Starting phenix.real_space_refine on Fri Jan 19 15:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/01_2024/6fq8_4299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/01_2024/6fq8_4299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/01_2024/6fq8_4299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/01_2024/6fq8_4299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/01_2024/6fq8_4299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/01_2024/6fq8_4299.pdb" } resolution = 4.8 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= 0.003 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 12 5.16 5 C 6575 2.51 5 N 2231 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11913 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 765 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 690 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 6.42, per 1000 atoms: 0.54 Number of scatterers: 11913 At special positions: 0 Unit cell: (77, 123.2, 110.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 294 15.00 O 2801 8.00 N 2231 7.00 C 6575 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: 6.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 75.1% alpha, 2.7% beta 145 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.625A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 47 through 77 removed outlier: 4.170A pdb=" N TYR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.563A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.374A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.726A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.678A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.845A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.687A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 47 through 76 removed outlier: 4.011A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.586A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 4.020A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.346A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.968A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.653A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.050A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.439A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.007A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.817A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.113A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 404 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.80 Time building geometry restraints manager: 6.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1837 1.33 - 1.45: 4571 1.45 - 1.57: 5708 1.57 - 1.69: 586 1.69 - 1.81: 22 Bond restraints: 12724 Sorted by residual: bond pdb=" C ARG E 42 " pdb=" N PRO E 43 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.19e-02 7.06e+03 1.31e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.97e+00 bond pdb=" C LEU E 65 " pdb=" N PRO E 66 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.36e-02 5.41e+03 5.41e+00 bond pdb=" C3' DT J 31 " pdb=" O3' DT J 31 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.06e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.489 -0.067 3.00e-02 1.11e+03 4.98e+00 ... (remaining 12719 not shown) Histogram of bond angle deviations from ideal: 94.35 - 102.06: 285 102.06 - 109.77: 4357 109.77 - 117.48: 6142 117.48 - 125.19: 6670 125.19 - 132.90: 1000 Bond angle restraints: 18454 Sorted by residual: angle pdb=" N LEU B 22 " pdb=" CA LEU B 22 " pdb=" C LEU B 22 " ideal model delta sigma weight residual 111.17 120.49 -9.32 1.41e+00 5.03e-01 4.37e+01 angle pdb=" O4' DA I 26 " pdb=" C1' DA I 26 " pdb=" N9 DA I 26 " ideal model delta sigma weight residual 108.40 100.85 7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" C ASP C 90 " pdb=" N GLU C 91 " pdb=" CA GLU C 91 " ideal model delta sigma weight residual 120.82 128.36 -7.54 1.50e+00 4.44e-01 2.53e+01 angle pdb=" OP1 DC J 10 " pdb=" P DC J 10 " pdb=" O5' DC J 10 " ideal model delta sigma weight residual 109.00 94.35 14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" N PRO E 43 " pdb=" CA PRO E 43 " pdb=" C PRO E 43 " ideal model delta sigma weight residual 111.26 118.60 -7.34 1.63e+00 3.76e-01 2.03e+01 ... (remaining 18449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.58: 5446 32.58 - 65.15: 1398 65.15 - 97.73: 37 97.73 - 130.30: 4 130.30 - 162.88: 2 Dihedral angle restraints: 6887 sinusoidal: 4725 harmonic: 2162 Sorted by residual: dihedral pdb=" CA VAL B 21 " pdb=" C VAL B 21 " pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 57.12 162.88 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 59.56 160.44 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 6884 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1523 0.070 - 0.140: 494 0.140 - 0.210: 84 0.210 - 0.280: 4 0.280 - 0.350: 5 Chirality restraints: 2110 Sorted by residual: chirality pdb=" C1' DG I 20 " pdb=" O4' DG I 20 " pdb=" C2' DG I 20 " pdb=" N9 DG I 20 " both_signs ideal model delta sigma weight residual False 2.42 2.07 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C1' DA J 16 " pdb=" O4' DA J 16 " pdb=" C2' DA J 16 " pdb=" N9 DA J 16 " both_signs ideal model delta sigma weight residual False 2.42 2.10 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1' DT I 33 " pdb=" O4' DT I 33 " pdb=" C2' DT I 33 " pdb=" N1 DT I 33 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2107 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 54 " 0.061 2.00e-02 2.50e+03 2.88e-02 2.07e+01 pdb=" N1 DT I 54 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DT I 54 " -0.021 2.00e-02 2.50e+03 pdb=" O2 DT I 54 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT I 54 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DT I 54 " 0.012 2.00e-02 2.50e+03 pdb=" O4 DT I 54 " 0.020 2.00e-02 2.50e+03 pdb=" C5 DT I 54 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 54 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 54 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.065 2.00e-02 2.50e+03 2.71e-02 2.02e+01 pdb=" N9 DA I 26 " 0.048 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.019 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.028 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -15 " 0.062 2.00e-02 2.50e+03 2.67e-02 1.96e+01 pdb=" N9 DA I -15 " -0.054 2.00e-02 2.50e+03 pdb=" C8 DA I -15 " -0.012 2.00e-02 2.50e+03 pdb=" N7 DA I -15 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I -15 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DA I -15 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -15 " 0.025 2.00e-02 2.50e+03 pdb=" N1 DA I -15 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -15 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DA I -15 " -0.011 2.00e-02 2.50e+03 pdb=" C4 DA I -15 " -0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2096 2.78 - 3.31: 11080 3.31 - 3.84: 25147 3.84 - 4.37: 28356 4.37 - 4.90: 39116 Nonbonded interactions: 105795 Sorted by model distance: nonbonded pdb=" OH TYR H 39 " pdb=" OP2 DG J -52 " model vdw 2.252 2.440 nonbonded pdb=" O2 DC I 61 " pdb=" N2 DG J -61 " model vdw 2.256 2.496 nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.277 2.440 nonbonded pdb=" O ILE B 50 " pdb=" OG1 THR B 54 " model vdw 2.278 2.440 nonbonded pdb=" OG SER C 18 " pdb=" O PHE C 25 " model vdw 2.320 2.440 ... (remaining 105790 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 40 through 132) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 20 through 100) selection = (chain 'F' and resid 20 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 13 through 117) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.690 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 39.300 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.008 0.074 12724 Z= 0.455 Angle : 1.161 14.650 18454 Z= 0.684 Chirality : 0.067 0.350 2110 Planarity : 0.008 0.041 1313 Dihedral : 26.946 162.875 5491 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.16 % Allowed : 1.30 % Favored : 98.54 % 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: -0.86 (0.27), residues: 728 helix: -0.24 (0.20), residues: 502 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS G 82 PHE 0.044 0.005 PHE A 104 TYR 0.034 0.003 TYR A 41 ARG 0.006 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9089 (tp30) cc_final: 0.8845 (tm-30) REVERT: A 100 LEU cc_start: 0.9661 (mt) cc_final: 0.9352 (pp) REVERT: B 31 LYS cc_start: 0.8792 (tttp) cc_final: 0.8568 (tmtt) REVERT: B 63 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 84 MET cc_start: 0.9144 (mmt) cc_final: 0.8793 (mpp) REVERT: C 38 ASN cc_start: 0.7504 (m-40) cc_final: 0.7167 (m-40) REVERT: C 64 GLU cc_start: 0.9468 (tt0) cc_final: 0.9213 (tp30) REVERT: D 54 LYS cc_start: 0.9408 (mttt) cc_final: 0.9084 (tmtt) REVERT: D 99 LEU cc_start: 0.9593 (mt) cc_final: 0.9326 (tp) REVERT: E 110 CYS cc_start: 0.8827 (m) cc_final: 0.8223 (m) REVERT: E 124 ILE cc_start: 0.9503 (mt) cc_final: 0.9259 (mp) REVERT: F 62 LEU cc_start: 0.9610 (mt) cc_final: 0.9184 (pp) REVERT: F 64 ASN cc_start: 0.9392 (m-40) cc_final: 0.8992 (t0) REVERT: F 68 ASP cc_start: 0.9423 (m-30) cc_final: 0.9068 (m-30) REVERT: F 72 TYR cc_start: 0.9186 (m-80) cc_final: 0.8865 (m-80) REVERT: F 81 VAL cc_start: 0.8490 (t) cc_final: 0.8265 (t) REVERT: F 84 MET cc_start: 0.8590 (mmm) cc_final: 0.7663 (ttp) REVERT: G 34 LEU cc_start: 0.9500 (mt) cc_final: 0.9267 (mt) REVERT: G 38 ASN cc_start: 0.7500 (m110) cc_final: 0.6328 (t0) REVERT: G 84 GLN cc_start: 0.8676 (tp40) cc_final: 0.8208 (tm-30) REVERT: G 94 ASN cc_start: 0.8077 (t0) cc_final: 0.7855 (t0) REVERT: G 95 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9263 (mmtm) REVERT: H 54 LYS cc_start: 0.9309 (tptm) cc_final: 0.8976 (tptt) REVERT: H 59 MET cc_start: 0.9382 (mmm) cc_final: 0.8843 (mmm) REVERT: H 65 ASP cc_start: 0.8494 (t0) cc_final: 0.8258 (t70) REVERT: H 66 VAL cc_start: 0.8933 (t) cc_final: 0.8710 (m) REVERT: H 81 ASN cc_start: 0.9315 (m-40) cc_final: 0.8926 (p0) REVERT: H 106 HIS cc_start: 0.9397 (m-70) cc_final: 0.9031 (m-70) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3237 time to fit residues: 94.2513 Evaluate side-chains 132 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 12724 Z= 0.252 Angle : 0.687 7.202 18454 Z= 0.409 Chirality : 0.039 0.166 2110 Planarity : 0.005 0.043 1313 Dihedral : 31.968 179.462 4038 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 728 helix: 1.15 (0.21), residues: 529 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 75 PHE 0.020 0.002 PHE A 104 TYR 0.036 0.003 TYR B 98 ARG 0.011 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9199 (tt0) cc_final: 0.8553 (tp-100) REVERT: A 100 LEU cc_start: 0.9789 (mt) cc_final: 0.9511 (mt) REVERT: B 63 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 84 MET cc_start: 0.9133 (mmt) cc_final: 0.8763 (mpp) REVERT: C 38 ASN cc_start: 0.7820 (m-40) cc_final: 0.7453 (m-40) REVERT: C 64 GLU cc_start: 0.9579 (tt0) cc_final: 0.9274 (tp30) REVERT: C 68 ASN cc_start: 0.9419 (m-40) cc_final: 0.9132 (m110) REVERT: D 54 LYS cc_start: 0.9416 (mttt) cc_final: 0.9105 (tmtt) REVERT: D 99 LEU cc_start: 0.9529 (mt) cc_final: 0.9177 (tp) REVERT: E 110 CYS cc_start: 0.8831 (m) cc_final: 0.8205 (m) REVERT: F 62 LEU cc_start: 0.9613 (mt) cc_final: 0.9413 (pp) REVERT: F 68 ASP cc_start: 0.9529 (m-30) cc_final: 0.9201 (m-30) REVERT: F 72 TYR cc_start: 0.9221 (m-80) cc_final: 0.8894 (m-80) REVERT: F 84 MET cc_start: 0.8365 (mmm) cc_final: 0.7476 (ttp) REVERT: G 38 ASN cc_start: 0.7803 (m110) cc_final: 0.6616 (t0) REVERT: G 84 GLN cc_start: 0.8373 (tp40) cc_final: 0.7896 (tm-30) REVERT: G 94 ASN cc_start: 0.8005 (t0) cc_final: 0.7695 (t0) REVERT: H 54 LYS cc_start: 0.9280 (tptm) cc_final: 0.8972 (tptt) REVERT: H 59 MET cc_start: 0.9354 (mmm) cc_final: 0.8927 (mmm) REVERT: H 81 ASN cc_start: 0.9168 (m-40) cc_final: 0.8864 (p0) REVERT: H 103 LEU cc_start: 0.8504 (mt) cc_final: 0.8252 (pp) REVERT: H 106 HIS cc_start: 0.9583 (m-70) cc_final: 0.8896 (m-70) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2880 time to fit residues: 64.3145 Evaluate side-chains 113 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 27 GLN F 75 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 79 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 12724 Z= 0.389 Angle : 0.800 8.898 18454 Z= 0.473 Chirality : 0.044 0.284 2110 Planarity : 0.006 0.055 1313 Dihedral : 32.851 178.647 4038 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 35.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.32 % Allowed : 0.81 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.28), residues: 728 helix: 0.64 (0.21), residues: 527 sheet: None (None), residues: 0 loop : -1.16 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 75 PHE 0.038 0.003 PHE A 104 TYR 0.018 0.003 TYR H 37 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 134 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9371 (tt0) cc_final: 0.8788 (tp-100) REVERT: A 100 LEU cc_start: 0.9797 (mt) cc_final: 0.9587 (mt) REVERT: A 108 ASN cc_start: 0.9061 (t0) cc_final: 0.8658 (m-40) REVERT: A 120 MET cc_start: 0.8596 (mtt) cc_final: 0.8316 (mtt) REVERT: B 62 LEU cc_start: 0.9498 (mm) cc_final: 0.9168 (mm) REVERT: B 63 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 84 MET cc_start: 0.9138 (mmt) cc_final: 0.8743 (mpp) REVERT: C 64 GLU cc_start: 0.9557 (tt0) cc_final: 0.9345 (tp30) REVERT: D 54 LYS cc_start: 0.9413 (mttt) cc_final: 0.9086 (tptp) REVERT: E 105 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8522 (mm-30) REVERT: E 110 CYS cc_start: 0.8862 (m) cc_final: 0.7955 (m) REVERT: F 62 LEU cc_start: 0.9756 (mt) cc_final: 0.9472 (pp) REVERT: F 72 TYR cc_start: 0.9256 (m-80) cc_final: 0.9025 (m-80) REVERT: F 81 VAL cc_start: 0.8772 (t) cc_final: 0.8393 (t) REVERT: G 94 ASN cc_start: 0.8022 (t0) cc_final: 0.7647 (t0) REVERT: H 54 LYS cc_start: 0.9344 (tptm) cc_final: 0.9028 (tptt) REVERT: H 59 MET cc_start: 0.9308 (mmm) cc_final: 0.8812 (mmm) REVERT: H 81 ASN cc_start: 0.9081 (m-40) cc_final: 0.8869 (p0) REVERT: H 103 LEU cc_start: 0.8706 (mt) cc_final: 0.8248 (mt) REVERT: H 106 HIS cc_start: 0.9623 (m-70) cc_final: 0.9144 (m-70) outliers start: 2 outliers final: 1 residues processed: 136 average time/residue: 0.2937 time to fit residues: 53.9921 Evaluate side-chains 101 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 12724 Z= 0.288 Angle : 0.703 12.039 18454 Z= 0.419 Chirality : 0.040 0.167 2110 Planarity : 0.005 0.048 1313 Dihedral : 32.928 177.544 4038 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.49 % Allowed : 2.11 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 728 helix: 0.99 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -1.25 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 31 PHE 0.021 0.003 PHE A 104 TYR 0.020 0.002 TYR B 72 ARG 0.005 0.001 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9291 (tt0) cc_final: 0.8857 (tp-100) REVERT: A 100 LEU cc_start: 0.9838 (mt) cc_final: 0.9558 (mt) REVERT: A 108 ASN cc_start: 0.8982 (t0) cc_final: 0.8608 (m-40) REVERT: B 62 LEU cc_start: 0.9430 (mm) cc_final: 0.9209 (mm) REVERT: B 63 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 84 MET cc_start: 0.9152 (mmt) cc_final: 0.8700 (mpp) REVERT: C 64 GLU cc_start: 0.9572 (tt0) cc_final: 0.9220 (tp30) REVERT: C 68 ASN cc_start: 0.9428 (m110) cc_final: 0.9121 (m110) REVERT: D 54 LYS cc_start: 0.9433 (mttt) cc_final: 0.9101 (tptp) REVERT: D 56 MET cc_start: 0.6463 (tpt) cc_final: 0.6242 (tpt) REVERT: E 92 LEU cc_start: 0.8766 (mt) cc_final: 0.8543 (mt) REVERT: E 104 PHE cc_start: 0.8831 (m-80) cc_final: 0.8480 (m-80) REVERT: E 105 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8538 (mm-30) REVERT: E 110 CYS cc_start: 0.8411 (m) cc_final: 0.7497 (m) REVERT: F 58 LEU cc_start: 0.9435 (tp) cc_final: 0.9060 (pp) REVERT: F 62 LEU cc_start: 0.9708 (mt) cc_final: 0.9280 (pp) REVERT: F 64 ASN cc_start: 0.8733 (t0) cc_final: 0.8305 (t0) REVERT: F 71 THR cc_start: 0.9714 (m) cc_final: 0.9505 (m) REVERT: F 72 TYR cc_start: 0.9273 (m-80) cc_final: 0.8933 (m-80) REVERT: F 81 VAL cc_start: 0.8725 (t) cc_final: 0.8460 (t) REVERT: F 84 MET cc_start: 0.8365 (mmm) cc_final: 0.7730 (ttp) REVERT: G 36 LYS cc_start: 0.9617 (mppt) cc_final: 0.9381 (mmtm) REVERT: G 84 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7614 (tm-30) REVERT: G 94 ASN cc_start: 0.8127 (t0) cc_final: 0.7825 (m-40) REVERT: H 54 LYS cc_start: 0.9326 (tptm) cc_final: 0.9095 (tptt) REVERT: H 59 MET cc_start: 0.9293 (mmm) cc_final: 0.8748 (mmm) REVERT: H 81 ASN cc_start: 0.9079 (m110) cc_final: 0.8870 (p0) REVERT: H 103 LEU cc_start: 0.8446 (mt) cc_final: 0.8083 (mt) REVERT: H 106 HIS cc_start: 0.9669 (m-70) cc_final: 0.9100 (m-70) outliers start: 3 outliers final: 0 residues processed: 138 average time/residue: 0.2877 time to fit residues: 53.4814 Evaluate side-chains 104 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 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 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12724 Z= 0.346 Angle : 0.763 11.258 18454 Z= 0.453 Chirality : 0.043 0.182 2110 Planarity : 0.006 0.063 1313 Dihedral : 33.440 178.914 4038 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 34.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 728 helix: 0.71 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS F 75 PHE 0.017 0.003 PHE E 78 TYR 0.022 0.003 TYR B 98 ARG 0.006 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9222 (tt0) cc_final: 0.8766 (tp-100) REVERT: A 100 LEU cc_start: 0.9801 (mt) cc_final: 0.9477 (mt) REVERT: A 120 MET cc_start: 0.8206 (mtt) cc_final: 0.7473 (mmt) REVERT: B 62 LEU cc_start: 0.9494 (mm) cc_final: 0.9257 (mm) REVERT: B 63 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 84 MET cc_start: 0.9149 (mmt) cc_final: 0.8690 (mpp) REVERT: C 64 GLU cc_start: 0.9559 (tt0) cc_final: 0.9327 (tp30) REVERT: D 54 LYS cc_start: 0.9460 (mttt) cc_final: 0.9128 (tptp) REVERT: E 104 PHE cc_start: 0.8889 (m-80) cc_final: 0.8541 (m-80) REVERT: E 105 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8593 (mm-30) REVERT: E 110 CYS cc_start: 0.8647 (m) cc_final: 0.7558 (m) REVERT: F 62 LEU cc_start: 0.9741 (mt) cc_final: 0.9480 (pp) REVERT: F 72 TYR cc_start: 0.9368 (m-80) cc_final: 0.8955 (m-80) REVERT: F 84 MET cc_start: 0.8236 (mmm) cc_final: 0.7518 (ttp) REVERT: G 36 LYS cc_start: 0.9661 (mppt) cc_final: 0.9413 (mmtm) REVERT: G 94 ASN cc_start: 0.8172 (t0) cc_final: 0.7801 (m-40) REVERT: H 54 LYS cc_start: 0.9371 (tptm) cc_final: 0.9100 (tptt) REVERT: H 59 MET cc_start: 0.9299 (mmm) cc_final: 0.8868 (mmm) REVERT: H 103 LEU cc_start: 0.8357 (mt) cc_final: 0.8113 (mt) REVERT: H 106 HIS cc_start: 0.9696 (m-70) cc_final: 0.9123 (m-70) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3086 time to fit residues: 50.0175 Evaluate side-chains 94 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12724 Z= 0.255 Angle : 0.695 12.272 18454 Z= 0.413 Chirality : 0.040 0.160 2110 Planarity : 0.005 0.065 1313 Dihedral : 33.410 178.613 4038 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 728 helix: 1.08 (0.21), residues: 520 sheet: None (None), residues: 0 loop : -1.53 (0.37), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 82 PHE 0.050 0.003 PHE A 104 TYR 0.024 0.002 TYR B 72 ARG 0.005 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9220 (tt0) cc_final: 0.8708 (tp-100) REVERT: A 120 MET cc_start: 0.8319 (mtt) cc_final: 0.7544 (mmt) REVERT: B 62 LEU cc_start: 0.9485 (mm) cc_final: 0.9205 (mm) REVERT: B 63 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7700 (mt-10) REVERT: B 84 MET cc_start: 0.9067 (mmt) cc_final: 0.8577 (mpp) REVERT: C 64 GLU cc_start: 0.9557 (tt0) cc_final: 0.9217 (tp30) REVERT: D 54 LYS cc_start: 0.9461 (mttt) cc_final: 0.9142 (tptm) REVERT: E 94 GLU cc_start: 0.9199 (mp0) cc_final: 0.8807 (mp0) REVERT: E 104 PHE cc_start: 0.8880 (m-80) cc_final: 0.8605 (m-80) REVERT: E 105 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8536 (mm-30) REVERT: E 110 CYS cc_start: 0.8584 (m) cc_final: 0.7302 (m) REVERT: F 58 LEU cc_start: 0.9393 (tp) cc_final: 0.8898 (pp) REVERT: F 62 LEU cc_start: 0.9658 (mt) cc_final: 0.9173 (pp) REVERT: F 64 ASN cc_start: 0.8715 (t0) cc_final: 0.8510 (t0) REVERT: F 72 TYR cc_start: 0.9270 (m-80) cc_final: 0.8748 (m-80) REVERT: F 84 MET cc_start: 0.8279 (mmm) cc_final: 0.7394 (ttp) REVERT: G 36 LYS cc_start: 0.9636 (mppt) cc_final: 0.9433 (mmtm) REVERT: G 84 GLN cc_start: 0.7497 (tp-100) cc_final: 0.7240 (tm-30) REVERT: G 94 ASN cc_start: 0.8219 (t0) cc_final: 0.7896 (m-40) REVERT: H 54 LYS cc_start: 0.9325 (tptm) cc_final: 0.8860 (tttm) REVERT: H 59 MET cc_start: 0.9244 (mmm) cc_final: 0.8761 (mmm) REVERT: H 103 LEU cc_start: 0.8301 (mt) cc_final: 0.8067 (mt) REVERT: H 106 HIS cc_start: 0.9656 (m-70) cc_final: 0.9095 (m-70) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.2974 time to fit residues: 51.7180 Evaluate side-chains 97 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN D 92 GLN E 85 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12724 Z= 0.243 Angle : 0.680 12.308 18454 Z= 0.403 Chirality : 0.039 0.155 2110 Planarity : 0.005 0.057 1313 Dihedral : 33.275 178.742 4038 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 0.75 (0.29), residues: 728 helix: 1.28 (0.21), residues: 521 sheet: None (None), residues: 0 loop : -1.50 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 82 PHE 0.035 0.003 PHE A 104 TYR 0.020 0.002 TYR B 72 ARG 0.006 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9216 (tt0) cc_final: 0.8760 (tp-100) REVERT: A 120 MET cc_start: 0.8396 (mtt) cc_final: 0.7506 (mmt) REVERT: B 54 THR cc_start: 0.9743 (m) cc_final: 0.9251 (m) REVERT: B 62 LEU cc_start: 0.9425 (mm) cc_final: 0.9218 (mm) REVERT: B 63 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 84 MET cc_start: 0.9058 (mmt) cc_final: 0.8567 (mpp) REVERT: C 64 GLU cc_start: 0.9550 (tt0) cc_final: 0.9217 (tp30) REVERT: C 68 ASN cc_start: 0.9504 (m-40) cc_final: 0.9103 (m110) REVERT: D 54 LYS cc_start: 0.9470 (mttt) cc_final: 0.9151 (tptm) REVERT: D 77 LEU cc_start: 0.9309 (tp) cc_final: 0.9100 (tp) REVERT: E 104 PHE cc_start: 0.8938 (m-80) cc_final: 0.8693 (m-80) REVERT: E 105 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8628 (mm-30) REVERT: E 110 CYS cc_start: 0.8772 (m) cc_final: 0.7498 (m) REVERT: F 58 LEU cc_start: 0.9381 (tp) cc_final: 0.8915 (pp) REVERT: F 62 LEU cc_start: 0.9561 (mt) cc_final: 0.9096 (pp) REVERT: F 72 TYR cc_start: 0.9298 (m-10) cc_final: 0.8846 (m-80) REVERT: F 84 MET cc_start: 0.8319 (mmm) cc_final: 0.7573 (ttp) REVERT: G 36 LYS cc_start: 0.9628 (mppt) cc_final: 0.9418 (mmtm) REVERT: G 84 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7123 (tm-30) REVERT: G 94 ASN cc_start: 0.8205 (t0) cc_final: 0.7890 (m-40) REVERT: G 100 VAL cc_start: 0.8061 (t) cc_final: 0.7846 (p) REVERT: H 54 LYS cc_start: 0.9268 (tptm) cc_final: 0.8784 (tttm) REVERT: H 59 MET cc_start: 0.9215 (mmm) cc_final: 0.8744 (mmm) REVERT: H 103 LEU cc_start: 0.8303 (mt) cc_final: 0.8083 (mt) REVERT: H 106 HIS cc_start: 0.9631 (m-70) cc_final: 0.9094 (m-70) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2990 time to fit residues: 49.9457 Evaluate side-chains 93 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 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 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12724 Z= 0.293 Angle : 0.722 12.569 18454 Z= 0.426 Chirality : 0.041 0.163 2110 Planarity : 0.005 0.083 1313 Dihedral : 33.516 179.838 4038 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 29.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 728 helix: 1.17 (0.21), residues: 519 sheet: None (None), residues: 0 loop : -1.67 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 75 PHE 0.031 0.003 PHE A 104 TYR 0.021 0.002 TYR D 39 ARG 0.009 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9267 (tt0) cc_final: 0.8774 (tp-100) REVERT: A 120 MET cc_start: 0.8334 (mtt) cc_final: 0.7802 (mmt) REVERT: B 63 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7768 (mt-10) REVERT: B 84 MET cc_start: 0.9132 (mmt) cc_final: 0.8592 (mpp) REVERT: B 92 ARG cc_start: 0.7897 (tmt170) cc_final: 0.7666 (tmm160) REVERT: C 64 GLU cc_start: 0.9555 (tt0) cc_final: 0.9213 (tp30) REVERT: C 68 ASN cc_start: 0.9411 (m-40) cc_final: 0.8933 (m110) REVERT: C 94 ASN cc_start: 0.9195 (t0) cc_final: 0.8980 (t0) REVERT: D 54 LYS cc_start: 0.9481 (mttt) cc_final: 0.9233 (tttp) REVERT: D 99 LEU cc_start: 0.9345 (mm) cc_final: 0.9130 (mm) REVERT: E 104 PHE cc_start: 0.8879 (m-10) cc_final: 0.8605 (m-80) REVERT: E 105 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8640 (mm-30) REVERT: E 110 CYS cc_start: 0.8752 (m) cc_final: 0.7642 (m) REVERT: F 58 LEU cc_start: 0.9442 (tp) cc_final: 0.8957 (pp) REVERT: F 62 LEU cc_start: 0.9567 (mt) cc_final: 0.9064 (pp) REVERT: F 72 TYR cc_start: 0.9271 (m-10) cc_final: 0.8926 (m-80) REVERT: F 84 MET cc_start: 0.8434 (mmm) cc_final: 0.8056 (mpp) REVERT: G 94 ASN cc_start: 0.8110 (t0) cc_final: 0.7749 (m-40) REVERT: H 54 LYS cc_start: 0.9277 (tptm) cc_final: 0.8794 (tttm) REVERT: H 59 MET cc_start: 0.9229 (mmm) cc_final: 0.8854 (mmm) REVERT: H 103 LEU cc_start: 0.8330 (mt) cc_final: 0.8090 (mt) REVERT: H 106 HIS cc_start: 0.9681 (m-70) cc_final: 0.9116 (m-70) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3022 time to fit residues: 48.2146 Evaluate side-chains 91 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 12724 Z= 0.361 Angle : 0.795 13.118 18454 Z= 0.469 Chirality : 0.044 0.178 2110 Planarity : 0.006 0.078 1313 Dihedral : 33.931 179.385 4038 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 38.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.29), residues: 728 helix: 0.63 (0.21), residues: 523 sheet: None (None), residues: 0 loop : -2.14 (0.37), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 82 PHE 0.028 0.003 PHE A 104 TYR 0.035 0.003 TYR D 39 ARG 0.014 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9234 (tt0) cc_final: 0.8833 (tp-100) REVERT: A 120 MET cc_start: 0.8078 (mtt) cc_final: 0.7552 (mtt) REVERT: B 63 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7837 (mt-10) REVERT: B 84 MET cc_start: 0.9213 (mmt) cc_final: 0.8703 (mpp) REVERT: B 92 ARG cc_start: 0.7959 (tmt170) cc_final: 0.7706 (tmm160) REVERT: C 64 GLU cc_start: 0.9583 (tt0) cc_final: 0.9301 (tp30) REVERT: C 94 ASN cc_start: 0.9212 (t0) cc_final: 0.8993 (t0) REVERT: D 54 LYS cc_start: 0.9475 (mttt) cc_final: 0.9155 (tptm) REVERT: E 94 GLU cc_start: 0.9212 (mp0) cc_final: 0.8806 (mp0) REVERT: E 104 PHE cc_start: 0.8958 (m-10) cc_final: 0.8735 (m-80) REVERT: E 105 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8709 (mm-30) REVERT: E 110 CYS cc_start: 0.8613 (m) cc_final: 0.7387 (m) REVERT: F 62 LEU cc_start: 0.9642 (mt) cc_final: 0.9226 (pp) REVERT: F 72 TYR cc_start: 0.9305 (m-10) cc_final: 0.9014 (m-80) REVERT: F 84 MET cc_start: 0.8464 (mmm) cc_final: 0.8089 (mpp) REVERT: G 94 ASN cc_start: 0.8027 (t0) cc_final: 0.7662 (t0) REVERT: H 54 LYS cc_start: 0.9337 (tptm) cc_final: 0.8935 (tttm) REVERT: H 59 MET cc_start: 0.9317 (mmm) cc_final: 0.9015 (mmm) REVERT: H 103 LEU cc_start: 0.8354 (mt) cc_final: 0.8109 (mt) REVERT: H 106 HIS cc_start: 0.9720 (m-70) cc_final: 0.9163 (m-70) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2707 time to fit residues: 39.7355 Evaluate side-chains 84 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.0070 chunk 64 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12724 Z= 0.309 Angle : 0.751 12.700 18454 Z= 0.445 Chirality : 0.042 0.166 2110 Planarity : 0.005 0.060 1313 Dihedral : 33.896 178.330 4038 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 31.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.29), residues: 728 helix: 0.79 (0.21), residues: 519 sheet: None (None), residues: 0 loop : -1.96 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 82 PHE 0.026 0.003 PHE A 104 TYR 0.018 0.002 TYR C 57 ARG 0.010 0.001 ARG G 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9199 (mpp) cc_final: 0.8971 (mpp) REVERT: A 93 GLN cc_start: 0.9288 (tt0) cc_final: 0.8727 (tp-100) REVERT: A 94 GLU cc_start: 0.9242 (pp20) cc_final: 0.8680 (pp20) REVERT: A 97 GLU cc_start: 0.8922 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 108 ASN cc_start: 0.8900 (m110) cc_final: 0.8610 (m-40) REVERT: A 120 MET cc_start: 0.8327 (mtt) cc_final: 0.7702 (mtt) REVERT: B 62 LEU cc_start: 0.9525 (mm) cc_final: 0.9292 (mm) REVERT: B 63 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 71 THR cc_start: 0.8946 (p) cc_final: 0.8694 (p) REVERT: B 84 MET cc_start: 0.9153 (mmt) cc_final: 0.8621 (mpp) REVERT: C 64 GLU cc_start: 0.9577 (tt0) cc_final: 0.9330 (tp30) REVERT: C 94 ASN cc_start: 0.9197 (t0) cc_final: 0.8940 (t0) REVERT: D 54 LYS cc_start: 0.9477 (mttt) cc_final: 0.9144 (tptm) REVERT: D 77 LEU cc_start: 0.9371 (tp) cc_final: 0.8914 (pp) REVERT: D 97 LEU cc_start: 0.9217 (tp) cc_final: 0.8753 (tt) REVERT: E 94 GLU cc_start: 0.9241 (mp0) cc_final: 0.8800 (mp0) REVERT: E 104 PHE cc_start: 0.8872 (m-10) cc_final: 0.8623 (m-80) REVERT: E 105 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8752 (mm-30) REVERT: E 110 CYS cc_start: 0.8591 (m) cc_final: 0.7357 (m) REVERT: F 62 LEU cc_start: 0.9621 (mt) cc_final: 0.9208 (pp) REVERT: F 72 TYR cc_start: 0.9363 (m-10) cc_final: 0.9018 (m-80) REVERT: F 84 MET cc_start: 0.8472 (mmm) cc_final: 0.8181 (mpp) REVERT: G 94 ASN cc_start: 0.7979 (t0) cc_final: 0.7646 (m-40) REVERT: H 54 LYS cc_start: 0.9247 (tptm) cc_final: 0.8771 (tttm) REVERT: H 59 MET cc_start: 0.9302 (mmm) cc_final: 0.8951 (mmm) REVERT: H 106 HIS cc_start: 0.9689 (m-70) cc_final: 0.9192 (m-70) REVERT: H 117 LYS cc_start: 0.9650 (ttpt) cc_final: 0.9401 (ptmt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2891 time to fit residues: 47.1949 Evaluate side-chains 88 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 23 optimal weight: 0.0170 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.043822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.037340 restraints weight = 153288.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038545 restraints weight = 101084.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039440 restraints weight = 72403.758| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12724 Z= 0.217 Angle : 0.683 11.973 18454 Z= 0.402 Chirality : 0.039 0.150 2110 Planarity : 0.005 0.053 1313 Dihedral : 33.458 179.452 4038 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.74 (0.30), residues: 728 helix: 1.35 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.75 (0.37), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.024 0.002 PHE A 104 TYR 0.028 0.002 TYR B 72 ARG 0.005 0.000 ARG G 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.20 seconds wall clock time: 35 minutes 0.53 seconds (2100.53 seconds total)