Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 11:43:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t79_10390/07_2023/6t79_10390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t79_10390/07_2023/6t79_10390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t79_10390/07_2023/6t79_10390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t79_10390/07_2023/6t79_10390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t79_10390/07_2023/6t79_10390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t79_10390/07_2023/6t79_10390.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 290 5.49 5 S 10 5.16 5 C 6732 2.51 5 N 2270 2.21 5 O 2819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 52": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 12121 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2959 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2986 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Time building chain proxies: 5.78, per 1000 atoms: 0.48 Number of scatterers: 12121 At special positions: 0 Unit cell: (84, 124.95, 115.5, 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 10 16.00 P 290 15.00 O 2819 8.00 N 2270 7.00 C 6732 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: 5.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 68.9% alpha, 3.1% beta 142 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.601A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.632A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.654A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.859A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.543A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.582A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.562A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.256A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.544A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.686A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.521A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.600A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.540A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.600A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.976A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.732A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.582A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.563A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.254A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.546A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.687A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.522A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.830A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.497A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.526A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.021A 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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.267A 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 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.927A 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 78 364 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 5.91 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: 2040 1.33 - 1.45: 4244 1.45 - 1.56: 6042 1.56 - 1.68: 580 1.68 - 1.80: 20 Bond restraints: 12926 Sorted by residual: bond pdb=" C ALA C 47 " pdb=" N PRO C 48 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" C ALA G 47 " pdb=" N PRO G 48 " ideal model delta sigma weight residual 1.336 1.378 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.36e+00 bond pdb=" C3' DT I 87 " pdb=" O3' DT I 87 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.81e+00 bond pdb=" C3' DG J 35 " pdb=" O3' DG J 35 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.24e+00 ... (remaining 12921 not shown) Histogram of bond angle deviations from ideal: 97.83 - 104.89: 1231 104.89 - 111.95: 6823 111.95 - 119.01: 3812 119.01 - 126.07: 5860 126.07 - 133.12: 961 Bond angle restraints: 18687 Sorted by residual: angle pdb=" CA GLU G 91 " pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " ideal model delta sigma weight residual 114.10 122.74 -8.64 2.00e+00 2.50e-01 1.87e+01 angle pdb=" CA GLU C 91 " pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " ideal model delta sigma weight residual 114.10 122.71 -8.61 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CB GLU C 91 " pdb=" CG GLU C 91 " pdb=" CD GLU C 91 " ideal model delta sigma weight residual 112.60 119.72 -7.12 1.70e+00 3.46e-01 1.76e+01 angle pdb=" CB GLU G 91 " pdb=" CG GLU G 91 " pdb=" CD GLU G 91 " ideal model delta sigma weight residual 112.60 119.68 -7.08 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA GLU G 61 " pdb=" CB GLU G 61 " pdb=" CG GLU G 61 " ideal model delta sigma weight residual 114.10 121.60 -7.50 2.00e+00 2.50e-01 1.41e+01 ... (remaining 18682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 5023 28.80 - 57.60: 1640 57.60 - 86.40: 122 86.40 - 115.20: 0 115.20 - 144.00: 5 Dihedral angle restraints: 6790 sinusoidal: 4542 harmonic: 2248 Sorted by residual: dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DT I 92 " pdb=" C3' DT I 92 " pdb=" O3' DT I 92 " pdb=" P DT I 93 " ideal model delta sinusoidal sigma weight residual 220.00 76.00 144.00 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" C4' DC I 13 " pdb=" C3' DC I 13 " pdb=" O3' DC I 13 " pdb=" P DT I 14 " ideal model delta sinusoidal sigma weight residual 220.00 76.90 143.10 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 6787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1420 0.041 - 0.082: 553 0.082 - 0.123: 116 0.123 - 0.164: 27 0.164 - 0.204: 5 Chirality restraints: 2121 Sorted by residual: chirality pdb=" C3' DT I 87 " pdb=" C4' DT I 87 " pdb=" O3' DT I 87 " pdb=" C2' DT I 87 " both_signs ideal model delta sigma weight residual False -2.66 -2.46 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB VAL D 108 " pdb=" CA VAL D 108 " pdb=" CG1 VAL D 108 " pdb=" CG2 VAL D 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CB VAL H 108 " pdb=" CA VAL H 108 " pdb=" CG1 VAL H 108 " pdb=" CG2 VAL H 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 2118 not shown) Planarity restraints: 1359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO C 80 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 121 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO G 80 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.038 5.00e-02 4.00e+02 ... (remaining 1356 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 799 2.72 - 3.27: 10004 3.27 - 3.81: 23673 3.81 - 4.36: 29233 4.36 - 4.90: 41366 Nonbonded interactions: 105075 Sorted by model distance: nonbonded pdb=" OE1 GLU C 61 " pdb=" CD2 LEU D 103 " model vdw 2.178 3.460 nonbonded pdb=" O ASP B 68 " pdb=" OG1 THR B 71 " model vdw 2.198 2.440 nonbonded pdb=" OE2 GLU C 61 " pdb=" CD2 LEU D 103 " model vdw 2.253 3.460 nonbonded pdb=" CE1 TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.293 3.340 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.309 2.440 ... (remaining 105070 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 1.750 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 36.190 Find NCS groups from input model: 0.510 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 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 : 0.006 0.063 12926 Z= 0.337 Angle : 0.848 8.642 18687 Z= 0.513 Chirality : 0.045 0.204 2121 Planarity : 0.007 0.069 1359 Dihedral : 28.256 144.003 5340 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.22), residues: 760 helix: -2.03 (0.16), residues: 535 sheet: None (None), residues: 0 loop : -1.90 (0.34), residues: 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.4082 time to fit residues: 91.2829 Evaluate side-chains 107 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 108 ASN A 113 HIS A 125 GLN D 46 HIS D 60 ASN D 92 GLN E 68 GLN E 108 ASN F 25 ASN F 75 HIS G 73 ASN H 46 HIS H 92 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 12926 Z= 0.259 Angle : 0.614 5.984 18687 Z= 0.372 Chirality : 0.035 0.158 2121 Planarity : 0.005 0.050 1359 Dihedral : 32.005 145.071 3784 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.40 % 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: -0.79 (0.27), residues: 760 helix: -0.02 (0.21), residues: 528 sheet: None (None), residues: 0 loop : -1.48 (0.35), residues: 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.917 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 119 average time/residue: 0.3075 time to fit residues: 48.9148 Evaluate side-chains 112 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1059 time to fit residues: 2.1074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN F 25 ASN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.055 12926 Z= 0.365 Angle : 0.680 5.838 18687 Z= 0.401 Chirality : 0.038 0.136 2121 Planarity : 0.005 0.046 1359 Dihedral : 32.366 142.783 3784 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 1.55 % 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: -0.41 (0.28), residues: 760 helix: 0.25 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 112 time to evaluate : 0.877 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 120 average time/residue: 0.3186 time to fit residues: 50.8349 Evaluate side-chains 108 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1081 time to fit residues: 1.4744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12926 Z= 0.222 Angle : 0.607 5.504 18687 Z= 0.367 Chirality : 0.035 0.139 2121 Planarity : 0.004 0.042 1359 Dihedral : 32.243 142.727 3784 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 1.71 % 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: 0.30 (0.29), residues: 760 helix: 0.78 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.13 (0.37), residues: 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 0.900 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 121 average time/residue: 0.3355 time to fit residues: 54.0442 Evaluate side-chains 113 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1927 time to fit residues: 2.2409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN G 73 ASN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 12926 Z= 0.211 Angle : 0.590 5.437 18687 Z= 0.357 Chirality : 0.034 0.150 2121 Planarity : 0.004 0.051 1359 Dihedral : 32.050 145.027 3784 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 1.71 % 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: 0.77 (0.29), residues: 760 helix: 1.18 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -1.09 (0.37), residues: 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 0.983 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 115 average time/residue: 0.3310 time to fit residues: 51.2746 Evaluate side-chains 106 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1095 time to fit residues: 1.7755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN F 25 ASN G 73 ASN H 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 12926 Z= 0.339 Angle : 0.660 6.454 18687 Z= 0.391 Chirality : 0.038 0.138 2121 Planarity : 0.005 0.040 1359 Dihedral : 32.294 142.467 3784 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 1.71 % 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: 0.38 (0.29), residues: 760 helix: 0.87 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.18 (0.36), residues: 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.143 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 109 average time/residue: 0.3210 time to fit residues: 47.5207 Evaluate side-chains 106 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1719 time to fit residues: 3.1258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 81 ASN E 108 ASN F 25 ASN G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12926 Z= 0.178 Angle : 0.585 5.304 18687 Z= 0.356 Chirality : 0.034 0.134 2121 Planarity : 0.004 0.040 1359 Dihedral : 32.060 144.108 3784 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer Outliers : 1.09 % 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: 1.07 (0.29), residues: 760 helix: 1.40 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.962 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 114 average time/residue: 0.3356 time to fit residues: 50.7747 Evaluate side-chains 102 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1028 time to fit residues: 1.2858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 94 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 79 HIS E 108 ASN F 25 ASN G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12926 Z= 0.215 Angle : 0.590 5.358 18687 Z= 0.357 Chirality : 0.034 0.165 2121 Planarity : 0.004 0.040 1359 Dihedral : 31.944 144.291 3784 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 1.24 % 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: 1.13 (0.29), residues: 760 helix: 1.44 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.867 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 104 average time/residue: 0.2956 time to fit residues: 42.1178 Evaluate side-chains 104 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1564 time to fit residues: 2.5543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 79 HIS F 25 ASN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 12926 Z= 0.277 Angle : 0.624 5.472 18687 Z= 0.373 Chirality : 0.036 0.156 2121 Planarity : 0.004 0.040 1359 Dihedral : 32.022 142.273 3784 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.62 % 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: 0.88 (0.29), residues: 760 helix: 1.23 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.921 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 108 average time/residue: 0.3182 time to fit residues: 46.9929 Evaluate side-chains 103 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1278 time to fit residues: 1.4331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 79 HIS F 25 ASN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 12926 Z= 0.282 Angle : 0.628 5.474 18687 Z= 0.375 Chirality : 0.036 0.151 2121 Planarity : 0.004 0.040 1359 Dihedral : 32.104 144.134 3784 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.78 % 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: 760 helix: 1.19 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.005 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 108 average time/residue: 0.3389 time to fit residues: 48.2667 Evaluate side-chains 105 residues out of total 645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1100 time to fit residues: 1.2044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS F 25 ASN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.154149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.114486 restraints weight = 18707.286| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.10 r_work: 0.3273 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 12926 Z= 0.241 Angle : 0.619 6.339 18687 Z= 0.372 Chirality : 0.035 0.153 2121 Planarity : 0.004 0.062 1359 Dihedral : 32.104 144.299 3784 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer Outliers : 0.78 % 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: 0.89 (0.29), residues: 760 helix: 1.25 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.98 (0.37), residues: 220 =============================================================================== Job complete usr+sys time: 2034.27 seconds wall clock time: 37 minutes 53.25 seconds (2273.25 seconds total)