Starting phenix.real_space_refine on Fri Feb 16 19:49:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njy_12427/02_2024/7njy_12427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njy_12427/02_2024/7njy_12427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njy_12427/02_2024/7njy_12427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njy_12427/02_2024/7njy_12427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njy_12427/02_2024/7njy_12427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njy_12427/02_2024/7njy_12427.pdb" } resolution = 2.94 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= 0.001 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: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 5346 2.51 5 N 1316 2.21 5 O 1399 1.98 5 H 8337 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "R ASP 32": "OD1" <-> "OD2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "a GLU 67": "OE1" <-> "OE2" Residue "a TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 177": "OE1" <-> "OE2" Residue "a PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 12 Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 979 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "d" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 952 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 58} Time building chain proxies: 7.63, per 1000 atoms: 0.46 Number of scatterers: 16426 At special positions: 0 Unit cell: (94.62, 78.85, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1399 8.00 N 1316 7.00 C 5346 6.00 H 8337 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: 15.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 2 sheets defined 87.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'L' and resid 4 through 46 removed outlier: 3.742A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 81 removed outlier: 3.501A pdb=" N PHE L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR L 55 " --> pdb=" O GLY L 51 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 4.146A pdb=" N ALA L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR L 68 " --> pdb=" O VAL L 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 46 Processing helix chain 'M' and resid 49 through 80 removed outlier: 4.588A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.629A pdb=" N TYR M 68 " --> pdb=" O VAL M 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 46 removed outlier: 3.630A pdb=" N ILE N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 80 removed outlier: 4.010A pdb=" N THR N 55 " --> pdb=" O GLY N 51 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.694A pdb=" N ALA N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR N 68 " --> pdb=" O VAL N 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 46 Processing helix chain 'O' and resid 49 through 80 removed outlier: 4.415A pdb=" N THR O 55 " --> pdb=" O GLY O 51 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.097A pdb=" N ALA O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 46 removed outlier: 3.651A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 81 removed outlier: 3.834A pdb=" N PHE P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix removed outlier: 3.677A pdb=" N ALA P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR P 68 " --> pdb=" O VAL P 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 46 removed outlier: 3.592A pdb=" N ILE Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 80 removed outlier: 3.854A pdb=" N THR Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Proline residue: Q 56 - end of helix Processing helix chain 'R' and resid 4 through 46 removed outlier: 3.658A pdb=" N ILE R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 81 removed outlier: 4.403A pdb=" N THR R 55 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix Processing helix chain 'S' and resid 4 through 46 Processing helix chain 'S' and resid 48 through 81 removed outlier: 4.602A pdb=" N ARG S 52 " --> pdb=" O GLU S 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix removed outlier: 3.536A pdb=" N ALA S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 46 removed outlier: 3.583A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 81 removed outlier: 4.039A pdb=" N THR T 55 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.930A pdb=" N ALA T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 51 Processing helix chain 'a' and resid 60 through 81 Processing helix chain 'a' and resid 88 through 106 Processing helix chain 'a' and resid 107 through 109 No H-bonds generated for 'chain 'a' and resid 107 through 109' Processing helix chain 'a' and resid 126 through 129 Processing helix chain 'a' and resid 130 through 154 removed outlier: 3.585A pdb=" N VAL a 134 " --> pdb=" O ASP a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 165 Processing helix chain 'a' and resid 167 through 169 No H-bonds generated for 'chain 'a' and resid 167 through 169' Processing helix chain 'a' and resid 170 through 204 Proline residue: a 182 - end of helix removed outlier: 3.667A pdb=" N LEU a 189 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY a 196 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA a 201 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 245 removed outlier: 5.656A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.644A pdb=" N ALA b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL b 49 " --> pdb=" O ILE b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 84 removed outlier: 3.736A pdb=" N GLN b 82 " --> pdb=" O VAL b 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 22 Processing helix chain 'd' and resid 22 through 61 Processing sheet with id=AA1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'a' and resid 112 through 114 795 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.02 Time building geometry restraints manager: 15.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8336 1.03 - 1.22: 1 1.22 - 1.42: 3359 1.42 - 1.61: 4843 1.61 - 1.81: 55 Bond restraints: 16594 Sorted by residual: bond pdb=" CB MET O 21 " pdb=" CG MET O 21 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" C THR a 220 " pdb=" O THR a 220 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 7.90e-01 bond pdb=" CB MET S 21 " pdb=" CG MET S 21 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 4.74e-01 bond pdb=" N PHE a 213 " pdb=" CA PHE a 213 " ideal model delta sigma weight residual 1.463 1.468 -0.005 6.90e-03 2.10e+04 4.29e-01 bond pdb=" CG LEU Q 72 " pdb=" CD2 LEU Q 72 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.07e-01 ... (remaining 16589 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 241 106.58 - 113.43: 19683 113.43 - 120.29: 5758 120.29 - 127.14: 4361 127.14 - 133.99: 73 Bond angle restraints: 30116 Sorted by residual: angle pdb=" C CYS a 144 " pdb=" N TYR a 145 " pdb=" CA TYR a 145 " ideal model delta sigma weight residual 121.14 116.45 4.69 1.75e+00 3.27e-01 7.20e+00 angle pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " pdb=" CG TYR a 145 " ideal model delta sigma weight residual 113.90 118.39 -4.49 1.80e+00 3.09e-01 6.24e+00 angle pdb=" N TYR a 145 " pdb=" CA TYR a 145 " pdb=" CB TYR a 145 " ideal model delta sigma weight residual 110.40 114.44 -4.04 1.63e+00 3.76e-01 6.14e+00 angle pdb=" CA TRP a 218 " pdb=" CB TRP a 218 " pdb=" CG TRP a 218 " ideal model delta sigma weight residual 113.60 110.25 3.35 1.90e+00 2.77e-01 3.11e+00 angle pdb=" C TYR a 145 " pdb=" N HIS a 146 " pdb=" CA HIS a 146 " ideal model delta sigma weight residual 120.29 117.92 2.37 1.42e+00 4.96e-01 2.79e+00 ... (remaining 30111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6790 17.56 - 35.12: 578 35.12 - 52.68: 264 52.68 - 70.24: 122 70.24 - 87.80: 5 Dihedral angle restraints: 7759 sinusoidal: 4150 harmonic: 3609 Sorted by residual: dihedral pdb=" CB GLU b 59 " pdb=" CG GLU b 59 " pdb=" CD GLU b 59 " pdb=" OE1 GLU b 59 " ideal model delta sinusoidal sigma weight residual 0.00 87.80 -87.80 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG a 188 " pdb=" CD ARG a 188 " pdb=" NE ARG a 188 " pdb=" CZ ARG a 188 " ideal model delta sinusoidal sigma weight residual 180.00 -136.53 -43.47 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU T 65 " pdb=" CG GLU T 65 " pdb=" CD GLU T 65 " pdb=" OE1 GLU T 65 " ideal model delta sinusoidal sigma weight residual 0.00 -84.72 84.72 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 7756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 826 0.027 - 0.053: 254 0.053 - 0.080: 176 0.080 - 0.107: 59 0.107 - 0.134: 7 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CA TYR a 145 " pdb=" N TYR a 145 " pdb=" C TYR a 145 " pdb=" CB TYR a 145 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA PRO L 47 " pdb=" N PRO L 47 " pdb=" C PRO L 47 " pdb=" CB PRO L 47 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA VAL a 58 " pdb=" N VAL a 58 " pdb=" C VAL a 58 " pdb=" CB VAL a 58 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.43e-01 ... (remaining 1319 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY a 191 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C GLY a 191 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY a 191 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN a 192 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG a 188 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ARG a 188 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG a 188 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU a 189 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 70 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C ILE P 70 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE P 70 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN P 71 " 0.008 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 968 2.21 - 2.80: 34814 2.80 - 3.40: 49880 3.40 - 4.00: 65112 4.00 - 4.60: 101376 Nonbonded interactions: 252150 Sorted by model distance: nonbonded pdb=" OD1 ASN a 132 " pdb=" H ASN b 28 " model vdw 1.608 1.850 nonbonded pdb=" OE1 GLN R 46 " pdb="HH22 ARG R 52 " model vdw 1.630 1.850 nonbonded pdb=" OD1 ASN b 28 " pdb=" H GLY b 29 " model vdw 1.655 1.850 nonbonded pdb=" O PHE T 78 " pdb=" HG1 THR T 82 " model vdw 1.670 1.850 nonbonded pdb="HE22 GLN S 86 " pdb=" OD2 ASP T 4 " model vdw 1.694 1.850 ... (remaining 252145 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 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.690 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: 0.240 Extract box with map and model: 25.480 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 57.370 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.003 0.035 8257 Z= 0.191 Angle : 0.471 5.169 11218 Z= 0.266 Chirality : 0.038 0.134 1322 Planarity : 0.004 0.038 1440 Dihedral : 13.384 87.801 2789 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.27), residues: 1094 helix: 1.49 (0.18), residues: 907 sheet: None (None), residues: 0 loop : 1.38 (0.53), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.014 0.001 PHE a 142 TYR 0.011 0.001 TYR a 145 ARG 0.004 0.001 ARG M 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7649 (mp10) cc_final: 0.6833 (mp10) REVERT: d 2 SER cc_start: 0.8219 (p) cc_final: 0.7940 (t) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 2.9533 time to fit residues: 375.7178 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 50 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8257 Z= 0.309 Angle : 0.535 5.567 11218 Z= 0.293 Chirality : 0.039 0.135 1322 Planarity : 0.004 0.030 1440 Dihedral : 3.747 14.540 1149 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.30 % Allowed : 8.16 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.26), residues: 1094 helix: 2.30 (0.17), residues: 944 sheet: None (None), residues: 0 loop : 1.92 (0.60), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.016 0.002 PHE S 74 TYR 0.031 0.001 TYR a 145 ARG 0.005 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7887 (mp10) cc_final: 0.7401 (mp10) REVERT: S 21 MET cc_start: 0.8305 (mmp) cc_final: 0.7981 (mmp) REVERT: a 72 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6674 (tp40) outliers start: 10 outliers final: 3 residues processed: 88 average time/residue: 2.5597 time to fit residues: 240.8059 Evaluate side-chains 80 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 234 SER Chi-restraints excluded: chain b residue 76 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.8636 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8257 Z= 0.252 Angle : 0.501 5.430 11218 Z= 0.273 Chirality : 0.038 0.134 1322 Planarity : 0.004 0.033 1440 Dihedral : 3.747 14.057 1149 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.42 % Allowed : 8.94 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.26), residues: 1094 helix: 2.65 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.92 (0.61), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.015 0.002 PHE S 74 TYR 0.027 0.001 TYR a 145 ARG 0.004 0.000 ARG L 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7918 (mp10) cc_final: 0.7523 (mp10) REVERT: a 72 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6683 (tp40) outliers start: 11 outliers final: 1 residues processed: 86 average time/residue: 2.7196 time to fit residues: 248.8188 Evaluate side-chains 78 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain a residue 72 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8651 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8257 Z= 0.296 Angle : 0.511 5.472 11218 Z= 0.279 Chirality : 0.038 0.134 1322 Planarity : 0.004 0.034 1440 Dihedral : 3.825 14.250 1149 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.42 % Allowed : 9.97 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.26), residues: 1094 helix: 2.82 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 1.17 (0.52), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.016 0.002 PHE a 142 TYR 0.024 0.001 TYR a 145 ARG 0.005 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7929 (mp10) cc_final: 0.7536 (mp10) REVERT: a 72 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6661 (tp40) outliers start: 11 outliers final: 3 residues processed: 85 average time/residue: 2.9492 time to fit residues: 266.2148 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 0.1980 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 52 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.8640 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8257 Z= 0.235 Angle : 0.492 5.413 11218 Z= 0.267 Chirality : 0.038 0.129 1322 Planarity : 0.004 0.038 1440 Dihedral : 3.789 14.275 1149 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 9.33 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.26), residues: 1094 helix: 2.80 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.89 (0.60), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.014 0.002 PHE a 142 TYR 0.022 0.001 TYR a 145 ARG 0.006 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7913 (mp10) cc_final: 0.7518 (mp10) REVERT: a 72 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6683 (tp40) REVERT: a 161 LYS cc_start: 0.8796 (tptp) cc_final: 0.8469 (ttmt) outliers start: 14 outliers final: 4 residues processed: 88 average time/residue: 2.7918 time to fit residues: 262.3435 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 103 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.8643 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8257 Z= 0.250 Angle : 0.499 6.207 11218 Z= 0.270 Chirality : 0.038 0.132 1322 Planarity : 0.004 0.038 1440 Dihedral : 3.794 14.312 1149 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.68 % Allowed : 9.72 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.02 (0.26), residues: 1094 helix: 2.96 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 1.08 (0.51), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.015 0.002 PHE a 142 TYR 0.022 0.001 TYR a 145 ARG 0.007 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 1.309 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7900 (mp10) cc_final: 0.7501 (mp10) REVERT: a 72 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6677 (tp40) REVERT: a 161 LYS cc_start: 0.8799 (tptp) cc_final: 0.8478 (ttmt) outliers start: 13 outliers final: 5 residues processed: 82 average time/residue: 2.7154 time to fit residues: 237.2247 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 41 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8633 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8257 Z= 0.213 Angle : 0.487 7.064 11218 Z= 0.262 Chirality : 0.038 0.130 1322 Planarity : 0.004 0.041 1440 Dihedral : 3.746 14.304 1149 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 10.36 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.26), residues: 1094 helix: 2.89 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.82 (0.59), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.014 0.001 PHE a 142 TYR 0.021 0.001 TYR a 145 ARG 0.008 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7911 (mp10) cc_final: 0.7508 (mp10) REVERT: R 45 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7067 (mtm-85) REVERT: a 72 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.6671 (tp40) REVERT: a 73 MET cc_start: 0.8978 (mmt) cc_final: 0.8572 (mmt) REVERT: a 161 LYS cc_start: 0.8795 (tptp) cc_final: 0.8477 (ttmt) outliers start: 14 outliers final: 6 residues processed: 85 average time/residue: 2.7326 time to fit residues: 247.3818 Evaluate side-chains 79 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 125 LYS Chi-restraints excluded: chain a residue 179 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.2980 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.8636 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8257 Z= 0.231 Angle : 0.500 8.363 11218 Z= 0.268 Chirality : 0.038 0.130 1322 Planarity : 0.004 0.038 1440 Dihedral : 3.737 14.257 1149 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 10.62 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.26), residues: 1094 helix: 3.06 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 1.04 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.014 0.001 PHE a 142 TYR 0.020 0.001 TYR a 145 ARG 0.007 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7936 (mp10) cc_final: 0.7535 (mp10) REVERT: a 72 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6681 (tp40) REVERT: a 161 LYS cc_start: 0.8793 (tptp) cc_final: 0.8476 (ttmt) outliers start: 14 outliers final: 6 residues processed: 82 average time/residue: 2.7857 time to fit residues: 242.8581 Evaluate side-chains 81 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 48 GLU Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 179 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8633 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8257 Z= 0.219 Angle : 0.493 8.586 11218 Z= 0.264 Chirality : 0.038 0.129 1322 Planarity : 0.004 0.067 1440 Dihedral : 3.727 14.236 1149 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.68 % Allowed : 11.01 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.26), residues: 1094 helix: 2.94 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.80 (0.58), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.002 0.001 HIS a 146 PHE 0.014 0.001 PHE a 142 TYR 0.020 0.001 TYR a 145 ARG 0.014 0.001 ARG R 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7935 (mp10) cc_final: 0.7530 (mp10) REVERT: a 72 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6684 (tp40) REVERT: a 161 LYS cc_start: 0.8792 (tptp) cc_final: 0.8474 (ttmt) outliers start: 13 outliers final: 5 residues processed: 83 average time/residue: 2.7742 time to fit residues: 245.0141 Evaluate side-chains 81 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 67 optimal weight: 0.1980 chunk 90 optimal weight: 0.1980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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: 0.8607 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8257 Z= 0.167 Angle : 0.483 8.661 11218 Z= 0.256 Chirality : 0.038 0.126 1322 Planarity : 0.004 0.057 1440 Dihedral : 3.626 14.201 1149 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.04 % Allowed : 11.27 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.47 (0.26), residues: 1094 helix: 3.10 (0.17), residues: 945 sheet: None (None), residues: 0 loop : 1.91 (0.59), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 218 HIS 0.002 0.000 HIS a 146 PHE 0.013 0.001 PHE P 54 TYR 0.020 0.001 TYR a 145 ARG 0.012 0.001 ARG R 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: M 46 GLN cc_start: 0.7910 (mp10) cc_final: 0.7505 (mp10) REVERT: R 45 ARG cc_start: 0.7833 (mtp-110) cc_final: 0.7270 (tmt170) REVERT: a 72 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6685 (tp40) REVERT: a 161 LYS cc_start: 0.8784 (tptp) cc_final: 0.8476 (ttmt) outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 2.7821 time to fit residues: 239.9816 Evaluate side-chains 80 residues out of total 772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 45 ARG Chi-restraints excluded: chain Q residue 72 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain a residue 72 GLN Chi-restraints excluded: chain a residue 179 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.068811 restraints weight = 43063.900| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.76 r_work: 0.2769 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8257 Z= 0.284 Angle : 0.516 8.293 11218 Z= 0.278 Chirality : 0.038 0.133 1322 Planarity : 0.004 0.051 1440 Dihedral : 3.734 14.266 1149 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.78 % Allowed : 11.92 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.25), residues: 1094 helix: 3.06 (0.17), residues: 909 sheet: None (None), residues: 0 loop : 1.09 (0.50), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 218 HIS 0.003 0.001 HIS a 146 PHE 0.016 0.002 PHE a 142 TYR 0.020 0.001 TYR a 145 ARG 0.012 0.001 ARG R 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5779.77 seconds wall clock time: 102 minutes 14.35 seconds (6134.35 seconds total)