Starting phenix.real_space_refine on Thu Nov 16 04:42:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/11_2023/6px3_20517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/11_2023/6px3_20517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/11_2023/6px3_20517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/11_2023/6px3_20517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/11_2023/6px3_20517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6px3_20517/11_2023/6px3_20517.pdb" } resolution = 4.1 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= 0.004 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 3 6.06 5 P 290 5.49 5 S 33 5.16 5 C 8074 2.51 5 N 2663 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "C GLU -56": "OE1" <-> "OE2" Residue "C GLU -8": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 14323 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1393 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 792 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 741 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2957 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2988 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "S" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1819 Unusual residues: {' ZN': 3} Classifications: {'peptide': 233, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 223, None: 3} Not linked: pdbres="THR S 325 " pdbres=" ZN S1001 " Not linked: pdbres=" ZN S1001 " pdbres=" ZN S1002 " Not linked: pdbres=" ZN S1002 " pdbres=" ZN S1003 " Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12981 SG CYS S 158 59.132 83.833 47.890 1.00358.91 S ATOM 13014 SG CYS S 163 61.737 82.243 50.744 1.00359.20 S ATOM 13051 SG CYS S 169 61.811 82.426 46.323 1.00377.57 S ATOM 12758 SG CYS S 129 58.755 80.167 51.153 1.00321.15 S ATOM 12772 SG CYS S 131 58.781 77.155 49.607 1.00322.61 S ATOM 12869 SG CYS S 143 60.681 80.024 47.354 1.00365.86 S ATOM 12910 SG CYS S 149 58.173 78.238 47.291 1.00299.48 S ATOM 13819 SG CYS S 261 37.845 88.685 19.012 1.00396.58 S ATOM 14198 SG CYS S 308 40.086 91.078 16.518 1.00413.35 S ATOM 14216 SG CYS S 310 40.442 89.010 15.411 1.00394.48 S ATOM 14250 SG CYS S 315 37.517 90.048 15.112 1.00394.57 S Time building chain proxies: 7.20, per 1000 atoms: 0.50 Number of scatterers: 14323 At special positions: 0 Unit cell: (93.6, 145.6, 131.04, 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 3 29.99 S 33 16.00 P 290 15.00 O 3260 8.00 N 2663 7.00 C 8074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 169 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 158 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 163 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 129 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 149 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 143 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 131 " pdb=" ZN S1003 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 308 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 315 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 310 " pdb="ZN ZN S1003 " - pdb=" SG CYS S 261 " Number of angles added : 18 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 56.8% alpha, 7.1% beta 143 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 6.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.962A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid -50 through -37 Processing helix chain 'C' and resid -35 through -33 No H-bonds generated for 'chain 'C' and resid -35 through -33' Processing helix chain 'C' and resid -17 through -12 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.561A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.632A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.003A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.926A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.392A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.521A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.547A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 155 removed outlier: 3.600A pdb=" N LYS S 155 " --> pdb=" O ARG S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 230 Processing helix chain 'S' and resid 252 through 256 removed outlier: 3.607A pdb=" N ARG S 255 " --> pdb=" O ASN S 252 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE S 256 " --> pdb=" O LEU S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 252 through 256' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.827A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid -60 through -56 removed outlier: 8.790A pdb=" N LEU C -5 " --> pdb=" O GLN C -70 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE C -68 " --> pdb=" O LEU C -5 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU C -3 " --> pdb=" O PHE C -68 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C -66 " --> pdb=" O LEU C -3 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N LEU C -1 " --> pdb=" O LYS C -66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.107A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.726A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.271A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 187 Processing sheet with id=AB5, first strand: chain 'S' and resid 205 through 208 removed outlier: 6.714A pdb=" N PHE S 205 " --> pdb=" O ALA S 282 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA S 282 " --> pdb=" O PHE S 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 212 through 214 466 hydrogen bonds defined for protein. 1341 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 6.56 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2342 1.33 - 1.45: 5126 1.45 - 1.57: 7067 1.57 - 1.69: 578 1.69 - 1.81: 48 Bond restraints: 15161 Sorted by residual: bond pdb=" C ASP S 134 " pdb=" N TRP S 135 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.23e-02 6.61e+03 2.29e+01 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.392 -0.058 1.51e-02 4.39e+03 1.47e+01 bond pdb=" C3' DC I 143 " pdb=" O3' DC I 143 " ideal model delta sigma weight residual 1.422 1.501 -0.079 3.00e-02 1.11e+03 6.86e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.95e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 ... (remaining 15156 not shown) Histogram of bond angle deviations from ideal: 97.98 - 105.43: 1428 105.43 - 112.88: 8338 112.88 - 120.33: 6273 120.33 - 127.78: 5216 127.78 - 135.23: 447 Bond angle restraints: 21702 Sorted by residual: angle pdb=" N PRO S 88 " pdb=" CA PRO S 88 " pdb=" CB PRO S 88 " ideal model delta sigma weight residual 103.00 110.46 -7.46 1.10e+00 8.26e-01 4.60e+01 angle pdb=" N PRO S 89 " pdb=" CA PRO S 89 " pdb=" CB PRO S 89 " ideal model delta sigma weight residual 103.38 110.41 -7.03 1.05e+00 9.07e-01 4.48e+01 angle pdb=" N PRO S 84 " pdb=" CA PRO S 84 " pdb=" CB PRO S 84 " ideal model delta sigma weight residual 103.00 110.25 -7.25 1.10e+00 8.26e-01 4.34e+01 angle pdb=" C SER S 122 " pdb=" N ASP S 123 " pdb=" CA ASP S 123 " ideal model delta sigma weight residual 122.61 129.80 -7.19 1.56e+00 4.11e-01 2.12e+01 angle pdb=" N VAL S 159 " pdb=" CA VAL S 159 " pdb=" C VAL S 159 " ideal model delta sigma weight residual 110.05 105.58 4.47 1.09e+00 8.42e-01 1.68e+01 ... (remaining 21697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 6620 34.59 - 69.19: 1484 69.19 - 103.78: 17 103.78 - 138.38: 0 138.38 - 172.97: 4 Dihedral angle restraints: 8125 sinusoidal: 5066 harmonic: 3059 Sorted by residual: dihedral pdb=" CA GLN S 172 " pdb=" C GLN S 172 " pdb=" N ARG S 173 " pdb=" CA ARG S 173 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLU S 133 " pdb=" C GLU S 133 " pdb=" N ASP S 134 " pdb=" CA ASP S 134 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 47.03 172.97 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1769 0.057 - 0.113: 550 0.113 - 0.170: 98 0.170 - 0.227: 25 0.227 - 0.283: 5 Chirality restraints: 2447 Sorted by residual: chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE G 111 " pdb=" CA ILE G 111 " pdb=" CG1 ILE G 111 " pdb=" CG2 ILE G 111 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA PRO S 88 " pdb=" N PRO S 88 " pdb=" C PRO S 88 " pdb=" CB PRO S 88 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2444 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 102 " -0.038 2.00e-02 2.50e+03 1.77e-02 9.39e+00 pdb=" N9 DG I 102 " 0.032 2.00e-02 2.50e+03 pdb=" C8 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 102 " 0.023 2.00e-02 2.50e+03 pdb=" C5 DG I 102 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 102 " -0.021 2.00e-02 2.50e+03 pdb=" O6 DG I 102 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 102 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 102 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG I 102 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DG I 102 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG I 102 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.040 2.00e-02 2.50e+03 1.77e-02 8.61e+00 pdb=" N9 DA I 20 " 0.039 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.012 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 106 " 0.037 2.00e-02 2.50e+03 1.60e-02 7.71e+00 pdb=" N9 DG J 106 " -0.037 2.00e-02 2.50e+03 pdb=" C8 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG J 106 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 106 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG J 106 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 106 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG J 106 " -0.010 2.00e-02 2.50e+03 pdb=" N2 DG J 106 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG J 106 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J 106 " -0.004 2.00e-02 2.50e+03 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 2 1.67 - 2.48: 35 2.48 - 3.28: 14016 3.28 - 4.09: 41685 4.09 - 4.90: 65863 Warning: very small nonbonded interaction distances. Nonbonded interactions: 121601 Sorted by model distance: nonbonded pdb=" O GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 0.861 3.040 nonbonded pdb=" O GLN C -23 " pdb=" CD GLU D 102 " model vdw 1.590 3.270 nonbonded pdb=" O GLY C -25 " pdb=" OD1 ASP C 90 " model vdw 1.742 3.040 nonbonded pdb=" C GLN C -23 " pdb=" OE2 GLU D 102 " model vdw 1.788 3.270 nonbonded pdb=" NE2 GLN C -23 " pdb=" CE1 HIS D 106 " model vdw 2.014 3.340 ... (remaining 121596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = (chain 'F' and resid 24 through 100) } ncs_group { reference = (chain 'D' and resid 27 through 120) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.89 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 3.860 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 47.590 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 15161 Z= 0.410 Angle : 0.941 10.225 21702 Z= 0.573 Chirality : 0.057 0.283 2447 Planarity : 0.007 0.056 1760 Dihedral : 26.807 172.971 6155 Min Nonbonded Distance : 0.861 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.45 % Favored : 95.45 % Rotamer: Outliers : 0.45 % Allowed : 5.76 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.23), residues: 1033 helix: 0.14 (0.19), residues: 564 sheet: -1.34 (0.57), residues: 71 loop : -1.49 (0.29), residues: 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 381 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 385 average time/residue: 0.3317 time to fit residues: 171.8685 Evaluate side-chains 216 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN C -32 GLN C 24 GLN D 79 HIS F 25 ASN G 24 GLN G 38 ASN G 89 ASN ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN S 171 ASN S 175 GLN S 215 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15161 Z= 0.291 Angle : 0.657 12.860 21702 Z= 0.384 Chirality : 0.038 0.163 2447 Planarity : 0.005 0.061 1760 Dihedral : 30.768 172.504 4085 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.34 % Allowed : 5.42 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1033 helix: 1.27 (0.21), residues: 582 sheet: -0.82 (0.61), residues: 66 loop : -1.32 (0.30), residues: 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 281 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 283 average time/residue: 0.3313 time to fit residues: 130.1434 Evaluate side-chains 190 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 126 optimal weight: 50.0000 chunk 104 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 92 GLN ** H 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 15161 Z= 0.396 Angle : 0.705 8.645 21702 Z= 0.413 Chirality : 0.041 0.177 2447 Planarity : 0.006 0.058 1760 Dihedral : 31.732 179.304 4085 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.11 % Allowed : 4.52 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1033 helix: 0.82 (0.21), residues: 574 sheet: -1.00 (0.60), residues: 70 loop : -1.09 (0.32), residues: 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.3025 time to fit residues: 104.4504 Evaluate side-chains 176 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 ASN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15161 Z= 0.236 Angle : 0.616 7.401 21702 Z= 0.366 Chirality : 0.037 0.164 2447 Planarity : 0.005 0.058 1760 Dihedral : 31.394 179.037 4085 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.23 % Allowed : 3.05 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1033 helix: 0.94 (0.21), residues: 579 sheet: -0.70 (0.58), residues: 76 loop : -1.17 (0.33), residues: 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 257 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 258 average time/residue: 0.2899 time to fit residues: 104.9986 Evaluate side-chains 184 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.262 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1712 time to fit residues: 1.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 0.0000 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 104 GLN H 44 GLN ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15161 Z= 0.299 Angle : 0.636 6.929 21702 Z= 0.376 Chirality : 0.038 0.156 2447 Planarity : 0.005 0.060 1760 Dihedral : 31.513 177.826 4085 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.23 % Allowed : 2.71 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1033 helix: 0.73 (0.21), residues: 586 sheet: -0.68 (0.58), residues: 76 loop : -1.24 (0.33), residues: 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 240 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.2940 time to fit residues: 99.9326 Evaluate side-chains 173 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15161 Z= 0.199 Angle : 0.599 7.078 21702 Z= 0.353 Chirality : 0.036 0.164 2447 Planarity : 0.004 0.060 1760 Dihedral : 31.259 179.910 4085 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.23 % Allowed : 2.37 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.27), residues: 1033 helix: 0.91 (0.21), residues: 582 sheet: -0.38 (0.59), residues: 76 loop : -1.12 (0.34), residues: 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 247 average time/residue: 0.3028 time to fit residues: 105.4014 Evaluate side-chains 186 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.142 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1685 time to fit residues: 1.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15161 Z= 0.221 Angle : 0.605 7.017 21702 Z= 0.356 Chirality : 0.037 0.180 2447 Planarity : 0.005 0.060 1760 Dihedral : 31.233 179.177 4085 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.34 % Allowed : 1.81 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.27), residues: 1033 helix: 0.90 (0.21), residues: 579 sheet: -0.27 (0.59), residues: 76 loop : -1.05 (0.34), residues: 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 232 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 233 average time/residue: 0.2878 time to fit residues: 95.0618 Evaluate side-chains 181 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1669 time to fit residues: 1.7224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15161 Z= 0.288 Angle : 0.654 7.026 21702 Z= 0.386 Chirality : 0.038 0.197 2447 Planarity : 0.005 0.058 1760 Dihedral : 31.526 179.769 4085 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.23 % Allowed : 1.24 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1033 helix: 0.61 (0.21), residues: 574 sheet: -0.65 (0.58), residues: 78 loop : -0.96 (0.34), residues: 381 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 0.2965 time to fit residues: 93.1407 Evaluate side-chains 166 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1762 time to fit residues: 1.7971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 50.0000 chunk 115 optimal weight: 0.0980 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 50.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 31 HIS C 104 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15161 Z= 0.318 Angle : 0.672 7.075 21702 Z= 0.397 Chirality : 0.039 0.170 2447 Planarity : 0.005 0.059 1760 Dihedral : 31.757 179.535 4085 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.11 % Allowed : 0.68 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1033 helix: 0.58 (0.21), residues: 570 sheet: -0.96 (0.59), residues: 71 loop : -0.81 (0.34), residues: 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 217 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.3012 time to fit residues: 92.7379 Evaluate side-chains 166 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 128 optimal weight: 40.0000 chunk 118 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN C 31 HIS C 104 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** S 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 15161 Z= 0.363 Angle : 0.713 7.369 21702 Z= 0.418 Chirality : 0.041 0.179 2447 Planarity : 0.005 0.057 1760 Dihedral : 32.074 179.051 4085 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 27.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.11 % Allowed : 0.45 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1033 helix: 0.31 (0.21), residues: 575 sheet: -1.08 (0.59), residues: 72 loop : -0.94 (0.34), residues: 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2830 time to fit residues: 84.7314 Evaluate side-chains 159 residues out of total 897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.108 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS C 104 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.040291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.027439 restraints weight = 135895.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.028248 restraints weight = 79235.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.028778 restraints weight = 58219.857| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15161 Z= 0.220 Angle : 0.658 7.609 21702 Z= 0.384 Chirality : 0.038 0.172 2447 Planarity : 0.005 0.061 1760 Dihedral : 31.717 179.825 4085 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.11 % Allowed : 0.34 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1033 helix: 0.48 (0.21), residues: 581 sheet: -0.64 (0.59), residues: 78 loop : -1.10 (0.33), residues: 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2867.74 seconds wall clock time: 53 minutes 3.24 seconds (3183.24 seconds total)