Starting phenix.real_space_refine on Sun Feb 18 14:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_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_4768/02_2024/6r94_4768_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r94_4768/02_2024/6r94_4768_trim_updated.pdb" } resolution = 3.5 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= 0.000 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-dev-5238/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: 13.34, per 1000 atoms: 0.60 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: 21.62 Conformation dependent library (CDL) restraints added in 1.4 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: 15.75 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: 8.58 Time building geometry restraints manager: 22.09 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: 8341 35.15 - 70.31: 1407 70.31 - 105.46: 17 105.46 - 140.61: 0 140.61 - 175.77: 4 Dihedral angle restraints: 9769 sinusoidal: 7200 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 9766 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 11.300 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 89.160 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.150 ------------------------------------------------------------------------------- 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 : 26.304 175.766 5814 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 % Allowed : 3.59 % Favored : 96.41 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.003 HIS H 50 PHE 0.021 0.003 PHE D 63 TYR 0.027 0.006 TYR A 100 ARG 0.024 0.003 ARG D 77 *********************** 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 : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8747 (mttt) cc_final: 0.8531 (mtpp) REVERT: D 120 THR cc_start: 0.8269 (t) cc_final: 0.7974 (p) REVERT: G 74 ASN cc_start: 0.6138 (m-40) cc_final: 0.5886 (m-40) REVERT: G 76 LYS cc_start: 0.8026 (mttt) cc_final: 0.7820 (mmtm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.8991 time to fit residues: 62.3701 Evaluate side-chains 50 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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: 0.7980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.6340 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13184 Z= 0.189 Angle : 0.625 10.761 19037 Z= 0.386 Chirality : 0.048 1.402 2154 Planarity : 0.003 0.032 1395 Dihedral : 28.814 176.719 4192 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.15 % Allowed : 4.64 % Favored : 95.21 % 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: 524 sheet: None (None), residues: 0 loop : -0.73 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 50 PHE 0.004 0.001 PHE H 66 TYR 0.012 0.001 TYR A 100 ARG 0.004 0.001 ARG C 43 *********************** 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 : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8770 (mttt) cc_final: 0.8514 (mmmm) REVERT: D 99 LEU cc_start: 0.6828 (tt) cc_final: 0.6617 (mt) REVERT: G 76 LYS cc_start: 0.8069 (mttt) cc_final: 0.7859 (mmtm) outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.8983 time to fit residues: 62.5997 Evaluate side-chains 53 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13184 Z= 0.289 Angle : 0.638 10.768 19037 Z= 0.392 Chirality : 0.050 1.406 2154 Planarity : 0.004 0.041 1395 Dihedral : 28.948 175.210 4192 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.60 % Allowed : 5.54 % Favored : 93.86 % 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: 2.57 (0.29), residues: 787 helix: 2.76 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.58 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS H 83 PHE 0.007 0.001 PHE G 26 TYR 0.017 0.002 TYR A 100 ARG 0.004 0.001 ARG E 41 *********************** REFINEMENT MACRO_CYCLE 3 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 71 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8796 (mttt) cc_final: 0.8580 (mmmm) REVERT: G 74 ASN cc_start: 0.5854 (m110) cc_final: 0.5580 (m-40) outliers start: 4 outliers final: 3 residues processed: 69 average time/residue: 0.9799 time to fit residues: 83.5269 Evaluate side-chains 69 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13184 Z= 0.227 Angle : 0.604 10.796 19037 Z= 0.375 Chirality : 0.049 1.411 2154 Planarity : 0.004 0.047 1395 Dihedral : 28.844 174.944 4192 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.20 % Allowed : 6.59 % Favored : 92.22 % 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: 2.70 (0.30), residues: 787 helix: 2.87 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -0.55 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 32 PHE 0.004 0.001 PHE E 85 TYR 0.011 0.001 TYR A 100 ARG 0.009 0.000 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 4 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 75 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8794 (mttt) cc_final: 0.8570 (mmmm) REVERT: A 132 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7156 (mtt180) REVERT: D 99 LEU cc_start: 0.6943 (tt) cc_final: 0.6618 (mt) REVERT: F 85 MET cc_start: 0.6134 (mmm) cc_final: 0.5883 (mmt) REVERT: H 86 LYS cc_start: 0.8330 (mptt) cc_final: 0.8092 (mtmm) outliers start: 8 outliers final: 6 residues processed: 69 average time/residue: 0.9472 time to fit residues: 81.1592 Evaluate side-chains 74 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 75 optimal weight: 0.1980 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13184 Z= 0.336 Angle : 0.638 10.839 19037 Z= 0.392 Chirality : 0.051 1.414 2154 Planarity : 0.004 0.052 1395 Dihedral : 28.956 173.555 4192 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.35 % Allowed : 7.19 % Favored : 91.47 % 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: 2.14 (0.29), residues: 787 helix: 2.47 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -0.82 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 47 PHE 0.006 0.001 PHE D 63 TYR 0.018 0.002 TYR A 100 ARG 0.006 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 5 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 77 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8798 (mttt) cc_final: 0.8556 (mmmm) REVERT: A 132 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7297 (mtt180) REVERT: G 36 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7488 (mtm-85) REVERT: H 86 LYS cc_start: 0.8352 (mptt) cc_final: 0.8115 (mtmm) REVERT: H 121 LYS cc_start: 0.7549 (tptm) cc_final: 0.7174 (ttmt) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.9832 time to fit residues: 85.1927 Evaluate side-chains 76 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13184 Z= 0.239 Angle : 0.605 10.907 19037 Z= 0.374 Chirality : 0.049 1.419 2154 Planarity : 0.004 0.049 1395 Dihedral : 28.902 173.183 4192 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.05 % Allowed : 7.93 % Favored : 91.02 % 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: 2.36 (0.30), residues: 787 helix: 2.70 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -0.83 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 32 PHE 0.005 0.001 PHE E 79 TYR 0.012 0.001 TYR A 100 ARG 0.004 0.000 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 6 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 76 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8798 (mttt) cc_final: 0.8553 (mmmm) REVERT: A 132 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7297 (mtt180) REVERT: G 36 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7538 (mtm-85) REVERT: H 86 LYS cc_start: 0.8347 (mptt) cc_final: 0.8104 (mtmm) REVERT: H 121 LYS cc_start: 0.7483 (tptm) cc_final: 0.7198 (tttp) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.9592 time to fit residues: 84.5929 Evaluate side-chains 76 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.0970 chunk 101 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13184 Z= 0.199 Angle : 0.594 10.903 19037 Z= 0.368 Chirality : 0.049 1.421 2154 Planarity : 0.003 0.047 1395 Dihedral : 28.885 172.151 4192 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.05 % Allowed : 8.53 % Favored : 90.42 % 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: 2.60 (0.30), residues: 787 helix: 2.89 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -0.77 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS G 32 PHE 0.004 0.001 PHE H 71 TYR 0.009 0.001 TYR A 100 ARG 0.003 0.000 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 7 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 80 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8796 (mttt) cc_final: 0.8546 (mmmm) REVERT: A 132 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7299 (mtt180) REVERT: D 119 TYR cc_start: 0.7719 (t80) cc_final: 0.6770 (t80) REVERT: G 36 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7583 (mtm-85) REVERT: H 86 LYS cc_start: 0.8344 (mptt) cc_final: 0.8107 (mtmm) REVERT: H 121 LYS cc_start: 0.7497 (tptm) cc_final: 0.7181 (tttp) outliers start: 7 outliers final: 5 residues processed: 75 average time/residue: 0.9204 time to fit residues: 85.7006 Evaluate side-chains 79 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13184 Z= 0.324 Angle : 0.629 10.913 19037 Z= 0.387 Chirality : 0.051 1.421 2154 Planarity : 0.004 0.052 1395 Dihedral : 28.940 172.197 4192 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.50 % Allowed : 8.68 % Favored : 89.82 % 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: 2.12 (0.30), residues: 787 helix: 2.51 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.92 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 47 PHE 0.007 0.001 PHE E 79 TYR 0.017 0.002 TYR A 100 ARG 0.007 0.000 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 8 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 89 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8798 (mttt) cc_final: 0.8547 (mmmm) REVERT: A 132 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7265 (mtt180) REVERT: B 26 ASN cc_start: 0.6707 (m-40) cc_final: 0.6396 (m-40) REVERT: D 119 TYR cc_start: 0.7721 (t80) cc_final: 0.6683 (t80) REVERT: G 36 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7572 (mtm-85) REVERT: H 86 LYS cc_start: 0.8387 (mptt) cc_final: 0.8161 (mtmm) REVERT: H 121 LYS cc_start: 0.7519 (tptm) cc_final: 0.7247 (tttp) outliers start: 10 outliers final: 8 residues processed: 82 average time/residue: 0.9371 time to fit residues: 94.4416 Evaluate side-chains 86 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 36 ARG Chi-restraints excluded: chain G residue 101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 0.0670 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13184 Z= 0.195 Angle : 0.591 10.927 19037 Z= 0.366 Chirality : 0.049 1.425 2154 Planarity : 0.003 0.048 1395 Dihedral : 28.870 171.987 4192 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.20 % Allowed : 8.98 % Favored : 89.82 % 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: 2.56 (0.30), residues: 787 helix: 2.88 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -0.84 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 32 PHE 0.004 0.001 PHE H 71 TYR 0.008 0.001 TYR A 100 ARG 0.003 0.000 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 9 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 82 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8769 (mttt) cc_final: 0.8529 (mmmm) REVERT: A 132 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: B 93 ARG cc_start: 0.7474 (mtp-110) cc_final: 0.6923 (ttp80) REVERT: D 119 TYR cc_start: 0.7710 (t80) cc_final: 0.6675 (t80) REVERT: G 36 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7606 (mtm-85) REVERT: H 48 GLN cc_start: 0.7930 (tm-30) cc_final: 0.6614 (tt0) REVERT: H 86 LYS cc_start: 0.8412 (mptt) cc_final: 0.8188 (mtmm) REVERT: H 121 LYS cc_start: 0.7582 (tptm) cc_final: 0.7262 (tttp) outliers start: 8 outliers final: 6 residues processed: 76 average time/residue: 0.9299 time to fit residues: 88.3992 Evaluate side-chains 82 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13184 Z= 0.246 Angle : 0.602 10.942 19037 Z= 0.373 Chirality : 0.049 1.427 2154 Planarity : 0.004 0.049 1395 Dihedral : 28.880 172.098 4192 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.65 % Allowed : 8.53 % Favored : 89.82 % 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: 2.44 (0.30), residues: 787 helix: 2.78 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 32 PHE 0.005 0.001 PHE E 79 TYR 0.013 0.001 TYR A 100 ARG 0.003 0.000 ARG E 53 ********************** REFINEMENT MACRO_CYCLE 10 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 85 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8776 (mttt) cc_final: 0.8528 (mmmm) REVERT: A 132 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7328 (mtt180) REVERT: B 93 ARG cc_start: 0.7511 (mtp-110) cc_final: 0.6913 (ttp80) REVERT: D 119 TYR cc_start: 0.7714 (t80) cc_final: 0.6657 (t80) REVERT: F 85 MET cc_start: 0.6263 (mmm) cc_final: 0.6044 (mmt) REVERT: G 36 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7560 (mtm-85) REVERT: H 86 LYS cc_start: 0.8448 (mptt) cc_final: 0.8221 (mtmm) REVERT: H 121 LYS cc_start: 0.7563 (tptm) cc_final: 0.7251 (tttp) outliers start: 11 outliers final: 8 residues processed: 77 average time/residue: 0.8677 time to fit residues: 83.9710 Evaluate side-chains 84 residues out of total 668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain F residue 28 GLN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 76 optimal weight: 0.0470 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.161252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116623 restraints weight = 51489.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122167 restraints weight = 20981.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.125681 restraints weight = 13320.375| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13184 Z= 0.195 Angle : 0.589 10.947 19037 Z= 0.365 Chirality : 0.049 1.429 2154 Planarity : 0.003 0.048 1395 Dihedral : 28.827 171.967 4192 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.05 % Allowed : 9.28 % Favored : 89.67 % 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: 2.65 (0.30), residues: 787 helix: 2.95 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 32 PHE 0.004 0.001 PHE H 71 TYR 0.008 0.001 TYR A 100 ARG 0.003 0.000 ARG G 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5378.24 seconds wall clock time: 95 minutes 34.44 seconds (5734.44 seconds total)