Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 06:00:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/04_2023/6r94_4768_trim_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 292 5.49 5 S 14 5.16 5 C 6879 2.51 5 N 2316 2.21 5 O 2871 1.98 5 H 9995 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 53": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ASP 107": "OD1" <-> "OD2" Residue "F ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 25": "OD1" <-> "OD2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H ARG 32": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22367 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 4611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 4589 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Conformer: "B" Number of residues, atoms: 145, 4568 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 bond proxies already assigned to first conformer: 4900 Chain: "J" Number of atoms: 4608 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 4565 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Conformer: "B" Number of residues, atoms: 145, 4586 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} bond proxies already assigned to first conformer: 4898 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1705 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1394 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1831 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "D" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1559 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1707 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1456 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1611 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Residues with excluded nonbonded symmetry interactions: 4 residue group: pdb=" P A DG I 97 " occ=0.50 ... (31 atoms not shown) pdb=" C1'B3DR I 97 " occ=0.50 residue group: pdb=" P A DA I 98 " occ=0.50 ... (30 atoms not shown) pdb=" C1'B3DR I 98 " occ=0.50 residue group: pdb=" P A3DR J 97 " occ=0.50 ... (31 atoms not shown) pdb=" C4 B DG J 97 " occ=0.50 residue group: pdb=" P A3DR J 98 " occ=0.50 ... (30 atoms not shown) pdb=" C4 B DA J 98 " occ=0.50 Time building chain proxies: 13.10, per 1000 atoms: 0.59 Number of scatterers: 22367 At special positions: 0 Unit cell: (124.7, 103.2, 129.86, 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) S 14 16.00 P 292 15.00 O 2871 8.00 N 2316 7.00 C 6879 6.00 H 9995 1.00 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: 19.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 60.1% alpha, 0.0% beta 141 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 11.97 Creating SS restraints... Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.724A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 76 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 54 through 81 Processing helix chain 'D' and resid 89 through 99 Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.887A pdb=" N LYS D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.630A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 51 through 76 Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 124 339 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for 3DR residue Warning, Cannot make NA restraints for 3DR residue Warning, Cannot make NA restraints for 3DR residue Warning, Cannot make NA restraints for 3DR residue Warning, Cannot make NA restraints for 3DR residue Warning, Cannot make NA restraints for 3DR residue Warning, Cannot make NA restraints for 3DR residue Restraints generated for nucleic acids: 339 hydrogen bonds 678 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 8.00 Time building geometry restraints manager: 19.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9991 1.03 - 1.22: 93 1.22 - 1.42: 5546 1.42 - 1.61: 7517 1.61 - 1.81: 32 Bond restraints: 23179 Sorted by residual: bond pdb=" C4'B3DR I 97 " pdb=" O4'B3DR I 97 " ideal model delta sigma weight residual 1.664 1.435 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C4'A3DR J 98 " pdb=" O4'A3DR J 98 " ideal model delta sigma weight residual 1.664 1.437 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4'A3DR J 97 " pdb=" O4'A3DR J 97 " ideal model delta sigma weight residual 1.664 1.437 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4'B3DR I 98 " pdb=" O4'B3DR I 98 " ideal model delta sigma weight residual 1.664 1.443 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C4'B3DR I 97 " pdb=" C3'B3DR I 97 " ideal model delta sigma weight residual 1.336 1.529 -0.193 2.00e-02 2.50e+03 9.33e+01 ... (remaining 23174 not shown) Histogram of bond angle deviations from ideal: 80.96 - 91.27: 6 91.27 - 101.58: 105 101.58 - 111.90: 26048 111.90 - 122.21: 12249 122.21 - 132.52: 3621 Bond angle restraints: 42029 Sorted by residual: angle pdb=" C SER H 33 " pdb=" CA SER H 33 " pdb=" HA SER H 33 " ideal model delta sigma weight residual 109.00 80.96 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" CB SER H 33 " pdb=" CA SER H 33 " pdb=" HA SER H 33 " ideal model delta sigma weight residual 109.00 82.20 26.80 3.00e+00 1.11e-01 7.98e+01 angle pdb=" CG1 VAL A 36 " pdb=" CB VAL A 36 " pdb=" HB VAL A 36 " ideal model delta sigma weight residual 108.00 81.81 26.19 3.00e+00 1.11e-01 7.62e+01 angle pdb=" CG2 VAL A 36 " pdb=" CB VAL A 36 " pdb=" HB VAL A 36 " ideal model delta sigma weight residual 108.00 82.04 25.96 3.00e+00 1.11e-01 7.49e+01 angle pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" HA SER H 33 " ideal model delta sigma weight residual 110.00 84.53 25.47 3.00e+00 1.11e-01 7.21e+01 ... (remaining 42024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 7256 35.15 - 70.31: 1168 70.31 - 105.46: 15 105.46 - 140.61: 0 140.61 - 175.77: 4 Dihedral angle restraints: 8443 sinusoidal: 5874 harmonic: 2569 Sorted by residual: dihedral pdb=" C SER H 33 " pdb=" N SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual -122.60 -155.65 33.05 0 2.50e+00 1.60e-01 1.75e+02 dihedral pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CA SER H 33 " pdb=" CB SER H 33 " ideal model delta harmonic sigma weight residual 122.80 153.93 -31.13 0 2.50e+00 1.60e-01 1.55e+02 dihedral pdb=" CA GLU E 134 " pdb=" C GLU E 134 " pdb=" N ARG E 135 " pdb=" CA ARG E 135 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 8440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 2152 0.285 - 0.571: 0 0.571 - 0.856: 0 0.856 - 1.141: 0 1.141 - 1.426: 2 Chirality restraints: 2154 Sorted by residual: chirality pdb=" CB VAL A 36 " pdb=" CA VAL A 36 " pdb=" CG1 VAL A 36 " pdb=" CG2 VAL A 36 " both_signs ideal model delta sigma weight residual False -2.63 -1.20 -1.43 2.00e-01 2.50e+01 5.09e+01 chirality pdb=" CA SER H 33 " pdb=" N SER H 33 " pdb=" C SER H 33 " pdb=" CB SER H 33 " both_signs ideal model delta sigma weight residual False 2.51 1.14 1.37 2.00e-01 2.50e+01 4.72e+01 chirality pdb=" CG LEU D 78 " pdb=" CB LEU D 78 " pdb=" CD1 LEU D 78 " pdb=" CD2 LEU D 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2151 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 125 " 0.037 2.00e-02 2.50e+03 7.25e-02 5.25e+01 pdb=" C ALA H 125 " -0.125 2.00e-02 2.50e+03 pdb=" O ALA H 125 " 0.047 2.00e-02 2.50e+03 pdb=" N LYS H 126 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 135 " -0.036 2.00e-02 2.50e+03 7.04e-02 4.95e+01 pdb=" C ARG E 135 " 0.122 2.00e-02 2.50e+03 pdb=" O ARG E 135 " -0.045 2.00e-02 2.50e+03 pdb=" N ALA E 136 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 135 " 0.034 2.00e-02 2.50e+03 6.78e-02 4.60e+01 pdb=" C ARG A 135 " -0.117 2.00e-02 2.50e+03 pdb=" O ARG A 135 " 0.044 2.00e-02 2.50e+03 pdb=" N ALA A 136 " 0.039 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 3058 2.26 - 2.85: 42228 2.85 - 3.43: 53442 3.43 - 4.02: 79651 4.02 - 4.60: 115530 Nonbonded interactions: 293909 Sorted by model distance: nonbonded pdb=" OD1 ASN F 65 " pdb="HH22 ARG F 68 " model vdw 1.680 1.850 nonbonded pdb=" OD2 ASP D 66 " pdb=" HH TYR F 99 " model vdw 1.705 1.850 nonbonded pdb="HH12 ARG G 82 " pdb=" O VAL G 108 " model vdw 1.728 1.850 nonbonded pdb=" OP1 DG J 68 " pdb="HH21 ARG E 43 " model vdw 1.742 1.850 nonbonded pdb=" OP2 DT J 52 " pdb=" HZ3 LYS F 21 " model vdw 1.745 1.850 ... (remaining 293904 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 36 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG \ 3 or name HD2 or name HD3 or name HE or name HH21 or name HH22)) or resid 130 th \ rough 136)) } ncs_group { reference = chain 'B' selection = (chain 'F' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 21 through 103) \ ) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 123) } ncs_group { reference = chain 'D' selection = (chain 'H' and ((resid 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name H \ E or name HH11 or name HH12 or name HH21 or name HH22)) or resid 31 through 123 \ or (resid 124 and (name N or name CA or name C or name O or name CB or name OG o \ r name HA or name HB2 or name HB3 or name HG )) or resid 125 through 126)) } ncs_group { reference = (chain 'I' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) selection = (chain 'J' and (resid 1 through 71 or resid 75 through 96 or resid 99 through 14 \ 5)) } 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=0.50 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: 1.760 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: 0.280 Extract box with map and model: 7.600 Check model and map are aligned: 0.340 Set scattering table: 0.190 Process input model: 80.860 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 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 : 0.012 0.229 13184 Z= 0.669 Angle : 1.005 12.473 19037 Z= 0.597 Chirality : 0.068 1.426 2154 Planarity : 0.008 0.072 1395 Dihedral : 26.381 175.766 5462 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.05 % Favored : 96.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: 0.29 (0.26), residues: 787 helix: 0.84 (0.20), residues: 521 sheet: None (None), residues: 0 loop : -1.01 (0.31), residues: 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.8884 time to fit residues: 61.9019 Evaluate side-chains 49 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13184 Z= 0.190 Angle : 0.628 10.721 19037 Z= 0.386 Chirality : 0.049 1.403 2154 Planarity : 0.003 0.032 1395 Dihedral : 29.458 176.167 3840 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.29), residues: 787 helix: 2.85 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -0.72 (0.33), residues: 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.9224 time to fit residues: 64.1674 Evaluate side-chains 53 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2382 time to fit residues: 1.9408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1538 > 50: distance: 237 - 282: 7.388 distance: 247 - 298: 6.680 distance: 261 - 322: 11.027 distance: 274 - 282: 10.496 distance: 275 - 341: 6.577 distance: 282 - 283: 8.252 distance: 282 - 289: 10.429 distance: 283 - 284: 8.390 distance: 283 - 286: 4.581 distance: 283 - 290: 5.044 distance: 284 - 298: 13.836 distance: 286 - 287: 3.426 distance: 286 - 291: 6.562 distance: 288 - 296: 3.272 distance: 298 - 299: 8.779 distance: 298 - 309: 9.110 distance: 299 - 300: 12.823 distance: 299 - 302: 4.001 distance: 299 - 310: 7.063 distance: 300 - 301: 6.094 distance: 300 - 322: 5.583 distance: 302 - 303: 7.889 distance: 302 - 311: 11.978 distance: 302 - 312: 14.588 distance: 303 - 304: 3.187 distance: 303 - 313: 4.073 distance: 303 - 314: 3.469 distance: 304 - 305: 3.094 distance: 304 - 315: 3.645 distance: 322 - 323: 8.755 distance: 322 - 330: 15.211 distance: 323 - 324: 7.354 distance: 323 - 326: 7.250 distance: 323 - 331: 11.572 distance: 324 - 325: 14.668 distance: 324 - 341: 10.379 distance: 326 - 327: 8.034 distance: 326 - 332: 6.646 distance: 326 - 333: 9.422 distance: 327 - 328: 3.331 distance: 327 - 334: 3.191 distance: 328 - 335: 5.430 distance: 341 - 342: 8.949 distance: 341 - 349: 18.122 distance: 342 - 343: 7.341 distance: 342 - 345: 19.397 distance: 342 - 350: 11.945 distance: 343 - 344: 20.016 distance: 343 - 360: 17.440 distance: 345 - 346: 10.233 distance: 345 - 351: 16.251 distance: 345 - 352: 18.455 distance: 346 - 348: 4.994 distance: 346 - 353: 6.863 distance: 347 - 355: 3.500 distance: 360 - 361: 24.293 distance: 360 - 368: 23.271 distance: 361 - 362: 21.831 distance: 361 - 364: 30.505 distance: 361 - 369: 21.285 distance: 362 - 363: 9.176 distance: 362 - 379: 7.032 distance: 364 - 365: 13.825 distance: 364 - 370: 5.637 distance: 364 - 371: 15.123 distance: 365 - 366: 10.511 distance: 365 - 367: 9.630 distance: 366 - 373: 4.501 distance: 366 - 374: 3.621 distance: 366 - 375: 3.489 distance: 367 - 376: 5.526 distance: 379 - 380: 17.415 distance: 379 - 385: 6.162 distance: 380 - 381: 4.413 distance: 380 - 383: 12.964 distance: 380 - 386: 7.945 distance: 381 - 382: 23.274 distance: 381 - 393: 13.557 distance: 383 - 384: 8.860 distance: 383 - 387: 9.282 distance: 383 - 388: 10.114 distance: 384 - 385: 5.909 distance: 384 - 390: 8.303 distance: 385 - 391: 4.608 distance: 385 - 392: 4.614 distance: 393 - 394: 8.878 distance: 393 - 397: 3.518 distance: 394 - 395: 16.401 distance: 394 - 398: 12.650 distance: 394 - 399: 16.616 distance: 395 - 396: 3.637 distance: 395 - 400: 23.483 distance: 400 - 401: 5.711 distance: 400 - 409: 18.972 distance: 401 - 402: 5.996 distance: 401 - 404: 9.917 distance: 401 - 410: 7.360 distance: 402 - 403: 18.845 distance: 402 - 415: 11.586 distance: 404 - 405: 9.668 distance: 404 - 411: 4.505 distance: 404 - 412: 14.894 distance: 405 - 406: 6.634 distance: 405 - 413: 4.713 distance: 405 - 414: 4.670 distance: 406 - 408: 3.184 distance: 415 - 416: 9.027 distance: 415 - 423: 17.584 distance: 416 - 417: 5.637 distance: 416 - 419: 10.368 distance: 416 - 424: 6.794 distance: 417 - 418: 24.880 distance: 417 - 434: 7.212 distance: 418 - 479: 22.034 distance: 419 - 420: 9.702 distance: 419 - 425: 7.191 distance: 419 - 426: 8.071 distance: 420 - 427: 3.496 distance: 434 - 435: 8.622 distance: 434 - 439: 20.399 distance: 435 - 436: 3.916 distance: 435 - 438: 8.871 distance: 435 - 440: 6.870 distance: 436 - 437: 6.341 distance: 437 - 489: 6.791 distance: 438 - 441: 8.332 distance: 438 - 442: 8.306