Starting phenix.real_space_refine on Tue Feb 13 17:54:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dce_30636/02_2024/7dce_30636_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dce_30636/02_2024/7dce_30636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dce_30636/02_2024/7dce_30636.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dce_30636/02_2024/7dce_30636.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dce_30636/02_2024/7dce_30636_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dce_30636/02_2024/7dce_30636_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 P 1 5.49 5 S 28 5.16 5 C 4602 2.51 5 N 1161 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 26": "OD1" <-> "OD2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "X TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 129": "OD1" <-> "OD2" Residue "X GLU 141": "OE1" <-> "OE2" Residue "X GLU 160": "OE1" <-> "OE2" Residue "X TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 180": "OD1" <-> "OD2" Residue "X PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 280": "NH1" <-> "NH2" Residue "X TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 350": "OD1" <-> "OD2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 65": "NH1" <-> "NH2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 112": "NH1" <-> "NH2" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 146": "NH1" <-> "NH2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L GLU 165": "OE1" <-> "OE2" Residue "L GLU 169": "OE1" <-> "OE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L GLU 217": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7102 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1032 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2837 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 17, 'TRANS': 336} Chain: "H" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1553 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1626 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 207} Chain: "X" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'DLP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.15, per 1000 atoms: 0.58 Number of scatterers: 7102 At special positions: 0 Unit cell: (113.295, 70.965, 117.03, 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 P 1 15.00 O 1310 8.00 N 1161 7.00 C 4602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 185 " distance=2.02 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 81 " - pdb=" SG CYS L 175 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " 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=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 10 sheets defined 36.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 205 through 229 removed outlier: 3.764A pdb=" N TRP B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 3.894A pdb=" N ILE B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 40 Processing helix chain 'X' and resid 44 through 70 Processing helix chain 'X' and resid 84 through 91 Processing helix chain 'X' and resid 96 through 111 Processing helix chain 'X' and resid 117 through 140 removed outlier: 3.594A pdb=" N ALA X 121 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 156 Processing helix chain 'X' and resid 161 through 187 Processing helix chain 'X' and resid 196 through 224 Proline residue: X 213 - end of helix Processing helix chain 'X' and resid 229 through 246 Processing helix chain 'X' and resid 256 through 269 removed outlier: 3.758A pdb=" N TRP X 259 " --> pdb=" O SER X 256 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG X 262 " --> pdb=" O TRP X 259 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL X 265 " --> pdb=" O ARG X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 284 through 305 Processing helix chain 'X' and resid 316 through 339 removed outlier: 3.859A pdb=" N LEU X 320 " --> pdb=" O LEU X 316 " (cutoff:3.500A) Proline residue: X 321 - end of helix Processing helix chain 'X' and resid 349 through 357 Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' 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 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 185 through 189 removed outlier: 4.389A pdb=" N GLY H 189 " --> pdb=" O SER H 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 189' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 95 through 98 No H-bonds generated for 'chain 'L' and resid 95 through 98' Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.514A pdb=" N LYS L 130 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 126 through 131' Processing helix chain 'L' and resid 187 through 192 Processing sheet with id= A, first strand: chain 'B' and resid 107 through 109 Processing sheet with id= B, first strand: chain 'B' and resid 113 through 117 removed outlier: 8.231A pdb=" N GLU B 114 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N THR B 199 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 116 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG B 201 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN B 182 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 136 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= D, first strand: chain 'H' and resid 106 through 108 removed outlier: 3.811A pdb=" N ALA H 32 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG H 37 " --> pdb=" O TRP H 46 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TRP H 46 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.005A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 150 through 153 Processing sheet with id= G, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.502A pdb=" N GLN L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 11 through 15 removed outlier: 6.271A pdb=" N GLU L 107 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA L 14 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL L 109 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 85 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'L' and resid 118 through 122 Processing sheet with id= J, first strand: chain 'L' and resid 148 through 154 removed outlier: 3.621A pdb=" N LYS L 211 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1038 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: 2.07 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1211 1.32 - 1.44: 2012 1.44 - 1.57: 4029 1.57 - 1.69: 2 1.69 - 1.82: 36 Bond restraints: 7290 Sorted by residual: bond pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 1.345 1.460 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C4 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" O4P DLP X 501 " pdb=" P DLP X 501 " ideal model delta sigma weight residual 1.649 1.605 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" CB VAL X 49 " pdb=" CG2 VAL X 49 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CA ALA X 285 " pdb=" C ALA X 285 " ideal model delta sigma weight residual 1.524 1.498 0.027 1.29e-02 6.01e+03 4.25e+00 ... (remaining 7285 not shown) Histogram of bond angle deviations from ideal: 97.55 - 104.90: 154 104.90 - 112.26: 3716 112.26 - 119.61: 2429 119.61 - 126.96: 3510 126.96 - 134.32: 135 Bond angle restraints: 9944 Sorted by residual: angle pdb=" N ALA X 285 " pdb=" CA ALA X 285 " pdb=" C ALA X 285 " ideal model delta sigma weight residual 111.40 103.05 8.35 1.22e+00 6.72e-01 4.68e+01 angle pdb=" N GLY H 98 " pdb=" CA GLY H 98 " pdb=" C GLY H 98 " ideal model delta sigma weight residual 112.37 100.25 12.12 1.84e+00 2.95e-01 4.34e+01 angle pdb=" N TRP X 340 " pdb=" CA TRP X 340 " pdb=" C TRP X 340 " ideal model delta sigma weight residual 111.24 118.00 -6.76 1.29e+00 6.01e-01 2.74e+01 angle pdb=" N ALA H 97 " pdb=" CA ALA H 97 " pdb=" C ALA H 97 " ideal model delta sigma weight residual 107.23 99.23 8.00 1.67e+00 3.59e-01 2.29e+01 angle pdb=" N GLU B 146 " pdb=" CA GLU B 146 " pdb=" C GLU B 146 " ideal model delta sigma weight residual 108.52 115.60 -7.08 1.52e+00 4.33e-01 2.17e+01 ... (remaining 9939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 4016 24.90 - 49.81: 222 49.81 - 74.71: 23 74.71 - 99.62: 9 99.62 - 124.52: 1 Dihedral angle restraints: 4271 sinusoidal: 1635 harmonic: 2636 Sorted by residual: dihedral pdb=" CB CYS L 81 " pdb=" SG CYS L 81 " pdb=" SG CYS L 175 " pdb=" CB CYS L 175 " ideal model delta sinusoidal sigma weight residual -86.00 -126.28 40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" N DLP X 501 " pdb=" C4 DLP X 501 " pdb=" C5 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sinusoidal sigma weight residual 288.95 164.43 124.52 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CB GLU L 199 " pdb=" CG GLU L 199 " pdb=" CD GLU L 199 " pdb=" OE1 GLU L 199 " ideal model delta sinusoidal sigma weight residual 0.00 86.84 -86.84 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 802 0.056 - 0.112: 253 0.112 - 0.168: 61 0.168 - 0.224: 12 0.224 - 0.280: 5 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA PRO X 253 " pdb=" N PRO X 253 " pdb=" C PRO X 253 " pdb=" CB PRO X 253 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA LEU X 236 " pdb=" N LEU X 236 " pdb=" C LEU X 236 " pdb=" CB LEU X 236 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA TRP X 212 " pdb=" N TRP X 212 " pdb=" C TRP X 212 " pdb=" CB TRP X 212 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1130 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 DLP X 501 " 0.062 2.00e-02 2.50e+03 1.21e-01 1.46e+02 pdb=" C22 DLP X 501 " -0.158 2.00e-02 2.50e+03 pdb=" C23 DLP X 501 " 0.159 2.00e-02 2.50e+03 pdb=" C24 DLP X 501 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 262 " 0.123 9.50e-02 1.11e+02 7.08e-02 2.67e+01 pdb=" NE ARG X 262 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG X 262 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG X 262 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG X 262 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 DLP X 501 " 0.044 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C42 DLP X 501 " -0.047 2.00e-02 2.50e+03 pdb=" C43 DLP X 501 " -0.040 2.00e-02 2.50e+03 pdb=" C44 DLP X 501 " 0.043 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1163 2.76 - 3.29: 6915 3.29 - 3.83: 11918 3.83 - 4.36: 13529 4.36 - 4.90: 23324 Nonbonded interactions: 56849 Sorted by model distance: nonbonded pdb=" OG SER L 125 " pdb=" OE1 GLU L 127 " model vdw 2.220 2.440 nonbonded pdb=" NE2 HIS X 182 " pdb=" OH TYR X 337 " model vdw 2.222 2.520 nonbonded pdb=" NH2 ARG B 184 " pdb=" OE1 GLN B 195 " model vdw 2.256 2.520 nonbonded pdb=" OH TYR X 37 " pdb=" NE2 GLN X 163 " model vdw 2.263 2.520 nonbonded pdb=" OD1 ASP X 12 " pdb=" NH2 ARG X 183 " model vdw 2.287 2.520 ... (remaining 56844 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 1.240 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.780 ------------------------------------------------------------------------------- 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 : 0.009 0.115 7290 Z= 0.620 Angle : 1.212 14.698 9944 Z= 0.665 Chirality : 0.060 0.280 1133 Planarity : 0.009 0.121 1234 Dihedral : 14.999 124.523 2563 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.44 % Favored : 92.34 % Rotamer: Outliers : 3.27 % Allowed : 10.07 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -3.04 (0.24), residues: 901 helix: -2.75 (0.24), residues: 309 sheet: -0.59 (0.29), residues: 259 loop : -2.24 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP X 303 HIS 0.010 0.003 HIS X 232 PHE 0.026 0.003 PHE L 102 TYR 0.028 0.003 TYR L 98 ARG 0.086 0.003 ARG X 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 242 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8162 (p0) REVERT: B 123 MET cc_start: 0.9055 (ttp) cc_final: 0.8611 (ttp) REVERT: B 160 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (p) REVERT: B 173 ASN cc_start: 0.8943 (t0) cc_final: 0.8709 (t0) REVERT: B 227 PHE cc_start: 0.8523 (t80) cc_final: 0.8154 (t80) REVERT: X 43 TYR cc_start: 0.7301 (p90) cc_final: 0.6745 (p90) REVERT: X 66 LEU cc_start: 0.9346 (mm) cc_final: 0.9072 (mp) REVERT: X 103 LEU cc_start: 0.9205 (mt) cc_final: 0.8900 (mt) REVERT: X 132 MET cc_start: 0.9183 (mmm) cc_final: 0.8786 (mmp) REVERT: X 145 GLN cc_start: 0.8767 (tp40) cc_final: 0.8462 (tp40) REVERT: X 209 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8574 (mp) REVERT: X 233 PHE cc_start: 0.8576 (t80) cc_final: 0.8246 (t80) REVERT: X 259 TRP cc_start: 0.6462 (t60) cc_final: 0.6063 (t-100) REVERT: X 299 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (mp) REVERT: X 326 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8511 (t) REVERT: H 28 LEU cc_start: 0.9142 (mt) cc_final: 0.8870 (mp) REVERT: H 33 MET cc_start: 0.8744 (mmm) cc_final: 0.8376 (mmt) REVERT: H 86 ASP cc_start: 0.8595 (m-30) cc_final: 0.8263 (m-30) REVERT: H 139 CYS cc_start: 0.6328 (m) cc_final: 0.6049 (m) REVERT: H 140 LEU cc_start: 0.9212 (tp) cc_final: 0.8795 (tt) REVERT: H 143 ASP cc_start: 0.7615 (m-30) cc_final: 0.7188 (m-30) REVERT: H 144 TYR cc_start: 0.8260 (p90) cc_final: 0.8026 (p90) REVERT: H 153 TRP cc_start: 0.7771 (m100) cc_final: 0.6836 (m100) REVERT: L 5 MET cc_start: 0.8959 (mmm) cc_final: 0.8100 (mmm) REVERT: L 91 SER cc_start: 0.9447 (t) cc_final: 0.9016 (m) REVERT: L 129 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7478 (mm) REVERT: L 180 SER cc_start: 0.7513 (p) cc_final: 0.7016 (p) REVERT: L 191 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8760 (mm-30) outliers start: 25 outliers final: 11 residues processed: 258 average time/residue: 0.1833 time to fit residues: 62.7389 Evaluate side-chains 183 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 326 CYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 205 HIS ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 306 HIS X 339 HIS H 163 HIS L 128 GLN L 164 GLN L 214 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7290 Z= 0.217 Angle : 0.710 10.567 9944 Z= 0.346 Chirality : 0.043 0.150 1133 Planarity : 0.005 0.057 1234 Dihedral : 8.555 117.374 1053 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.40 % Allowed : 16.73 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.35 (0.27), residues: 901 helix: 0.69 (0.29), residues: 310 sheet: 0.26 (0.31), residues: 252 loop : -1.44 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.007 0.001 HIS X 288 PHE 0.029 0.002 PHE L 213 TYR 0.028 0.002 TYR L 33 ARG 0.008 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8923 (OUTLIER) cc_final: 0.8289 (p0) REVERT: B 173 ASN cc_start: 0.8934 (t0) cc_final: 0.8707 (t0) REVERT: B 227 PHE cc_start: 0.8474 (t80) cc_final: 0.8091 (t80) REVERT: X 43 TYR cc_start: 0.7327 (p90) cc_final: 0.6586 (p90) REVERT: X 154 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8226 (mp) REVERT: X 181 TYR cc_start: 0.9495 (t80) cc_final: 0.9046 (t80) REVERT: X 237 TRP cc_start: 0.8636 (t60) cc_final: 0.8238 (t60) REVERT: X 259 TRP cc_start: 0.6422 (t60) cc_final: 0.6057 (t-100) REVERT: X 275 ASN cc_start: 0.7472 (t0) cc_final: 0.7261 (t0) REVERT: H 28 LEU cc_start: 0.9123 (mt) cc_final: 0.8895 (mp) REVERT: H 86 ASP cc_start: 0.8552 (m-30) cc_final: 0.8242 (m-30) REVERT: H 139 CYS cc_start: 0.5566 (m) cc_final: 0.5144 (m) REVERT: H 153 TRP cc_start: 0.7825 (m100) cc_final: 0.7206 (m100) REVERT: L 191 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8713 (mm-30) outliers start: 26 outliers final: 15 residues processed: 203 average time/residue: 0.1537 time to fit residues: 44.0343 Evaluate side-chains 182 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 169 THR Chi-restraints excluded: chain X residue 170 SER Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 HIS B 117 ASN ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 163 GLN ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7290 Z= 0.237 Angle : 0.666 7.933 9944 Z= 0.323 Chirality : 0.042 0.168 1133 Planarity : 0.005 0.048 1234 Dihedral : 7.725 112.766 1029 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.23 % Allowed : 20.65 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.77 (0.28), residues: 901 helix: 1.79 (0.30), residues: 309 sheet: 0.84 (0.31), residues: 252 loop : -0.95 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 110 HIS 0.004 0.001 HIS X 182 PHE 0.018 0.002 PHE L 213 TYR 0.018 0.002 TYR X 122 ARG 0.005 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8673 (p0) REVERT: B 227 PHE cc_start: 0.8473 (t80) cc_final: 0.8172 (t80) REVERT: X 43 TYR cc_start: 0.7157 (p90) cc_final: 0.6354 (p90) REVERT: X 163 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8247 (mt0) REVERT: X 167 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7305 (mt) REVERT: X 237 TRP cc_start: 0.8712 (t60) cc_final: 0.8304 (t60) REVERT: X 242 LEU cc_start: 0.8694 (tt) cc_final: 0.8230 (mm) REVERT: X 259 TRP cc_start: 0.6460 (t60) cc_final: 0.6096 (t-100) REVERT: H 28 LEU cc_start: 0.9237 (mt) cc_final: 0.8923 (mp) REVERT: H 86 ASP cc_start: 0.8631 (m-30) cc_final: 0.8338 (m-30) REVERT: H 144 TYR cc_start: 0.8550 (p90) cc_final: 0.7944 (p90) REVERT: H 153 TRP cc_start: 0.7828 (m100) cc_final: 0.7345 (m100) REVERT: L 112 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7743 (ttp-170) REVERT: L 141 ASN cc_start: 0.8761 (t0) cc_final: 0.8295 (t0) REVERT: L 190 TYR cc_start: 0.7996 (t80) cc_final: 0.7697 (t80) REVERT: L 191 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8699 (mm-30) outliers start: 40 outliers final: 27 residues processed: 203 average time/residue: 0.1567 time to fit residues: 44.4902 Evaluate side-chains 187 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 163 GLN Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 169 THR Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 252 MET Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 23 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 ASN ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 288 HIS L 38 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7290 Z= 0.431 Angle : 0.727 9.681 9944 Z= 0.357 Chirality : 0.044 0.315 1133 Planarity : 0.005 0.047 1234 Dihedral : 7.877 113.074 1029 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 7.45 % Allowed : 20.78 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.85 (0.28), residues: 901 helix: 1.77 (0.29), residues: 307 sheet: 0.98 (0.31), residues: 252 loop : -0.88 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 210 HIS 0.004 0.001 HIS X 288 PHE 0.025 0.002 PHE L 213 TYR 0.016 0.002 TYR L 37 ARG 0.004 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 164 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 43 TYR cc_start: 0.7423 (p90) cc_final: 0.6563 (p90) REVERT: X 163 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: X 181 TYR cc_start: 0.9453 (t80) cc_final: 0.9185 (t80) REVERT: X 252 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7944 (ptm) REVERT: X 259 TRP cc_start: 0.6606 (t60) cc_final: 0.6168 (t-100) REVERT: H 28 LEU cc_start: 0.9330 (mt) cc_final: 0.8952 (mp) REVERT: H 86 ASP cc_start: 0.8650 (m-30) cc_final: 0.8185 (m-30) REVERT: H 144 TYR cc_start: 0.8686 (p90) cc_final: 0.8343 (p90) REVERT: H 153 TRP cc_start: 0.7840 (m100) cc_final: 0.7126 (m100) REVERT: L 141 ASN cc_start: 0.8688 (t0) cc_final: 0.8219 (t0) outliers start: 57 outliers final: 43 residues processed: 199 average time/residue: 0.1678 time to fit residues: 46.3416 Evaluate side-chains 197 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 163 GLN Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 252 MET Chi-restraints excluded: chain X residue 260 LEU Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 20.0000 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 170 HIS B 173 ASN ** X 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7290 Z= 0.177 Angle : 0.640 11.497 9944 Z= 0.306 Chirality : 0.042 0.333 1133 Planarity : 0.004 0.045 1234 Dihedral : 7.494 108.147 1027 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.23 % Allowed : 22.48 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.19 (0.28), residues: 901 helix: 2.27 (0.29), residues: 305 sheet: 1.07 (0.31), residues: 245 loop : -0.78 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.017 0.001 PHE L 122 TYR 0.015 0.001 TYR L 33 ARG 0.005 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7573 (ttp80) REVERT: B 201 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7837 (ptm160) REVERT: X 43 TYR cc_start: 0.7344 (p90) cc_final: 0.6446 (p90) REVERT: X 85 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8664 (pp) REVERT: X 114 GLU cc_start: 0.8795 (tp30) cc_final: 0.8360 (tp30) REVERT: X 180 ASP cc_start: 0.8801 (m-30) cc_final: 0.8467 (m-30) REVERT: X 181 TYR cc_start: 0.9295 (t80) cc_final: 0.9040 (t80) REVERT: X 242 LEU cc_start: 0.8649 (tt) cc_final: 0.8201 (mm) REVERT: X 259 TRP cc_start: 0.6236 (t60) cc_final: 0.5829 (t-100) REVERT: H 28 LEU cc_start: 0.9240 (mt) cc_final: 0.8847 (mp) REVERT: H 86 ASP cc_start: 0.8694 (m-30) cc_final: 0.8297 (m-30) REVERT: H 106 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8769 (p) REVERT: H 144 TYR cc_start: 0.8577 (p90) cc_final: 0.8288 (p90) REVERT: L 141 ASN cc_start: 0.8755 (t0) cc_final: 0.8226 (t0) outliers start: 40 outliers final: 25 residues processed: 190 average time/residue: 0.1689 time to fit residues: 43.6529 Evaluate side-chains 184 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.0060 chunk 45 optimal weight: 6.9990 chunk 83 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 105 GLN L 71 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7290 Z= 0.255 Angle : 0.662 12.480 9944 Z= 0.318 Chirality : 0.042 0.349 1133 Planarity : 0.004 0.045 1234 Dihedral : 7.350 106.636 1026 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.49 % Allowed : 22.75 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.27 (0.28), residues: 901 helix: 2.28 (0.29), residues: 306 sheet: 1.14 (0.32), residues: 242 loop : -0.68 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP X 110 HIS 0.004 0.001 HIS X 182 PHE 0.017 0.001 PHE L 122 TYR 0.018 0.001 TYR X 122 ARG 0.007 0.001 ARG L 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 156 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7645 (ttp80) REVERT: X 43 TYR cc_start: 0.7389 (p90) cc_final: 0.6456 (p90) REVERT: X 85 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8704 (pp) REVERT: X 181 TYR cc_start: 0.9349 (t80) cc_final: 0.9131 (t80) REVERT: X 205 LEU cc_start: 0.9242 (tp) cc_final: 0.8952 (tp) REVERT: X 242 LEU cc_start: 0.8658 (tt) cc_final: 0.8212 (mm) REVERT: X 259 TRP cc_start: 0.6207 (t60) cc_final: 0.5812 (t-100) REVERT: H 28 LEU cc_start: 0.9282 (mt) cc_final: 0.8891 (mp) REVERT: H 86 ASP cc_start: 0.8722 (m-30) cc_final: 0.8338 (m-30) REVERT: H 106 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8803 (p) REVERT: H 144 TYR cc_start: 0.8621 (p90) cc_final: 0.8392 (p90) REVERT: L 141 ASN cc_start: 0.8641 (t0) cc_final: 0.8161 (t0) outliers start: 42 outliers final: 35 residues processed: 183 average time/residue: 0.1738 time to fit residues: 43.3660 Evaluate side-chains 188 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 227 SER Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 92 GLN X 163 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7290 Z= 0.345 Angle : 0.697 13.030 9944 Z= 0.336 Chirality : 0.043 0.353 1133 Planarity : 0.004 0.044 1234 Dihedral : 7.467 107.389 1026 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.80 % Allowed : 22.09 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.12 (0.28), residues: 901 helix: 2.08 (0.28), residues: 313 sheet: 1.07 (0.33), residues: 236 loop : -0.73 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 110 HIS 0.004 0.001 HIS X 182 PHE 0.018 0.002 PHE L 122 TYR 0.012 0.002 TYR L 37 ARG 0.005 0.001 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 151 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7805 (ttp80) REVERT: X 26 ASP cc_start: 0.8305 (t0) cc_final: 0.8014 (t0) REVERT: X 85 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8732 (pp) REVERT: X 242 LEU cc_start: 0.8678 (tt) cc_final: 0.8241 (mm) REVERT: X 259 TRP cc_start: 0.6263 (t60) cc_final: 0.5849 (t-100) REVERT: H 28 LEU cc_start: 0.9330 (mt) cc_final: 0.8892 (mp) REVERT: H 86 ASP cc_start: 0.8729 (m-30) cc_final: 0.8239 (m-30) REVERT: L 141 ASN cc_start: 0.8619 (t0) cc_final: 0.8153 (t0) outliers start: 52 outliers final: 44 residues processed: 185 average time/residue: 0.1724 time to fit residues: 44.2665 Evaluate side-chains 188 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 227 SER Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 260 LEU Chi-restraints excluded: chain X residue 276 VAL Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 163 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7290 Z= 0.215 Angle : 0.667 13.293 9944 Z= 0.315 Chirality : 0.043 0.347 1133 Planarity : 0.004 0.046 1234 Dihedral : 7.325 105.515 1026 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.23 % Allowed : 23.79 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.29 (0.28), residues: 901 helix: 2.24 (0.29), residues: 313 sheet: 1.26 (0.33), residues: 236 loop : -0.73 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 153 HIS 0.003 0.001 HIS X 182 PHE 0.020 0.001 PHE L 122 TYR 0.028 0.002 TYR H 144 ARG 0.005 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 155 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7577 (ttp80) REVERT: X 242 LEU cc_start: 0.8614 (tt) cc_final: 0.8210 (mm) REVERT: X 259 TRP cc_start: 0.6209 (t60) cc_final: 0.5806 (t-100) REVERT: H 28 LEU cc_start: 0.9266 (mt) cc_final: 0.8814 (mp) REVERT: H 86 ASP cc_start: 0.8752 (m-30) cc_final: 0.8336 (m-30) REVERT: H 106 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8751 (p) REVERT: L 141 ASN cc_start: 0.8692 (t0) cc_final: 0.8167 (t0) outliers start: 40 outliers final: 34 residues processed: 183 average time/residue: 0.1616 time to fit residues: 41.7190 Evaluate side-chains 185 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 17 VAL Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 227 SER Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 276 VAL Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP 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: 0.7980 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7290 Z= 0.185 Angle : 0.679 13.071 9944 Z= 0.316 Chirality : 0.043 0.345 1133 Planarity : 0.004 0.044 1234 Dihedral : 7.114 101.371 1026 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.05 % Allowed : 26.01 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.51 (0.29), residues: 901 helix: 2.42 (0.29), residues: 306 sheet: 1.43 (0.33), residues: 239 loop : -0.60 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.012 0.001 PHE L 213 TYR 0.021 0.001 TYR H 144 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 26 ASP cc_start: 0.8092 (t0) cc_final: 0.7877 (t0) REVERT: X 242 LEU cc_start: 0.8559 (tt) cc_final: 0.8188 (mm) REVERT: X 259 TRP cc_start: 0.6047 (t60) cc_final: 0.5663 (t-100) REVERT: H 28 LEU cc_start: 0.9227 (mt) cc_final: 0.8756 (mp) REVERT: H 86 ASP cc_start: 0.8807 (m-30) cc_final: 0.8539 (m-30) REVERT: H 106 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8697 (p) REVERT: L 141 ASN cc_start: 0.8555 (t0) cc_final: 0.8046 (t0) outliers start: 31 outliers final: 25 residues processed: 173 average time/residue: 0.1551 time to fit residues: 37.9133 Evaluate side-chains 174 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 227 SER Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 276 VAL Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 10 optimal weight: 0.0470 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7290 Z= 0.171 Angle : 0.676 13.090 9944 Z= 0.313 Chirality : 0.043 0.359 1133 Planarity : 0.004 0.046 1234 Dihedral : 6.935 97.794 1026 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.27 % Allowed : 26.67 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.58 (0.29), residues: 901 helix: 2.47 (0.29), residues: 308 sheet: 1.46 (0.33), residues: 239 loop : -0.56 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 PHE 0.018 0.001 PHE X 118 TYR 0.018 0.001 TYR H 144 ARG 0.006 0.000 ARG H 9 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 205 LEU cc_start: 0.9217 (tp) cc_final: 0.8928 (tp) REVERT: X 242 LEU cc_start: 0.8485 (tt) cc_final: 0.8112 (mm) REVERT: X 259 TRP cc_start: 0.5921 (t60) cc_final: 0.5568 (t-100) REVERT: H 28 LEU cc_start: 0.9226 (mt) cc_final: 0.8766 (mp) REVERT: H 86 ASP cc_start: 0.8879 (m-30) cc_final: 0.8659 (m-30) REVERT: H 106 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8652 (p) REVERT: L 141 ASN cc_start: 0.8681 (t0) cc_final: 0.8123 (t0) outliers start: 25 outliers final: 23 residues processed: 171 average time/residue: 0.1555 time to fit residues: 37.5188 Evaluate side-chains 175 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 227 SER Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 91 SER Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 163 GLN ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.143112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105868 restraints weight = 12647.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109905 restraints weight = 11089.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.109441 restraints weight = 8379.024| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 7290 Z= 0.406 Angle : 0.767 12.668 9944 Z= 0.367 Chirality : 0.046 0.363 1133 Planarity : 0.005 0.044 1234 Dihedral : 7.342 101.835 1026 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.31 % Allowed : 26.41 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.32 (0.29), residues: 901 helix: 2.20 (0.29), residues: 306 sheet: 1.29 (0.33), residues: 242 loop : -0.63 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 110 HIS 0.004 0.001 HIS B 170 PHE 0.017 0.002 PHE H 91 TYR 0.023 0.002 TYR L 98 ARG 0.005 0.001 ARG B 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1639.62 seconds wall clock time: 30 minutes 42.16 seconds (1842.16 seconds total)