Starting phenix.real_space_refine on Tue Jun 25 05:54:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rqf_19440/06_2024/8rqf_19440_updated.pdb" } resolution = 3.41 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= 0.059 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4466 2.51 5 N 1137 2.21 5 O 1303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 152": "OD1" <-> "OD2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6950 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2315 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 16, 'TRANS': 284} Chain: "H" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1690 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "L" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1630 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 10, 'TRANS': 201} Chain: "K" Number of atoms: 930 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Conformer: "B" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} bond proxies already assigned to first conformer: 931 Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 365 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 7, 'TRANS': 38} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'BJU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BJU:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.70, per 1000 atoms: 0.82 Number of scatterers: 6950 At special positions: 0 Unit cell: (81.9, 75.4, 139.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1303 8.00 N 1137 7.00 C 4466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 10 sheets defined 29.2% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 44 removed outlier: 3.933A pdb=" N VAL A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 56 Processing helix chain 'A' and resid 60 through 82 Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 130 through 141 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 179 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 181 through 216 removed outlier: 4.679A pdb=" N ARG A 185 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 203 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS A 212 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE A 214 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 216 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 Proline residue: A 230 - end of helix removed outlier: 3.696A pdb=" N PHE A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.889A pdb=" N LEU A 270 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN A 271 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 310 removed outlier: 3.515A pdb=" N GLY A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix removed outlier: 5.317A pdb=" N PHE A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.883A pdb=" N GLY A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 188 through 191 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'K' and resid 84 through 86 No H-bonds generated for 'chain 'K' and resid 84 through 86' Processing sheet with id= A, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.659A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 107 through 109 removed outlier: 3.642A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 58 " --> pdb=" O SER H 50 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 120 through 123 Processing sheet with id= D, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.537A pdb=" N THR H 151 " --> pdb=" O ASN H 199 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL H 198 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 207 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS H 200 " --> pdb=" O THR H 205 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.561A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR L 72 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 85 through 88 removed outlier: 6.393A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.743A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER L 176 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER L 162 " --> pdb=" O SER L 176 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 144 through 149 removed outlier: 3.569A pdb=" N TYR L 192 " --> pdb=" O PHE L 209 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.773A pdb=" N LEU K 18 " --> pdb=" O MET K 82 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 107 through 109 removed outlier: 4.068A pdb=" N ALA K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA K 40 " --> pdb=" O ARG K 45 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ARG K 45 " --> pdb=" O ALA K 40 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 647 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: 1.63 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1088 1.30 - 1.43: 1915 1.43 - 1.56: 4043 1.56 - 1.68: 5 1.68 - 1.81: 65 Bond restraints: 7116 Sorted by residual: bond pdb=" C CYS A 125 " pdb=" O CYS A 125 " ideal model delta sigma weight residual 1.237 1.176 0.060 1.17e-02 7.31e+03 2.65e+01 bond pdb=" CA SER A 119 " pdb=" CB SER A 119 " ideal model delta sigma weight residual 1.528 1.451 0.078 1.59e-02 3.96e+03 2.39e+01 bond pdb=" C ILE A 120 " pdb=" O ILE A 120 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.19e-02 7.06e+03 1.67e+01 bond pdb=" C VAL A 121 " pdb=" O VAL A 121 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.11e-02 8.12e+03 1.61e+01 bond pdb=" CA SER A 126 " pdb=" CB SER A 126 " ideal model delta sigma weight residual 1.531 1.469 0.061 1.72e-02 3.38e+03 1.27e+01 ... (remaining 7111 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.79: 190 105.79 - 112.85: 3773 112.85 - 119.92: 2324 119.92 - 126.98: 3291 126.98 - 134.04: 86 Bond angle restraints: 9664 Sorted by residual: angle pdb=" CA MET A 122 " pdb=" C MET A 122 " pdb=" N THR A 123 " ideal model delta sigma weight residual 117.07 124.66 -7.59 1.14e+00 7.69e-01 4.43e+01 angle pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 117.07 123.35 -6.28 1.14e+00 7.69e-01 3.03e+01 angle pdb=" N SER A 119 " pdb=" CA SER A 119 " pdb=" C SER A 119 " ideal model delta sigma weight residual 111.36 105.69 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" CA MET A 122 " pdb=" C MET A 122 " pdb=" O MET A 122 " ideal model delta sigma weight residual 120.82 115.42 5.40 1.05e+00 9.07e-01 2.65e+01 angle pdb=" CA VAL A 121 " pdb=" C VAL A 121 " pdb=" N MET A 122 " ideal model delta sigma weight residual 116.72 122.24 -5.52 1.10e+00 8.26e-01 2.51e+01 ... (remaining 9659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 3700 18.04 - 36.08: 421 36.08 - 54.12: 92 54.12 - 72.16: 19 72.16 - 90.20: 6 Dihedral angle restraints: 4238 sinusoidal: 1618 harmonic: 2620 Sorted by residual: dihedral pdb=" CA LEU A 246 " pdb=" C LEU A 246 " pdb=" N ASN A 247 " pdb=" CA ASN A 247 " ideal model delta harmonic sigma weight residual -180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CB CYS H 140 " pdb=" SG CYS H 140 " pdb=" SG CYS H 196 " pdb=" CB CYS H 196 " ideal model delta sinusoidal sigma weight residual 93.00 135.07 -42.07 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA HIS B 40 " pdb=" C HIS B 40 " pdb=" N TRP B 41 " pdb=" CA TRP B 41 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 4235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 888 0.051 - 0.103: 168 0.103 - 0.154: 31 0.154 - 0.206: 2 0.206 - 0.257: 4 Chirality restraints: 1093 Sorted by residual: chirality pdb=" CA THR A 123 " pdb=" N THR A 123 " pdb=" C THR A 123 " pdb=" CB THR A 123 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA SER A 119 " pdb=" N SER A 119 " pdb=" C SER A 119 " pdb=" CB SER A 119 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1090 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 119 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER A 119 " -0.059 2.00e-02 2.50e+03 pdb=" O SER A 119 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 120 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 256 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C MET A 256 " -0.045 2.00e-02 2.50e+03 pdb=" O MET A 256 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 257 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 291 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C ILE A 291 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 291 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 292 " -0.016 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 831 2.75 - 3.29: 6569 3.29 - 3.83: 10999 3.83 - 4.36: 12692 4.36 - 4.90: 22989 Nonbonded interactions: 54080 Sorted by model distance: nonbonded pdb=" OD1 ASP A 24 " pdb=" O HOH A 401 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.224 2.440 nonbonded pdb=" O PRO L 8 " pdb=" OG1 THR L 102 " model vdw 2.275 2.440 nonbonded pdb=" NH1 ARG L 66 " pdb=" O GLY L 68 " model vdw 2.281 2.520 nonbonded pdb=" OE1 GLN L 27 " pdb=" OH TYR L 93 " model vdw 2.301 2.440 ... (remaining 54075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.870 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.740 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.004 0.078 7116 Z= 0.263 Angle : 0.670 8.121 9664 Z= 0.391 Chirality : 0.044 0.257 1093 Planarity : 0.004 0.035 1216 Dihedral : 16.106 90.197 2559 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.26 % Allowed : 23.03 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.28), residues: 895 helix: 0.43 (0.31), residues: 276 sheet: 0.69 (0.38), residues: 203 loop : -1.26 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 PHE 0.023 0.001 PHE H 122 TYR 0.019 0.001 TYR L 93 ARG 0.004 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.8299 (tpp) cc_final: 0.8097 (mmm) REVERT: A 151 LYS cc_start: 0.8365 (pttt) cc_final: 0.7221 (tttp) REVERT: A 180 ARG cc_start: 0.7034 (mmt-90) cc_final: 0.6023 (mtm180) REVERT: A 184 MET cc_start: 0.4806 (tmt) cc_final: 0.3438 (mtm) REVERT: A 192 MET cc_start: 0.4945 (tpt) cc_final: 0.4315 (mtt) REVERT: K 34 MET cc_start: 0.8444 (mtt) cc_final: 0.8195 (mtt) REVERT: K 82 SER cc_start: 0.7009 (m) cc_final: 0.6763 (t) REVERT: B 46 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7527 (mtpt) outliers start: 2 outliers final: 2 residues processed: 106 average time/residue: 0.2429 time to fit residues: 33.1438 Evaluate side-chains 97 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 198 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7116 Z= 0.182 Angle : 0.542 6.820 9664 Z= 0.283 Chirality : 0.042 0.123 1093 Planarity : 0.005 0.035 1216 Dihedral : 4.782 46.483 997 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.33 % Allowed : 22.25 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.28), residues: 895 helix: 0.21 (0.30), residues: 277 sheet: 0.92 (0.37), residues: 213 loop : -1.20 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 146 TYR 0.018 0.001 TYR L 93 ARG 0.006 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.722 Fit side-chains revert: symmetry clash REVERT: A 34 MET cc_start: 0.7945 (tpp) cc_final: 0.7714 (ttm) REVERT: A 151 LYS cc_start: 0.8374 (pttt) cc_final: 0.7229 (tttp) REVERT: A 180 ARG cc_start: 0.6859 (mmt-90) cc_final: 0.5877 (mtm180) REVERT: A 192 MET cc_start: 0.4881 (tpt) cc_final: 0.4247 (mtt) REVERT: A 213 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7715 (t) REVERT: A 271 ASN cc_start: 0.8351 (t0) cc_final: 0.7776 (m-40) REVERT: L 156 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.8001 (t) REVERT: K 82 SER cc_start: 0.7025 (m) cc_final: 0.6782 (t) REVERT: B 46 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7531 (mtpt) outliers start: 18 outliers final: 13 residues processed: 110 average time/residue: 0.2093 time to fit residues: 30.2923 Evaluate side-chains 105 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 208 SER Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.0020 chunk 79 optimal weight: 7.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7116 Z= 0.195 Angle : 0.516 6.883 9664 Z= 0.268 Chirality : 0.041 0.123 1093 Planarity : 0.004 0.037 1216 Dihedral : 4.635 46.227 997 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.59 % Allowed : 22.38 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 895 helix: 0.18 (0.31), residues: 274 sheet: 0.77 (0.36), residues: 220 loop : -1.11 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE H 146 TYR 0.017 0.001 TYR L 93 ARG 0.006 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8377 (pttt) cc_final: 0.7245 (tttp) REVERT: A 180 ARG cc_start: 0.6826 (mmt-90) cc_final: 0.5783 (mtm180) REVERT: A 184 MET cc_start: 0.4335 (tmt) cc_final: 0.3275 (ttp) REVERT: A 192 MET cc_start: 0.4919 (tpt) cc_final: 0.4223 (mtt) REVERT: A 213 SER cc_start: 0.7934 (OUTLIER) cc_final: 0.7633 (t) REVERT: A 271 ASN cc_start: 0.8315 (t0) cc_final: 0.7777 (m-40) REVERT: L 106 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8606 (mt) REVERT: L 156 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8060 (t) REVERT: B 46 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7542 (mtpt) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.2088 time to fit residues: 29.8293 Evaluate side-chains 106 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 86 optimal weight: 0.0570 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7116 Z= 0.165 Angle : 0.494 6.929 9664 Z= 0.255 Chirality : 0.040 0.122 1093 Planarity : 0.004 0.034 1216 Dihedral : 4.478 46.217 997 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.20 % Allowed : 23.29 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.29), residues: 895 helix: 0.36 (0.31), residues: 267 sheet: 0.87 (0.36), residues: 220 loop : -0.94 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 37 TYR 0.016 0.001 TYR L 93 ARG 0.004 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 0.741 Fit side-chains REVERT: A 151 LYS cc_start: 0.8356 (pttt) cc_final: 0.7198 (tttp) REVERT: A 180 ARG cc_start: 0.6830 (mmt-90) cc_final: 0.5764 (mtm180) REVERT: A 184 MET cc_start: 0.4467 (tmt) cc_final: 0.3382 (ttp) REVERT: A 192 MET cc_start: 0.4934 (tpt) cc_final: 0.4245 (mtt) REVERT: A 213 SER cc_start: 0.7859 (OUTLIER) cc_final: 0.7259 (t) REVERT: A 271 ASN cc_start: 0.8304 (t0) cc_final: 0.7768 (m-40) REVERT: L 106 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8586 (mt) REVERT: L 156 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.8066 (t) REVERT: B 46 LYS cc_start: 0.8185 (mmtm) cc_final: 0.7522 (mtpt) outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 0.2085 time to fit residues: 28.2471 Evaluate side-chains 100 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 156 SER Chi-restraints excluded: chain L residue 196 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7993 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7116 Z= 0.205 Angle : 0.516 6.955 9664 Z= 0.265 Chirality : 0.041 0.123 1093 Planarity : 0.004 0.037 1216 Dihedral : 4.543 46.532 997 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.59 % Allowed : 23.42 % Favored : 74.00 % 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: -0.17 (0.29), residues: 895 helix: 0.35 (0.31), residues: 267 sheet: 0.89 (0.36), residues: 221 loop : -0.97 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 41 HIS 0.003 0.001 HIS H 35 PHE 0.010 0.001 PHE A 285 TYR 0.019 0.001 TYR L 93 ARG 0.003 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8392 (pttt) cc_final: 0.7252 (tttp) REVERT: A 180 ARG cc_start: 0.6888 (mmt-90) cc_final: 0.5817 (mtm180) REVERT: A 184 MET cc_start: 0.4557 (tmt) cc_final: 0.3505 (ttp) REVERT: A 192 MET cc_start: 0.4947 (tpt) cc_final: 0.4269 (mtt) REVERT: A 213 SER cc_start: 0.7905 (OUTLIER) cc_final: 0.7304 (t) REVERT: A 271 ASN cc_start: 0.8319 (t0) cc_final: 0.7826 (m-40) REVERT: L 106 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8638 (mt) REVERT: B 46 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7549 (mtpt) outliers start: 20 outliers final: 17 residues processed: 108 average time/residue: 0.2057 time to fit residues: 29.2035 Evaluate side-chains 109 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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: 0.7969 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7116 Z= 0.169 Angle : 0.493 6.965 9664 Z= 0.253 Chirality : 0.040 0.124 1093 Planarity : 0.004 0.035 1216 Dihedral : 4.455 47.421 997 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.46 % Allowed : 23.80 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.29), residues: 895 helix: 0.39 (0.31), residues: 267 sheet: 0.93 (0.36), residues: 221 loop : -0.96 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE H 146 TYR 0.018 0.001 TYR L 93 ARG 0.002 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8370 (pttt) cc_final: 0.7214 (tttp) REVERT: A 180 ARG cc_start: 0.6875 (mmt-90) cc_final: 0.5818 (mtm180) REVERT: A 184 MET cc_start: 0.4613 (tmt) cc_final: 0.3544 (ttp) REVERT: A 192 MET cc_start: 0.4959 (tpt) cc_final: 0.4291 (mtt) REVERT: A 213 SER cc_start: 0.7876 (OUTLIER) cc_final: 0.7259 (t) REVERT: A 271 ASN cc_start: 0.8319 (t0) cc_final: 0.7819 (m-40) REVERT: L 106 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8595 (mt) REVERT: B 46 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7521 (mtpt) outliers start: 19 outliers final: 14 residues processed: 101 average time/residue: 0.2042 time to fit residues: 27.2831 Evaluate side-chains 103 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 85 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7116 Z= 0.237 Angle : 0.527 6.942 9664 Z= 0.270 Chirality : 0.041 0.124 1093 Planarity : 0.004 0.038 1216 Dihedral : 4.596 47.377 997 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.59 % Allowed : 23.42 % Favored : 74.00 % 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: -0.24 (0.29), residues: 895 helix: 0.33 (0.31), residues: 267 sheet: 0.88 (0.36), residues: 223 loop : -1.07 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 41 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 285 TYR 0.021 0.001 TYR L 93 ARG 0.004 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8411 (pttt) cc_final: 0.7259 (tttp) REVERT: A 180 ARG cc_start: 0.6918 (mmt-90) cc_final: 0.5853 (mtm180) REVERT: A 184 MET cc_start: 0.4695 (tmt) cc_final: 0.3630 (ttp) REVERT: A 192 MET cc_start: 0.4936 (tpt) cc_final: 0.4182 (mtt) REVERT: A 212 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8115 (mmtt) REVERT: A 213 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7376 (t) REVERT: A 271 ASN cc_start: 0.8342 (t0) cc_final: 0.7869 (m-40) REVERT: B 46 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7554 (mtpt) outliers start: 20 outliers final: 18 residues processed: 110 average time/residue: 0.2077 time to fit residues: 29.8731 Evaluate side-chains 113 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 3 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7116 Z= 0.242 Angle : 0.538 6.939 9664 Z= 0.274 Chirality : 0.042 0.125 1093 Planarity : 0.004 0.038 1216 Dihedral : 4.648 47.942 997 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.10 % Allowed : 23.03 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.29), residues: 895 helix: 0.25 (0.31), residues: 268 sheet: 0.84 (0.36), residues: 223 loop : -1.11 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 41 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE H 146 TYR 0.020 0.001 TYR L 93 ARG 0.004 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8423 (pttt) cc_final: 0.7267 (tttp) REVERT: A 180 ARG cc_start: 0.6906 (mmt-90) cc_final: 0.5866 (mtm180) REVERT: A 184 MET cc_start: 0.4634 (tmt) cc_final: 0.3594 (ttp) REVERT: A 192 MET cc_start: 0.4913 (tpt) cc_final: 0.4192 (mtt) REVERT: A 212 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8160 (mmtt) REVERT: A 213 SER cc_start: 0.8038 (OUTLIER) cc_final: 0.7462 (t) REVERT: A 271 ASN cc_start: 0.8381 (t0) cc_final: 0.7920 (m-40) REVERT: B 46 LYS cc_start: 0.8226 (mmtm) cc_final: 0.7563 (mtpt) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.2099 time to fit residues: 31.0829 Evaluate side-chains 116 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.0670 chunk 58 optimal weight: 3.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7116 Z= 0.345 Angle : 0.600 6.881 9664 Z= 0.307 Chirality : 0.044 0.129 1093 Planarity : 0.004 0.040 1216 Dihedral : 4.973 47.799 997 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.98 % Allowed : 22.64 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.28), residues: 895 helix: -0.04 (0.30), residues: 272 sheet: 0.62 (0.36), residues: 225 loop : -1.29 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 41 HIS 0.003 0.001 HIS B 40 PHE 0.016 0.002 PHE H 146 TYR 0.025 0.002 TYR L 93 ARG 0.006 0.000 ARG K 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8478 (pttt) cc_final: 0.7361 (tttp) REVERT: A 180 ARG cc_start: 0.6974 (mmt-90) cc_final: 0.5922 (mtm180) REVERT: A 184 MET cc_start: 0.4730 (tmt) cc_final: 0.3660 (ttp) REVERT: A 192 MET cc_start: 0.4972 (tpt) cc_final: 0.4241 (mtt) REVERT: A 212 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8242 (mmtt) REVERT: A 213 SER cc_start: 0.8124 (OUTLIER) cc_final: 0.7608 (t) REVERT: A 271 ASN cc_start: 0.8493 (t0) cc_final: 0.8031 (m-40) REVERT: L 145 LYS cc_start: 0.7750 (tttp) cc_final: 0.7221 (ttpp) REVERT: L 155 GLN cc_start: 0.7295 (mp10) cc_final: 0.6917 (mp10) REVERT: B 46 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7588 (mtpt) outliers start: 23 outliers final: 20 residues processed: 112 average time/residue: 0.2087 time to fit residues: 30.4451 Evaluate side-chains 115 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 93 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 10 optimal weight: 0.2980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7116 Z= 0.169 Angle : 0.518 6.889 9664 Z= 0.263 Chirality : 0.041 0.123 1093 Planarity : 0.004 0.037 1216 Dihedral : 4.635 47.065 997 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.85 % Allowed : 22.64 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.28), residues: 895 helix: 0.14 (0.31), residues: 274 sheet: 0.97 (0.37), residues: 217 loop : -1.29 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 32 HIS 0.002 0.001 HIS H 35 PHE 0.010 0.001 PHE H 146 TYR 0.018 0.001 TYR L 93 ARG 0.004 0.000 ARG K 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8410 (pttt) cc_final: 0.7250 (tttp) REVERT: A 180 ARG cc_start: 0.6939 (mmt-90) cc_final: 0.5899 (mtm180) REVERT: A 184 MET cc_start: 0.4693 (tmt) cc_final: 0.3636 (ttp) REVERT: A 192 MET cc_start: 0.4935 (tpt) cc_final: 0.4221 (mtt) REVERT: A 212 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8170 (mmtt) REVERT: A 213 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7523 (t) REVERT: A 271 ASN cc_start: 0.8459 (t0) cc_final: 0.8022 (m-40) REVERT: L 155 GLN cc_start: 0.7295 (mp10) cc_final: 0.7070 (mp10) REVERT: L 160 GLN cc_start: 0.7235 (mt0) cc_final: 0.6909 (mt0) REVERT: B 46 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7563 (mtpt) outliers start: 22 outliers final: 19 residues processed: 112 average time/residue: 0.2133 time to fit residues: 31.1742 Evaluate side-chains 113 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain H residue 205 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.167353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.129016 restraints weight = 22323.040| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 6.44 r_work: 0.3082 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7116 Z= 0.167 Angle : 0.508 6.966 9664 Z= 0.257 Chirality : 0.040 0.122 1093 Planarity : 0.004 0.038 1216 Dihedral : 4.439 46.780 997 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.72 % Allowed : 22.90 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.29), residues: 895 helix: 0.36 (0.31), residues: 271 sheet: 1.02 (0.37), residues: 213 loop : -1.23 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 32 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 285 TYR 0.017 0.001 TYR L 93 ARG 0.004 0.000 ARG K 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.51 seconds wall clock time: 34 minutes 58.06 seconds (2098.06 seconds total)