 - 113.56: 2824 113.56 - 119.59: 1154 119.59 - 125.62: 2126 125.62 - 131.66: 36 Bond angle restraints: 6288 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 112.96 104.63 8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CG1 VAL G 16 " pdb=" CB VAL G 16 " pdb=" CG2 VAL G 16 " ideal model delta sigma weight residual 110.80 101.49 9.31 2.20e+00 2.07e-01 1.79e+01 angle pdb=" CG1 VAL H 16 " pdb=" CB VAL H 16 " pdb=" CG2 VAL H 16 " ideal model delta sigma weight residual 110.80 101.54 9.26 2.20e+00 2.07e-01 1.77e+01 angle pdb=" C ALA F 18 " pdb=" N ALA F 19 " pdb=" CA ALA F 19 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ALA C 18 " pdb=" N ALA C 19 " pdb=" CA ALA C 19 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 ... (remaining 6283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2404 16.64 - 33.29: 265 33.29 - 49.93: 50 49.93 - 66.58: 8 66.58 - 83.22: 7 Dihedral angle restraints: 2734 sinusoidal: 877 harmonic: 1857 Sorted by residual: dihedral pdb=" CA ALA G 19 " pdb=" C ALA G 19 " pdb=" N GLU G 20 " pdb=" CA GLU G 20 " ideal model delta harmonic sigma weight residual 180.00 113.95 66.05 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA ALA C 19 " pdb=" C ALA C 19 " pdb=" N GLU C 20 " pdb=" CA GLU C 20 " ideal model delta harmonic sigma weight residual 180.00 128.01 51.99 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA ALA I 19 " pdb=" C ALA I 19 " pdb=" N GLU I 20 " pdb=" CA GLU I 20 " ideal model delta harmonic sigma weight residual 180.00 128.78 51.22 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 2731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 494 0.057 - 0.115: 260 0.115 - 0.172: 68 0.172 - 0.230: 10 0.230 - 0.287: 7 Chirality restraints: 839 Sorted by residual: chirality pdb=" CB THR I 81 " pdb=" CA THR I 81 " pdb=" OG1 THR I 81 " pdb=" CG2 THR I 81 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB THR B 92 " pdb=" CA THR B 92 " pdb=" OG1 THR B 92 " pdb=" CG2 THR B 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR D 92 " pdb=" CA THR D 92 " pdb=" OG1 THR D 92 " pdb=" CG2 THR D 92 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 836 not shown) Planarity restraints: 778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 18 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" C ALA G 18 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA G 18 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA G 19 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 19 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C ALA J 19 " 0.041 2.00e-02 2.50e+03 pdb=" O ALA J 19 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU J 20 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 18 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ALA F 18 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA F 18 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA F 19 " 0.013 2.00e-02 2.50e+03 ... (remaining 775 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 141 2.68 - 3.23: 3871 3.23 - 3.79: 6452 3.79 - 4.34: 8026 4.34 - 4.90: 15387 Nonbonded interactions: 33877 Sorted by model distance: nonbonded pdb=" OG SER G 87 " pdb=" O ALA F 18 " model vdw 2.122 2.440 nonbonded pdb=" O SER E 9 " pdb=" OG SER E 9 " model vdw 2.294 2.440 nonbonded pdb=" O SER C 9 " pdb=" OG SER C 9 " model vdw 2.297 2.440 nonbonded pdb=" O SER B 9 " pdb=" OG SER B 9 " model vdw 2.299 2.440 nonbonded pdb=" O SER D 9 " pdb=" OG SER D 9 " model vdw 2.301 2.440 ... (remaining 33872 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' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'B' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'C' and (resid 9 through 24 or resid 36 through 93)) selection = chain 'D' selection = (chain 'E' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'F' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'G' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'H' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'I' and (resid 9 through 24 or resid 36 through 93)) selection = (chain 'J' and (resid 9 through 24 or resid 36 through 93)) } 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: 1.490 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.650 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.880 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.009 0.078 4671 Z= 0.610 Angle : 1.226 9.311 6288 Z= 0.718 Chirality : 0.072 0.287 839 Planarity : 0.005 0.025 778 Dihedral : 15.078 83.221 1556 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 18.94 % Favored : 80.91 % Rotamer: Outliers : 2.61 % Allowed : 11.33 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.94 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 50 TYR 0.028 0.005 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.519 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 104 average time/residue: 0.1937 time to fit residues: 24.6643 Evaluate side-chains 86 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0441 time to fit residues: 1.2993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN H 65 ASN C 50 HIS C 62 GLN C 79 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN D 79 GLN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN F 62 GLN A 50 HIS ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4671 Z= 0.210 Angle : 0.724 5.854 6288 Z= 0.403 Chirality : 0.051 0.139 839 Planarity : 0.002 0.019 778 Dihedral : 8.645 48.345 679 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.12 % Favored : 83.88 % Rotamer: Outliers : 5.45 % Allowed : 13.73 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.013 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.525 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 94 average time/residue: 0.1478 time to fit residues: 18.1356 Evaluate side-chains 78 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0459 time to fit residues: 1.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.0170 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 overall best weight: 3.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 4671 Z= 0.405 Angle : 0.793 5.516 6288 Z= 0.449 Chirality : 0.054 0.217 839 Planarity : 0.003 0.016 778 Dihedral : 8.832 43.317 679 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.03 % Favored : 79.97 % Rotamer: Outliers : 5.01 % Allowed : 16.99 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.46 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.019 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 0.522 Fit side-chains outliers start: 23 outliers final: 16 residues processed: 85 average time/residue: 0.1456 time to fit residues: 16.6771 Evaluate side-chains 78 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0505 time to fit residues: 2.1973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4671 Z= 0.216 Angle : 0.674 5.556 6288 Z= 0.378 Chirality : 0.051 0.140 839 Planarity : 0.002 0.010 778 Dihedral : 7.789 35.161 679 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.18 % Favored : 84.82 % Rotamer: Outliers : 3.05 % Allowed : 20.48 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.011 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.542 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 75 average time/residue: 0.1401 time to fit residues: 14.1664 Evaluate side-chains 71 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.518 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0513 time to fit residues: 1.3087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 34 optimal weight: 0.0270 chunk 59 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 ASN C 62 GLN ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 4671 Z= 0.190 Angle : 0.631 5.684 6288 Z= 0.353 Chirality : 0.050 0.133 839 Planarity : 0.002 0.016 778 Dihedral : 7.090 28.908 679 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.59 % Favored : 83.41 % Rotamer: Outliers : 3.27 % Allowed : 19.61 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 50 TYR 0.011 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.548 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 74 average time/residue: 0.1315 time to fit residues: 13.2409 Evaluate side-chains 66 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0432 time to fit residues: 1.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.0870 chunk 16 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN I 62 GLN J 62 GLN G 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN A 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 4671 Z= 0.155 Angle : 0.597 5.397 6288 Z= 0.333 Chirality : 0.050 0.133 839 Planarity : 0.002 0.016 778 Dihedral : 6.573 26.352 679 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.96 % Favored : 84.04 % Rotamer: Outliers : 3.70 % Allowed : 19.83 % Favored : 76.47 % 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 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 50 TYR 0.009 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.525 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 79 average time/residue: 0.1390 time to fit residues: 14.7291 Evaluate side-chains 66 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.522 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0829 time to fit residues: 1.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 0.0370 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 chunk 41 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 overall best weight: 1.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN I 62 GLN G 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4671 Z= 0.228 Angle : 0.631 5.381 6288 Z= 0.355 Chirality : 0.051 0.159 839 Planarity : 0.002 0.013 778 Dihedral : 6.850 28.300 679 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.21 % Favored : 82.79 % Rotamer: Outliers : 2.40 % Allowed : 20.26 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.013 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.541 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1241 time to fit residues: 11.6540 Evaluate side-chains 62 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0579 time to fit residues: 1.2605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 63 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 37 optimal weight: 0.0570 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN E 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN A 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4671 Z= 0.130 Angle : 0.569 5.509 6288 Z= 0.317 Chirality : 0.050 0.134 839 Planarity : 0.002 0.013 778 Dihedral : 6.058 23.842 679 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.34 % Favored : 84.66 % Rotamer: Outliers : 0.44 % Allowed : 21.35 % Favored : 78.21 % 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: -3.73 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 TYR 0.007 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.524 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.1215 time to fit residues: 10.8300 Evaluate side-chains 58 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.546 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0689 time to fit residues: 0.8144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN I 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4671 Z= 0.325 Angle : 0.687 5.239 6288 Z= 0.387 Chirality : 0.052 0.138 839 Planarity : 0.002 0.010 778 Dihedral : 7.126 29.828 679 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.94 % Favored : 81.06 % Rotamer: Outliers : 1.31 % Allowed : 21.13 % Favored : 77.56 % 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: -3.79 (0.29), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 TYR 0.017 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.526 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.1182 time to fit residues: 10.5370 Evaluate side-chains 60 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.494 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0555 time to fit residues: 1.1162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 4671 Z= 0.551 Angle : 0.872 5.709 6288 Z= 0.497 Chirality : 0.059 0.151 839 Planarity : 0.004 0.012 778 Dihedral : 8.395 36.101 679 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.26 % Favored : 75.74 % Rotamer: Outliers : 0.22 % Allowed : 21.35 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 TYR 0.023 0.004 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.507 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.1372 time to fit residues: 10.2142 Evaluate side-chains 54 residues out of total 459 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0502 time to fit residues: 0.7816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.159886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.136313 restraints weight = 6818.525| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.62 r_work: 0.4141 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4671 Z= 0.230 Angle : 0.685 6.027 6288 Z= 0.383 Chirality : 0.052 0.144 839 Planarity : 0.002 0.010 778 Dihedral : 7.255 31.817 679 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.37 % Favored : 82.63 % Rotamer: Outliers : 1.53 % Allowed : 22.00 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.08 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 TYR 0.012 0.002 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1313.42 seconds wall clock time: 24 minutes 40.78 seconds (1480.78 seconds total)