Starting phenix.real_space_refine on Sat Dec 9 18:01:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/12_2023/6fq8_4299.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/12_2023/6fq8_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_4299/12_2023/6fq8_4299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/12_2023/6fq8_4299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/12_2023/6fq8_4299.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6fq8_4299/12_2023/6fq8_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-1.21rc1-5172/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: 6.57, per 1000 atoms: 0.55 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: 7.46 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: 6.19 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: 4.65 Time building geometry restraints manager: 7.67 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: 0.310 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: 1.700 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 41.300 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- 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 : 0.944 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 outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.3367 time to fit residues: 99.2461 Evaluate side-chains 114 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0492 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2560 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= 0.246 Angle : 0.689 8.012 18454 Z= 0.409 Chirality : 0.039 0.167 2110 Planarity : 0.005 0.045 1313 Dihedral : 31.887 179.108 4038 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.16 % Allowed : 0.97 % 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: 0.76 (0.29), residues: 728 helix: 1.12 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 82 PHE 0.019 0.003 PHE C 25 TYR 0.032 0.002 TYR B 98 ARG 0.006 0.001 ARG G 29 *********************** 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 160 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.005 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 outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.3168 time to fit residues: 68.6223 Evaluate side-chains 95 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.073 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1332 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 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: 9.1996 ------------------------------------------------------------------------------- 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 108 ASN F 27 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 79 HIS H 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 12724 Z= 0.430 Angle : 0.853 10.128 18454 Z= 0.500 Chirality : 0.047 0.242 2110 Planarity : 0.007 0.063 1313 Dihedral : 33.088 178.136 4038 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 41.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.32 % Allowed : 1.30 % 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: -0.05 (0.28), residues: 728 helix: 0.49 (0.21), residues: 523 sheet: None (None), residues: 0 loop : -1.22 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS C 31 PHE 0.028 0.003 PHE A 104 TYR 0.024 0.003 TYR C 57 ARG 0.008 0.001 ARG F 67 *********************** 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 132 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.868 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 outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.2764 time to fit residues: 50.0369 Evaluate side-chains 84 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1065 time to fit residues: 1.2690 ------------------------------------------------------------------------------- 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: 0.0770 chunk 46 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 overall best weight: 4.0944 ------------------------------------------------------------------------------- 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** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4477 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= 0.249 Angle : 0.698 12.078 18454 Z= 0.414 Chirality : 0.040 0.169 2110 Planarity : 0.005 0.052 1313 Dihedral : 32.912 177.280 4038 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.16 % Allowed : 2.27 % Favored : 97.57 % 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: 0.49 (0.29), residues: 728 helix: 0.98 (0.21), residues: 526 sheet: None (None), residues: 0 loop : -1.32 (0.39), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.002 HIS H 106 PHE 0.018 0.002 PHE A 104 TYR 0.018 0.002 TYR B 72 ARG 0.007 0.001 ARG F 67 *********************** 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 132 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.978 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 outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2912 time to fit residues: 52.1813 Evaluate side-chains 88 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0413 ------------------------------------------------------------------------------- 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: 5.9990 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 12724 Z= 0.305 Angle : 0.722 11.876 18454 Z= 0.428 Chirality : 0.041 0.171 2110 Planarity : 0.006 0.066 1313 Dihedral : 33.166 179.773 4038 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 31.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 1.02 (0.21), residues: 515 sheet: None (None), residues: 0 loop : -1.30 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 82 PHE 0.015 0.002 PHE E 78 TYR 0.020 0.002 TYR H 37 ARG 0.006 0.001 ARG A 69 *********************** 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 118 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.954 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 outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.3109 time to fit residues: 50.0689 Evaluate side-chains 74 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0209 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12724 Z= 0.319 Angle : 0.751 12.300 18454 Z= 0.444 Chirality : 0.042 0.170 2110 Planarity : 0.006 0.104 1313 Dihedral : 33.489 178.417 4038 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 32.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: 0.31 (0.29), residues: 728 helix: 0.94 (0.21), residues: 515 sheet: None (None), residues: 0 loop : -1.55 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS G 31 PHE 0.042 0.003 PHE A 104 TYR 0.031 0.003 TYR F 72 ARG 0.012 0.001 ARG F 67 *********************** 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 117 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.871 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 outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2808 time to fit residues: 45.0953 Evaluate side-chains 78 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9813 ------------------------------------------------------------------------------- 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: 6.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN E 85 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5788 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= 0.247 Angle : 0.705 12.626 18454 Z= 0.415 Chirality : 0.040 0.182 2110 Planarity : 0.006 0.071 1313 Dihedral : 33.355 179.933 4038 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 24.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 0.56 (0.29), residues: 728 helix: 1.17 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.67 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.036 0.002 PHE A 104 TYR 0.020 0.002 TYR A 99 ARG 0.009 0.001 ARG F 67 *********************** 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 120 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.021 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 outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2749 time to fit residues: 45.6229 Evaluate side-chains 78 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0618 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 0.0370 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 6.0066 ------------------------------------------------------------------------------- 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 ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12724 Z= 0.306 Angle : 0.738 12.652 18454 Z= 0.435 Chirality : 0.042 0.187 2110 Planarity : 0.006 0.086 1313 Dihedral : 33.517 179.719 4038 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 31.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 0.15 (0.29), residues: 728 helix: 0.86 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.82 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 82 PHE 0.038 0.003 PHE A 104 TYR 0.025 0.002 TYR B 72 ARG 0.007 0.001 ARG E 116 *********************** 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 115 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.984 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 outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2753 time to fit residues: 43.7961 Evaluate side-chains 78 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0921 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 12724 Z= 0.337 Angle : 0.778 13.415 18454 Z= 0.457 Chirality : 0.044 0.194 2110 Planarity : 0.006 0.089 1313 Dihedral : 33.852 177.987 4038 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 35.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: -0.12 (0.29), residues: 728 helix: 0.72 (0.21), residues: 516 sheet: None (None), residues: 0 loop : -2.02 (0.37), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.002 HIS H 106 PHE 0.041 0.003 PHE A 104 TYR 0.027 0.003 TYR C 50 ARG 0.009 0.001 ARG F 67 *********************** 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 112 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.930 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 outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2662 time to fit residues: 42.3599 Evaluate side-chains 78 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0539 ------------------------------------------------------------------------------- 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: 3.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 overall best weight: 4.1586 ------------------------------------------------------------------------------- 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 E 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12724 Z= 0.257 Angle : 0.719 12.931 18454 Z= 0.422 Chirality : 0.041 0.194 2110 Planarity : 0.005 0.066 1313 Dihedral : 33.654 179.297 4038 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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: 0.39 (0.29), residues: 728 helix: 1.10 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.88 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 82 PHE 0.039 0.003 PHE A 104 TYR 0.022 0.002 TYR F 72 ARG 0.005 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 119 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.961 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 outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2605 time to fit residues: 43.5637 Evaluate side-chains 76 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0091 ------------------------------------------------------------------------------- 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: 4.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.039899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.033814 restraints weight = 164915.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.034871 restraints weight = 109293.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035648 restraints weight = 78814.816| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12724 Z= 0.316 Angle : 0.760 12.942 18454 Z= 0.445 Chirality : 0.043 0.205 2110 Planarity : 0.006 0.087 1313 Dihedral : 33.803 179.306 4038 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 33.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: 0.09 (0.29), residues: 728 helix: 0.86 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.98 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS A 113 PHE 0.039 0.003 PHE A 104 TYR 0.019 0.003 TYR B 72 ARG 0.009 0.001 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.89 seconds wall clock time: 35 minutes 39.84 seconds (2139.84 seconds total)