Starting phenix.real_space_refine on Thu Nov 16 10:48:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/11_2023/6wua_21908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/11_2023/6wua_21908.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/6wua_21908/11_2023/6wua_21908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/11_2023/6wua_21908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/11_2023/6wua_21908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wua_21908/11_2023/6wua_21908.pdb" } resolution = 3.2 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= -0.001 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 402 5.49 5 S 20 5.16 5 C 7975 2.51 5 N 2807 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c GLU 25": "OE1" <-> "OE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 46": "OE1" <-> "OE2" Residue "s GLU 20": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15195 Number of models: 1 Model: "" Number of chains: 9 Chain: "a" Number of atoms: 8569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 8569 Classifications: {'RNA': 402} Modifications used: {'rna2p_pur': 33, 'rna2p_pyr': 39, 'rna3p_pur': 177, 'rna3p_pyr': 153} Link IDs: {'rna2p': 71, 'rna3p': 330} Chain breaks: 1 Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1610 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 4, 'TRANS': 199} Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1229 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 120} Chain: "j" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 800 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "m" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 104} Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "s" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 634 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14249 SG CYS n 24 57.908 83.292 49.350 1.00 17.98 S ATOM 14275 SG CYS n 27 61.128 84.467 48.757 1.00 19.90 S ATOM 14387 SG CYS n 40 60.686 82.934 52.027 1.00 18.14 S ATOM 14412 SG CYS n 43 59.723 86.442 51.550 1.00 17.83 S Time building chain proxies: 8.68, per 1000 atoms: 0.57 Number of scatterers: 15195 At special positions: 0 Unit cell: (109.7, 132.737, 127.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 20 16.00 P 402 15.00 O 3990 8.00 N 2807 7.00 C 7975 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: 7.26 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " Number of angles added : 6 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 42.4% alpha, 20.4% beta 123 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'c' and resid 28 through 42 Processing helix chain 'c' and resid 45 through 50 Processing helix chain 'c' and resid 72 through 77 Processing helix chain 'c' and resid 82 through 95 removed outlier: 4.201A pdb=" N LYS c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU c 93 " --> pdb=" O GLU c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.565A pdb=" N ARG c 126 " --> pdb=" O LEU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.662A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 159 removed outlier: 3.635A pdb=" N GLY c 158 " --> pdb=" O ARG c 155 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 53 removed outlier: 3.704A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.515A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 128 removed outlier: 4.082A pdb=" N LYS g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 149 through 153 removed outlier: 3.674A pdb=" N HIS g 153 " --> pdb=" O ALA g 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.556A pdb=" N ILE i 39 " --> pdb=" O VAL i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 44 through 49 Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 73 through 91 removed outlier: 3.741A pdb=" N GLY i 77 " --> pdb=" O ALA i 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE i 79 " --> pdb=" O GLN i 75 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 95 Processing helix chain 'i' and resid 96 through 101 removed outlier: 3.601A pdb=" N ALA i 101 " --> pdb=" O ALA i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 Processing helix chain 'j' and resid 82 through 89 removed outlier: 3.711A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.703A pdb=" N VAL m 37 " --> pdb=" O VAL m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 59 removed outlier: 3.557A pdb=" N ASP m 54 " --> pdb=" O ASN m 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU m 59 " --> pdb=" O ALA m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 63 Processing helix chain 'm' and resid 68 through 81 removed outlier: 3.840A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 92 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 4 through 12 removed outlier: 3.751A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 20 removed outlier: 3.796A pdb=" N ALA n 20 " --> pdb=" O SER n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 49 removed outlier: 3.985A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU n 46 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 70 through 75 removed outlier: 3.801A pdb=" N PHE s 74 " --> pdb=" O LEU s 71 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA s 75 " --> pdb=" O GLY s 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 58 removed outlier: 3.958A pdb=" N THR c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE c 67 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 165 removed outlier: 3.552A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL c 197 " --> pdb=" O GLU c 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'g' and resid 74 through 79 removed outlier: 3.580A pdb=" N GLU g 74 " --> pdb=" O VAL g 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 6 through 12 removed outlier: 6.540A pdb=" N LYS i 27 " --> pdb=" O VAL i 63 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL i 65 " --> pdb=" O LYS i 27 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL i 67 " --> pdb=" O THR i 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 40 through 52 removed outlier: 6.457A pdb=" N LEU j 73 " --> pdb=" O PRO j 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 33 through 34 Processing sheet with id=AB1, first strand: chain 's' and resid 32 through 33 removed outlier: 3.684A pdb=" N TYR s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) 273 hydrogen bonds defined for protein. 768 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 494 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 6.61 Time building geometry restraints manager: 7.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1771 1.32 - 1.44: 6560 1.44 - 1.56: 7140 1.56 - 1.68: 802 1.68 - 1.80: 36 Bond restraints: 16309 Sorted by residual: bond pdb=" CA PRO i 40 " pdb=" C PRO i 40 " ideal model delta sigma weight residual 1.527 1.502 0.025 1.35e-02 5.49e+03 3.36e+00 bond pdb=" N ALA m 106 " pdb=" CA ALA m 106 " ideal model delta sigma weight residual 1.457 1.441 0.017 1.10e-02 8.26e+03 2.27e+00 bond pdb=" C5 G a1237 " pdb=" C6 G a1237 " ideal model delta sigma weight residual 1.419 1.391 0.028 2.00e-02 2.50e+03 1.95e+00 bond pdb=" O3' G a1237 " pdb=" P C a1238 " ideal model delta sigma weight residual 1.607 1.588 0.019 1.50e-02 4.44e+03 1.65e+00 bond pdb=" P G a1237 " pdb=" O5' G a1237 " ideal model delta sigma weight residual 1.593 1.574 0.019 1.50e-02 4.44e+03 1.60e+00 ... (remaining 16304 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.29: 2449 106.29 - 113.37: 9470 113.37 - 120.44: 6380 120.44 - 127.52: 4867 127.52 - 134.59: 797 Bond angle restraints: 23963 Sorted by residual: angle pdb=" N PRO j 43 " pdb=" CA PRO j 43 " pdb=" C PRO j 43 " ideal model delta sigma weight residual 112.47 120.95 -8.48 2.06e+00 2.36e-01 1.70e+01 angle pdb=" C PRO i 40 " pdb=" N HIS i 41 " pdb=" CA HIS i 41 " ideal model delta sigma weight residual 121.54 113.84 7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" N VAL c 75 " pdb=" CA VAL c 75 " pdb=" C VAL c 75 " ideal model delta sigma weight residual 113.71 110.15 3.56 9.50e-01 1.11e+00 1.40e+01 angle pdb=" C3' U a1226 " pdb=" O3' U a1226 " pdb=" P U a1227 " ideal model delta sigma weight residual 120.20 124.97 -4.77 1.50e+00 4.44e-01 1.01e+01 angle pdb=" C2' G a1019 " pdb=" C1' G a1019 " pdb=" N9 G a1019 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.50e+00 4.44e-01 1.00e+01 ... (remaining 23958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 8516 33.72 - 67.44: 435 67.44 - 101.17: 33 101.17 - 134.89: 3 134.89 - 168.61: 3 Dihedral angle restraints: 8990 sinusoidal: 6599 harmonic: 2391 Sorted by residual: dihedral pdb=" O4' U a1040 " pdb=" C1' U a1040 " pdb=" N1 U a1040 " pdb=" C2 U a1040 " ideal model delta sinusoidal sigma weight residual 200.00 53.67 146.33 1 1.50e+01 4.44e-03 7.82e+01 dihedral pdb=" O4' C a1173 " pdb=" C1' C a1173 " pdb=" N1 C a1173 " pdb=" C2 C a1173 " ideal model delta sinusoidal sigma weight residual 200.00 65.56 134.44 1 1.50e+01 4.44e-03 7.25e+01 dihedral pdb=" O4' U a1152 " pdb=" C1' U a1152 " pdb=" N1 U a1152 " pdb=" C2 U a1152 " ideal model delta sinusoidal sigma weight residual 200.00 67.00 133.00 1 1.50e+01 4.44e-03 7.18e+01 ... (remaining 8987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2274 0.051 - 0.102: 608 0.102 - 0.153: 102 0.153 - 0.203: 17 0.203 - 0.254: 4 Chirality restraints: 3005 Sorted by residual: chirality pdb=" CA PRO j 43 " pdb=" N PRO j 43 " pdb=" C PRO j 43 " pdb=" CB PRO j 43 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' A a 974 " pdb=" C4' A a 974 " pdb=" O3' A a 974 " pdb=" C2' A a 974 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1' U a1226 " pdb=" O4' U a1226 " pdb=" C2' U a1226 " pdb=" N1 U a1226 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3002 not shown) Planarity restraints: 1570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU j 42 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO j 43 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G a1019 " -0.038 2.00e-02 2.50e+03 1.59e-02 7.56e+00 pdb=" N9 G a1019 " 0.036 2.00e-02 2.50e+03 pdb=" C8 G a1019 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G a1019 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G a1019 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G a1019 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G a1019 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G a1019 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G a1019 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G a1019 " 0.005 2.00e-02 2.50e+03 pdb=" N3 G a1019 " 0.009 2.00e-02 2.50e+03 pdb=" C4 G a1019 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU j 92 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.16e+00 pdb=" N PRO j 93 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO j 93 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO j 93 " 0.029 5.00e-02 4.00e+02 ... (remaining 1567 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 114 2.57 - 3.16: 11330 3.16 - 3.74: 25652 3.74 - 4.32: 37749 4.32 - 4.90: 53156 Nonbonded interactions: 128001 Sorted by model distance: nonbonded pdb=" O2 U a 976 " pdb=" O2' G a1237 " model vdw 1.992 2.440 nonbonded pdb=" N2 G a1019 " pdb=" N6 A a1052 " model vdw 2.033 2.560 nonbonded pdb=" O4 U a 966 " pdb=" NZ LYS m 103 " model vdw 2.141 2.520 nonbonded pdb=" N1 G a1181 " pdb=" OP2 A a1184 " model vdw 2.166 2.520 nonbonded pdb=" O2' C a1038 " pdb=" O5' U a1039 " model vdw 2.182 2.440 ... (remaining 127996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.750 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: 18.540 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 50.170 Find NCS groups from input model: 0.300 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.007 0.048 16309 Z= 0.414 Angle : 0.813 8.484 23963 Z= 0.424 Chirality : 0.047 0.254 3005 Planarity : 0.006 0.070 1570 Dihedral : 16.543 168.610 7452 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.38 % Favored : 84.49 % Rotamer: Outliers : 14.80 % Allowed : 15.80 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.24), residues: 819 helix: -2.49 (0.24), residues: 306 sheet: -2.26 (0.38), residues: 139 loop : -3.57 (0.27), residues: 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 153 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 57 residues processed: 233 average time/residue: 0.3417 time to fit residues: 109.1163 Evaluate side-chains 166 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 109 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.1991 time to fit residues: 19.2900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN g 64 GLN g 86 GLN i 66 ASN i 81 HIS m 50 ASN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 HIS ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 63 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16309 Z= 0.218 Angle : 0.638 6.831 23963 Z= 0.334 Chirality : 0.040 0.201 3005 Planarity : 0.005 0.059 1570 Dihedral : 14.537 170.517 5760 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 3.59 % Allowed : 25.14 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -2.98 (0.27), residues: 819 helix: -1.01 (0.28), residues: 307 sheet: -1.30 (0.40), residues: 147 loop : -3.16 (0.29), residues: 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 1.108 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 136 average time/residue: 0.2926 time to fit residues: 58.6253 Evaluate side-chains 104 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1390 time to fit residues: 3.9753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 109 optimal weight: 0.2980 chunk 117 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 108 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 61 ASN ** c 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16309 Z= 0.307 Angle : 0.704 7.536 23963 Z= 0.364 Chirality : 0.043 0.229 3005 Planarity : 0.006 0.072 1570 Dihedral : 14.675 166.432 5760 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 6.18 % Allowed : 24.86 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -2.57 (0.28), residues: 819 helix: -0.69 (0.29), residues: 309 sheet: -0.94 (0.41), residues: 143 loop : -2.98 (0.29), residues: 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 95 time to evaluate : 1.086 Fit side-chains outliers start: 43 outliers final: 22 residues processed: 130 average time/residue: 0.2571 time to fit residues: 51.2093 Evaluate side-chains 111 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1476 time to fit residues: 7.1485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16309 Z= 0.235 Angle : 0.638 7.101 23963 Z= 0.333 Chirality : 0.040 0.207 3005 Planarity : 0.005 0.063 1570 Dihedral : 14.473 168.053 5760 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.59 % Allowed : 27.73 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -2.17 (0.28), residues: 819 helix: -0.30 (0.30), residues: 304 sheet: -0.56 (0.41), residues: 147 loop : -2.88 (0.30), residues: 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.034 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 122 average time/residue: 0.2413 time to fit residues: 45.3107 Evaluate side-chains 104 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1358 time to fit residues: 3.1353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 1 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16309 Z= 0.195 Angle : 0.589 9.358 23963 Z= 0.307 Chirality : 0.038 0.191 3005 Planarity : 0.005 0.067 1570 Dihedral : 14.273 169.665 5760 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.59 % Allowed : 28.02 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.93 (0.29), residues: 819 helix: -0.16 (0.30), residues: 317 sheet: -0.33 (0.42), residues: 147 loop : -2.81 (0.30), residues: 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.983 Fit side-chains outliers start: 25 outliers final: 13 residues processed: 120 average time/residue: 0.2516 time to fit residues: 46.5641 Evaluate side-chains 106 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1291 time to fit residues: 4.3398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 86 GLN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16309 Z= 0.347 Angle : 0.733 9.408 23963 Z= 0.377 Chirality : 0.045 0.239 3005 Planarity : 0.006 0.074 1570 Dihedral : 14.612 165.306 5760 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 2.59 % Allowed : 29.17 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.99 (0.29), residues: 819 helix: -0.19 (0.30), residues: 304 sheet: -0.29 (0.42), residues: 145 loop : -2.80 (0.29), residues: 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.032 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 106 average time/residue: 0.2538 time to fit residues: 41.4018 Evaluate side-chains 96 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1398 time to fit residues: 3.1484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 0.0070 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16309 Z= 0.128 Angle : 0.534 8.187 23963 Z= 0.279 Chirality : 0.035 0.180 3005 Planarity : 0.004 0.060 1570 Dihedral : 14.111 172.972 5760 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.86 % Allowed : 30.89 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.55 (0.29), residues: 819 helix: 0.10 (0.31), residues: 320 sheet: -0.03 (0.43), residues: 141 loop : -2.57 (0.30), residues: 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.354 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 102 average time/residue: 0.2549 time to fit residues: 40.2909 Evaluate side-chains 92 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4772 time to fit residues: 1.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 90 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 86 GLN g 153 HIS ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16309 Z= 0.139 Angle : 0.525 8.046 23963 Z= 0.274 Chirality : 0.034 0.181 3005 Planarity : 0.004 0.066 1570 Dihedral : 13.935 172.796 5760 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 1.44 % Allowed : 30.17 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.34 (0.29), residues: 819 helix: 0.32 (0.31), residues: 318 sheet: 0.14 (0.43), residues: 141 loop : -2.50 (0.30), residues: 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.093 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 102 average time/residue: 0.2620 time to fit residues: 40.8948 Evaluate side-chains 97 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1434 time to fit residues: 2.3266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 153 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16309 Z= 0.150 Angle : 0.531 8.049 23963 Z= 0.277 Chirality : 0.035 0.180 3005 Planarity : 0.004 0.067 1570 Dihedral : 13.863 173.142 5760 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.57 % Allowed : 31.18 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.19 (0.30), residues: 819 helix: 0.42 (0.31), residues: 318 sheet: 0.14 (0.44), residues: 143 loop : -2.38 (0.31), residues: 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.950 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 0.2515 time to fit residues: 39.3326 Evaluate side-chains 90 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1406 time to fit residues: 1.6408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.0170 chunk 9 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 153 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16309 Z= 0.196 Angle : 0.574 8.320 23963 Z= 0.298 Chirality : 0.037 0.196 3005 Planarity : 0.005 0.068 1570 Dihedral : 13.930 171.693 5760 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.43 % Allowed : 31.61 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.20 (0.30), residues: 819 helix: 0.46 (0.31), residues: 311 sheet: 0.25 (0.43), residues: 147 loop : -2.47 (0.30), residues: 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.117 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 93 average time/residue: 0.2356 time to fit residues: 35.3705 Evaluate side-chains 89 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1347 time to fit residues: 1.6256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 chunk 39 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 83 optimal weight: 0.0070 chunk 5 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.6804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063545 restraints weight = 50843.397| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.41 r_work: 0.3040 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16309 Z= 0.317 Angle : 0.697 9.362 23963 Z= 0.359 Chirality : 0.043 0.236 3005 Planarity : 0.005 0.069 1570 Dihedral : 14.335 167.782 5760 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 0.43 % Allowed : 32.04 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.63 % 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: -1.47 (0.29), residues: 819 helix: 0.19 (0.30), residues: 308 sheet: 0.06 (0.43), residues: 149 loop : -2.54 (0.30), residues: 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2666.33 seconds wall clock time: 49 minutes 50.38 seconds (2990.38 seconds total)