Starting phenix.real_space_refine (version: dev) on Wed Apr 6 23:18:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pcq_20304/04_2022/6pcq_20304_neut_updated.pdb" } resolution = 2.6 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= -0.018 sd= 1.268 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 72125 Number of models: 1 Model: "" Number of chains: 8 Chain: "I" Number of atoms: 62206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62206 Classifications: {'RNA': 2897} Modifications used: {'rna3p': 15, 'rna2p': 6, 'rna3p_pur': 1384, 'rna3p_pyr': 1061, 'rna2p_pur': 280, 'rna2p_pyr': 151} Link IDs: {'rna3p': 2459, 'rna2p': 437} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 104, 'rna2p': 13} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2076 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Chain: "O" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'O8J': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.84, per 1000 atoms: 0.41 Number of scatterers: 72125 At special positions: 0 Unit cell: (229.439, 221.984, 190.509, 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 22 16.00 P 3015 15.00 O 22269 8.00 N 13318 7.00 C 33501 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 29.38 Conformation dependent library (CDL) restraints added in 1.3 seconds 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 18.7% alpha, 13.9% beta 886 base pairs and 1620 stacking pairs defined. Time for finding SS restraints: 36.38 Creating SS restraints... Processing helix chain 'K' and resid 198 through 202 removed outlier: 3.674A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 79 through 84 removed outlier: 4.438A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 4.081A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 92 through 98' Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.915A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 19 No H-bonds generated for 'chain 'M' and resid 16 through 19' Processing helix chain 'M' and resid 25 through 39 Processing helix chain 'M' and resid 98 through 114 removed outlier: 3.657A pdb=" N VAL M 113 " --> pdb=" O LEU M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 141 Processing helix chain 'M' and resid 155 through 160 removed outlier: 3.770A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 190 through 200 removed outlier: 3.550A pdb=" N GLU M 197 " --> pdb=" O VAL M 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 62 through 69 Processing helix chain 'N' and resid 98 through 101 Processing helix chain 'N' and resid 121 through 124 No H-bonds generated for 'chain 'N' and resid 121 through 124' Processing helix chain 'O' and resid 25 through 37 removed outlier: 4.382A pdb=" N GLU O 31 " --> pdb=" O ARG O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 71 removed outlier: 4.534A pdb=" N ARG O 69 " --> pdb=" O GLY O 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP O 71 " --> pdb=" O LYS O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 107 Proline residue: O 97 - end of helix removed outlier: 4.371A pdb=" N VAL O 100 " --> pdb=" O ARG O 96 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE O 101 " --> pdb=" O PRO O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 121 removed outlier: 3.847A pdb=" N PHE O 119 " --> pdb=" O GLY O 115 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 135 No H-bonds generated for 'chain 'O' and resid 133 through 135' Processing sheet with id= A, first strand: chain 'K' and resid 3 through 5 Processing sheet with id= B, first strand: chain 'K' and resid 34 through 36 Processing sheet with id= C, first strand: chain 'K' and resid 101 through 105 removed outlier: 6.489A pdb=" N LEU K 95 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VAL K 78 " --> pdb=" O LEU K 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 129 through 131 Processing sheet with id= E, first strand: chain 'K' and resid 181 through 185 removed outlier: 6.438A pdb=" N ARG K 175 " --> pdb=" O ILE K 164 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE K 164 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.318A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'M' and resid 118 through 121 removed outlier: 6.003A pdb=" N VAL M 186 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL M 121 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N MET M 188 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 169 through 172 removed outlier: 4.754A pdb=" N THR N 112 " --> pdb=" O ASP N 200 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASP N 200 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL N 26 " --> pdb=" O VAL N 9 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET N 11 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL N 24 " --> pdb=" O MET N 11 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG N 13 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE N 22 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL N 189 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP N 181 " --> pdb=" O LEU N 186 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LYS N 190 " --> pdb=" O VAL N 177 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 177 " --> pdb=" O LYS N 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 80 through 83 removed outlier: 6.277A pdb=" N THR N 51 " --> pdb=" O VAL N 34 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL N 34 " --> pdb=" O THR N 51 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 115 through 119 removed outlier: 5.610A pdb=" N MET N 165 " --> pdb=" O LYS N 116 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE N 118 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY N 163 " --> pdb=" O PHE N 118 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 15 through 19 removed outlier: 6.736A pdb=" N TYR O 53 " --> pdb=" O TYR O 16 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL O 18 " --> pdb=" O TYR O 53 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE O 55 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 73 through 76 138 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2200 hydrogen bonds 3592 hydrogen bond angles 0 basepair planarities 886 basepair parallelities 1620 stacking parallelities Total time for adding SS restraints: 139.39 Time building geometry restraints manager: 31.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.55: 73899 1.55 - 1.88: 6096 1.88 - 2.21: 0 2.21 - 2.55: 0 2.55 - 2.88: 1 Bond restraints: 79996 Sorted by residual: bond pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 1.332 2.878 -1.546 1.36e-02 5.41e+03 1.29e+04 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.805 1.410 0.395 2.00e-02 2.50e+03 3.91e+02 bond pdb=" C4 5MU I1939 " pdb=" C5 5MU I1939 " ideal model delta sigma weight residual 1.805 1.412 0.393 2.00e-02 2.50e+03 3.85e+02 bond pdb=" N1 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.638 1.366 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" N1 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.638 1.367 0.271 2.00e-02 2.50e+03 1.83e+02 ... (remaining 79991 not shown) Histogram of bond angle deviations from ideal: 52.46 - 72.58: 1 72.58 - 92.70: 0 92.70 - 112.81: 62561 112.81 - 132.93: 60582 132.93 - 153.05: 20 Bond angle restraints: 123164 Sorted by residual: angle pdb=" O ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 122.59 52.46 70.13 1.33e+00 5.65e-01 2.78e+03 angle pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " ideal model delta sigma weight residual 116.84 153.05 -36.21 1.71e+00 3.42e-01 4.48e+02 angle pdb=" C ASN K 226 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " ideal model delta sigma weight residual 121.97 137.23 -15.26 1.80e+00 3.09e-01 7.19e+01 angle pdb=" C1' 1MG I 745 " pdb=" N9 1MG I 745 " pdb=" C4 1MG I 745 " ideal model delta sigma weight residual 103.27 126.50 -23.23 3.00e+00 1.11e-01 6.00e+01 angle pdb=" C1' 2MA I2503 " pdb=" N9 2MA I2503 " pdb=" C4 2MA I2503 " ideal model delta sigma weight residual 103.49 126.23 -22.74 3.00e+00 1.11e-01 5.75e+01 ... (remaining 123159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 39459 35.81 - 71.63: 1108 71.63 - 107.44: 99 107.44 - 143.26: 7 143.26 - 179.07: 5 Dihedral angle restraints: 40678 sinusoidal: 38001 harmonic: 2677 Sorted by residual: dihedral pdb=" CA ASN K 226 " pdb=" C ASN K 226 " pdb=" N VAL K 228 " pdb=" CA VAL K 228 " ideal model delta harmonic sigma weight residual 180.00 64.29 115.71 0 5.00e+00 4.00e-02 5.36e+02 dihedral pdb=" O4' C I 323 " pdb=" C1' C I 323 " pdb=" N1 C I 323 " pdb=" C2 C I 323 " ideal model delta sinusoidal sigma weight residual 232.00 52.93 179.07 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I1340 " pdb=" C1' U I1340 " pdb=" N1 U I1340 " pdb=" C2 U I1340 " ideal model delta sinusoidal sigma weight residual 232.00 60.36 171.64 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 40675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 12440 0.030 - 0.061: 3471 0.061 - 0.091: 150 0.091 - 0.121: 81 0.121 - 0.152: 9 Chirality restraints: 16151 Sorted by residual: chirality pdb=" C30 O8J I3001 " pdb=" C29 O8J I3001 " pdb=" C31 O8J I3001 " pdb=" N34 O8J I3001 " both_signs ideal model delta sigma weight residual False -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" C3' G I 271 " pdb=" C4' G I 271 " pdb=" O3' G I 271 " pdb=" C2' G I 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE K 135 " pdb=" N ILE K 135 " pdb=" C ILE K 135 " pdb=" CB ILE K 135 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 16148 not shown) Planarity restraints: 4335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.029 2.00e-02 2.50e+03 6.03e-01 8.19e+03 pdb=" C4' 2MG I2445 " -0.466 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.783 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.572 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.237 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.879 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.191 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.953 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.037 2.00e-02 2.50e+03 5.76e-01 7.46e+03 pdb=" C4' 2MG I1835 " -0.436 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.645 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.574 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.910 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.227 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG I2251 " 0.038 2.00e-02 2.50e+03 5.68e-01 7.27e+03 pdb=" C4' OMG I2251 " 0.430 2.00e-02 2.50e+03 pdb=" O4' OMG I2251 " 0.611 2.00e-02 2.50e+03 pdb=" C3' OMG I2251 " -0.595 2.00e-02 2.50e+03 pdb=" O3' OMG I2251 " -0.570 2.00e-02 2.50e+03 pdb=" C2' OMG I2251 " -0.206 2.00e-02 2.50e+03 pdb=" O2' OMG I2251 " 0.916 2.00e-02 2.50e+03 pdb=" C1' OMG I2251 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG I2251 " -0.857 2.00e-02 2.50e+03 ... (remaining 4332 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 559 2.56 - 3.15: 53330 3.15 - 3.73: 146379 3.73 - 4.32: 206568 4.32 - 4.90: 267183 Nonbonded interactions: 674019 Sorted by model distance: nonbonded pdb=" O2' A I2799 " pdb=" OP2 G I2801 " model vdw 1.976 2.440 nonbonded pdb=" O2* PSU I1911 " pdb=" OP1 A I1912 " model vdw 1.981 3.040 nonbonded pdb=" O2' G I1715 " pdb=" O6 G I1743 " model vdw 1.986 2.440 nonbonded pdb=" O2' G I1826 " pdb=" OP2 U I1971 " model vdw 1.996 2.440 nonbonded pdb=" O2' U I1061 " pdb=" OP2 G I1063 " model vdw 2.007 2.440 ... (remaining 674014 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3015 5.49 5 S 22 5.16 5 C 33501 2.51 5 N 13318 2.21 5 O 22269 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 9.430 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: 0.050 Extract box with map and model: 46.550 Check model and map are aligned: 0.790 Convert atoms to be neutral: 0.470 Process input model: 276.720 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 346.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.546 79996 Z= 0.430 Angle : 0.450 70.132 123164 Z= 0.256 Chirality : 0.024 0.152 16151 Planarity : 0.023 0.603 4335 Dihedral : 12.703 179.074 38974 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.22), residues: 949 helix: -3.79 (0.21), residues: 167 sheet: -2.17 (0.40), residues: 152 loop : -2.60 (0.21), residues: 630 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1898 Ramachandran restraints generated. 949 Oldfield, 0 Emsley, 949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 2.053 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 225 average time/residue: 1.5242 time to fit residues: 456.0587 Evaluate side-chains 148 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 4 average time/residue: 0.5559 time to fit residues: 5.7631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 333 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 309 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 358 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 58 HIS K 134 ASN K 153 GLN M 115 GLN N 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.108 79996 Z= 0.499 Angle : 0.832 14.258 123164 Z= 0.424 Chirality : 0.046 0.347 16151 Planarity : 0.008 0.137 4335 Dihedral : 14.193 179.734 37178 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.15 % Favored : 92.53 % Rotamer Outliers : 6.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.69 (0.24), residues: 951 helix: -2.10 (0.32), residues: 179 sheet: -1.33 (0.41), residues: 145 loop : -1.88 (0.22), residues: 627 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 2.081 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 19 residues processed: 199 average time/residue: 1.4586 time to fit residues: 387.1362 Evaluate side-chains 160 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 7 average time/residue: 0.5522 time to fit residues: 8.6694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 199 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 153 GLN K 239 ASN M 41 GLN M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 79996 Z= 0.286 Angle : 0.641 13.885 123164 Z= 0.340 Chirality : 0.035 0.323 16151 Planarity : 0.007 0.132 4335 Dihedral : 13.901 179.694 37178 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.62 % Favored : 93.17 % Rotamer Outliers : 6.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.91 (0.26), residues: 951 helix: -1.01 (0.36), residues: 180 sheet: -1.00 (0.42), residues: 145 loop : -1.46 (0.24), residues: 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 2.083 Fit side-chains outliers start: 46 outliers final: 21 residues processed: 184 average time/residue: 1.4479 time to fit residues: 357.8231 Evaluate side-chains 158 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 5 average time/residue: 0.7119 time to fit residues: 7.5069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 355 optimal weight: 0.0770 chunk 270 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 360 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 341 optimal weight: 0.0030 chunk 102 optimal weight: 10.0000 overall best weight: 4.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 79996 Z= 0.299 Angle : 0.657 14.043 123164 Z= 0.349 Chirality : 0.036 0.285 16151 Planarity : 0.007 0.131 4335 Dihedral : 14.037 179.545 37178 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.15 % Favored : 92.64 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.58 (0.26), residues: 951 helix: -0.47 (0.38), residues: 179 sheet: -0.93 (0.42), residues: 145 loop : -1.29 (0.24), residues: 627 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 169 time to evaluate : 2.117 Fit side-chains outliers start: 47 outliers final: 25 residues processed: 197 average time/residue: 1.4718 time to fit residues: 388.3015 Evaluate side-chains 172 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 7 average time/residue: 0.6874 time to fit residues: 9.7695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 317 optimal weight: 5.9990 chunk 216 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 243 HIS M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 126 ASN O 47 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.105 79996 Z= 0.497 Angle : 0.819 14.045 123164 Z= 0.417 Chirality : 0.045 0.332 16151 Planarity : 0.008 0.138 4335 Dihedral : 14.607 179.127 37178 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.68 % Favored : 92.11 % Rotamer Outliers : 6.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.81 (0.25), residues: 951 helix: -0.84 (0.37), residues: 181 sheet: -0.91 (0.41), residues: 136 loop : -1.43 (0.23), residues: 634 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 152 time to evaluate : 2.105 Fit side-chains outliers start: 47 outliers final: 24 residues processed: 186 average time/residue: 1.4369 time to fit residues: 359.9589 Evaluate side-chains 165 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 5 average time/residue: 0.5473 time to fit residues: 6.7009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 128 optimal weight: 7.9990 chunk 343 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 382 optimal weight: 7.9990 chunk 317 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 21 ASN K 239 ASN M 115 GLN M 156 ASN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 ASN O 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 79996 Z= 0.316 Angle : 0.670 13.953 123164 Z= 0.354 Chirality : 0.037 0.285 16151 Planarity : 0.007 0.133 4335 Dihedral : 14.330 179.755 37178 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.26 % Favored : 92.53 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.53 (0.26), residues: 951 helix: -0.41 (0.39), residues: 179 sheet: -0.72 (0.41), residues: 145 loop : -1.31 (0.24), residues: 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 2.108 Fit side-chains outliers start: 40 outliers final: 26 residues processed: 188 average time/residue: 1.4909 time to fit residues: 380.5056 Evaluate side-chains 163 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 2.102 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 7 average time/residue: 0.8508 time to fit residues: 11.0806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 368 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 217 optimal weight: 40.0000 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 30.0000 chunk 321 optimal weight: 1.9990 chunk 213 optimal weight: 40.0000 chunk 380 optimal weight: 8.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN M 156 ASN M 195 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.120 79996 Z= 0.549 Angle : 0.861 14.066 123164 Z= 0.435 Chirality : 0.047 0.350 16151 Planarity : 0.008 0.140 4335 Dihedral : 14.862 178.980 37178 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.31 % Favored : 91.48 % Rotamer Outliers : 5.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.25), residues: 951 helix: -1.02 (0.36), residues: 189 sheet: -1.03 (0.40), residues: 155 loop : -1.54 (0.24), residues: 607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 2.078 Fit side-chains outliers start: 39 outliers final: 25 residues processed: 174 average time/residue: 1.3673 time to fit residues: 326.3099 Evaluate side-chains 165 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 2.791 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 6 average time/residue: 0.9360 time to fit residues: 10.6795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 235 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 242 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN K 260 ASN M 115 GLN M 156 ASN M 195 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 185 ASN O 128 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 79996 Z= 0.377 Angle : 0.712 13.988 123164 Z= 0.372 Chirality : 0.039 0.301 16151 Planarity : 0.007 0.136 4335 Dihedral : 14.552 179.767 37178 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.47 % Favored : 92.32 % Rotamer Outliers : 5.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.76 (0.26), residues: 951 helix: -0.67 (0.38), residues: 187 sheet: -0.95 (0.40), residues: 155 loop : -1.44 (0.24), residues: 609 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 148 time to evaluate : 2.131 Fit side-chains outliers start: 42 outliers final: 26 residues processed: 177 average time/residue: 1.3496 time to fit residues: 326.2400 Evaluate side-chains 168 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 142 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.8034 time to fit residues: 7.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 346 optimal weight: 0.2980 chunk 364 optimal weight: 0.9980 chunk 332 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 213 optimal weight: 40.0000 chunk 154 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 320 optimal weight: 0.9980 chunk 335 optimal weight: 8.9990 chunk 353 optimal weight: 0.0030 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 239 ASN M 115 GLN M 156 ASN M 195 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 185 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.065 79996 Z= 0.129 Angle : 0.562 13.882 123164 Z= 0.307 Chirality : 0.029 0.260 16151 Planarity : 0.006 0.125 4335 Dihedral : 14.203 179.834 37178 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.94 % Favored : 92.85 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.28 (0.27), residues: 951 helix: -0.05 (0.40), residues: 184 sheet: -0.90 (0.40), residues: 151 loop : -1.10 (0.25), residues: 616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 2.165 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 180 average time/residue: 1.4628 time to fit residues: 357.4214 Evaluate side-chains 172 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.5086 time to fit residues: 4.5293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 232 optimal weight: 10.0000 chunk 375 optimal weight: 7.9990 chunk 228 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 362 optimal weight: 0.0770 chunk 313 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 overall best weight: 6.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 GLN M 195 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN O 58 ASN O 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.104 79996 Z= 0.470 Angle : 0.792 14.016 123164 Z= 0.405 Chirality : 0.044 0.326 16151 Planarity : 0.008 0.138 4335 Dihedral : 14.610 179.679 37178 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.10 % Favored : 91.69 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.69 (0.26), residues: 951 helix: -0.67 (0.37), residues: 189 sheet: -0.97 (0.40), residues: 149 loop : -1.34 (0.24), residues: 613 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 2.151 Fit side-chains outliers start: 30 outliers final: 25 residues processed: 177 average time/residue: 1.4962 time to fit residues: 359.1734 Evaluate side-chains 168 residues out of total 760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 5 average time/residue: 0.8709 time to fit residues: 8.6096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 395 random chunks: chunk 248 optimal weight: 8.9990 chunk 333 optimal weight: 0.0470 chunk 95 optimal weight: 7.9990 chunk 288 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN M 115 GLN ** N 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099826 restraints weight = 131972.756| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 0.61 r_work: 0.3314 rms_B_bonded: 0.59 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 0.63 restraints_weight: 0.2500 r_work: 0.3300 rms_B_bonded: 0.71 restraints_weight: 0.1250 r_work: 0.3293 rms_B_bonded: 0.81 restraints_weight: 0.0625 r_work: 0.3286 rms_B_bonded: 0.93 restraints_weight: 0.0312 r_work: 0.3278 rms_B_bonded: 1.06 restraints_weight: 0.0156 r_work: 0.3270 rms_B_bonded: 1.22 restraints_weight: 0.0078 r_work: 0.3262 rms_B_bonded: 1.38 restraints_weight: 0.0039 r_work: 0.3253 rms_B_bonded: 1.57 restraints_weight: 0.0020 r_work: 0.3244 rms_B_bonded: 1.77 restraints_weight: 0.0010 r_work: 0.3234 rms_B_bonded: 1.98 restraints_weight: 0.0005 r_work: 0.3224 rms_B_bonded: 2.22 restraints_weight: 0.0002 r_work: 0.3212 rms_B_bonded: 2.49 restraints_weight: 0.0001 r_work: 0.3200 rms_B_bonded: 2.77 restraints_weight: 0.0001 r_work: 0.3187 rms_B_bonded: 3.09 restraints_weight: 0.0000 r_work: 0.3173 rms_B_bonded: 3.44 restraints_weight: 0.0000 r_work: 0.3158 rms_B_bonded: 3.82 restraints_weight: 0.0000 r_work: 0.3142 rms_B_bonded: 4.24 restraints_weight: 0.0000 r_work: 0.3124 rms_B_bonded: 4.71 restraints_weight: 0.0000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 79996 Z= 0.313 Angle : 0.674 13.949 123164 Z= 0.357 Chirality : 0.037 0.288 16151 Planarity : 0.007 0.134 4335 Dihedral : 14.456 179.758 37178 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.68 % Favored : 92.11 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.26), residues: 951 helix: -0.51 (0.38), residues: 187 sheet: -0.90 (0.41), residues: 149 loop : -1.25 (0.24), residues: 615 =============================================================================== Job complete usr+sys time: 9420.14 seconds wall clock time: 171 minutes 7.06 seconds (10267.06 seconds total)