Starting phenix.real_space_refine on Tue Feb 13 23:39:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tko_10515/02_2024/6tko_10515_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tko_10515/02_2024/6tko_10515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tko_10515/02_2024/6tko_10515.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tko_10515/02_2024/6tko_10515.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tko_10515/02_2024/6tko_10515_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tko_10515/02_2024/6tko_10515_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 C 5177 2.51 5 N 1358 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 139": "NH1" <-> "NH2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8085 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2241 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TPO:plan-1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2684 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1529 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1606 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.59 Number of scatterers: 8085 At special positions: 0 Unit cell: (126.5, 106.7, 104.5, 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 36 16.00 P 6 15.00 O 1508 8.00 N 1358 7.00 C 5177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " 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: 3.16 Conformation dependent library (CDL) restraints added in 1.5 seconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 18 sheets defined 24.9% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 45 through 68 removed outlier: 3.957A pdb=" N VAL A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 104 removed outlier: 3.923A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 111 through 143 removed outlier: 3.938A pdb=" N GLU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 152 removed outlier: 4.221A pdb=" N SER A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 179 removed outlier: 4.237A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 217 through 241 Processing helix chain 'A' and resid 281 through 315 removed outlier: 3.708A pdb=" N PHE A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.696A pdb=" N VAL A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 315 " --> pdb=" O ILE A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 removed outlier: 3.904A pdb=" N ASN A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER A 336 " --> pdb=" O GLY A 332 " (cutoff:3.500A) Proline residue: A 340 - end of helix Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' 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 123 through 128 Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.685A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 9 through 12 Processing sheet with id= B, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.895A pdb=" N GLU B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 76 through 78 removed outlier: 4.039A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 144 through 147 removed outlier: 3.547A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 146 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 166 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.635A pdb=" N ALA B 201 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 214 through 218 Processing sheet with id= G, first strand: chain 'B' and resid 255 through 258 removed outlier: 7.093A pdb=" N VAL B 328 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILE B 231 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS B 326 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 233 " --> pdb=" O LYS B 324 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS B 324 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B 235 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS B 322 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLN B 237 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SER B 320 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 236 through 241 Processing sheet with id= I, first strand: chain 'B' and resid 53 through 58 removed outlier: 6.678A pdb=" N VAL B 55 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN B 85 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU B 57 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN B 83 " --> pdb=" O LEU B 57 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= K, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.539A pdb=" N TYR H 97 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA H 95 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 130 through 134 Processing sheet with id= M, first strand: chain 'H' and resid 161 through 164 Processing sheet with id= N, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= O, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.305A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ALA L 14 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLU L 106 " --> pdb=" O ALA L 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'L' and resid 86 through 90 removed outlier: 6.344A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.512A pdb=" N ASN L 139 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER L 175 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 146 through 150 345 hydrogen bonds defined for protein. 966 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: 2.64 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2531 1.34 - 1.46: 1273 1.46 - 1.57: 4417 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 8271 Sorted by residual: bond pdb=" OG1 TPO A1360 " pdb=" P TPO A1360 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" OG1 TPO A1359 " pdb=" P TPO A1359 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O2P SEP A1363 " pdb=" P SEP A1363 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O3P SEP A1363 " pdb=" P SEP A1363 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O3P SEP A1362 " pdb=" P SEP A1362 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.53e+01 ... (remaining 8266 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 318 107.39 - 114.03: 4764 114.03 - 120.68: 3201 120.68 - 127.33: 2897 127.33 - 133.98: 99 Bond angle restraints: 11279 Sorted by residual: angle pdb=" CB SEP A1364 " pdb=" OG SEP A1364 " pdb=" P SEP A1364 " ideal model delta sigma weight residual 110.00 121.71 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CB SEP A1363 " pdb=" OG SEP A1363 " pdb=" P SEP A1363 " ideal model delta sigma weight residual 110.00 120.85 -10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" CB SEP A1357 " pdb=" OG SEP A1357 " pdb=" P SEP A1357 " ideal model delta sigma weight residual 110.00 120.57 -10.57 3.00e+00 1.11e-01 1.24e+01 angle pdb=" CB SEP A1362 " pdb=" OG SEP A1362 " pdb=" P SEP A1362 " ideal model delta sigma weight residual 110.00 120.51 -10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" OG1 TPO A1359 " pdb=" P TPO A1359 " pdb=" O1P TPO A1359 " ideal model delta sigma weight residual 100.43 109.13 -8.70 3.00e+00 1.11e-01 8.41e+00 ... (remaining 11274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4589 17.44 - 34.89: 286 34.89 - 52.33: 51 52.33 - 69.77: 8 69.77 - 87.22: 14 Dihedral angle restraints: 4948 sinusoidal: 1863 harmonic: 3085 Sorted by residual: dihedral pdb=" CB CYS A 44 " pdb=" SG CYS A 44 " pdb=" SG CYS A 103 " pdb=" CB CYS A 103 " ideal model delta sinusoidal sigma weight residual 93.00 36.03 56.97 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA ASP B 78 " pdb=" CB ASP B 78 " pdb=" CG ASP B 78 " pdb=" OD1 ASP B 78 " ideal model delta sinusoidal sigma weight residual -30.00 -82.26 52.26 1 2.00e+01 2.50e-03 9.31e+00 dihedral pdb=" CA ARG A 345 " pdb=" CB ARG A 345 " pdb=" CG ARG A 345 " pdb=" CD ARG A 345 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1136 0.055 - 0.109: 143 0.109 - 0.164: 28 0.164 - 0.218: 0 0.218 - 0.273: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" C12 H98 A2001 " pdb=" C11 H98 A2001 " pdb=" C13 H98 A2001 " pdb=" O4 H98 A2001 " both_signs ideal model delta sigma weight residual False -2.43 -2.70 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C2 H98 A2001 " pdb=" C1 H98 A2001 " pdb=" C3 H98 A2001 " pdb=" N1 H98 A2001 " both_signs ideal model delta sigma weight residual False 2.57 2.71 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1305 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 275 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO B 276 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 218 " 0.012 5.00e-02 4.00e+02 1.82e-02 5.28e-01 pdb=" N PRO A 219 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.012 5.00e-02 4.00e+02 1.79e-02 5.15e-01 pdb=" N PRO H 159 " -0.031 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.010 5.00e-02 4.00e+02 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 93 2.64 - 3.21: 7471 3.21 - 3.77: 12423 3.77 - 4.34: 17158 4.34 - 4.90: 28461 Nonbonded interactions: 65606 Sorted by model distance: nonbonded pdb=" OG SER B 13 " pdb=" OD1 ASN B 15 " model vdw 2.079 2.440 nonbonded pdb=" OG SER H 36 " pdb=" OG SER H 102 " model vdw 2.096 2.440 nonbonded pdb=" O HIS L 190 " pdb=" NH1 ARG L 212 " model vdw 2.255 2.520 nonbonded pdb=" OH TYR A 193 " pdb=" O VAL A 202 " model vdw 2.279 2.440 nonbonded pdb=" O PHE B 277 " pdb=" ND2 ASN B 281 " model vdw 2.285 2.520 ... (remaining 65601 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=0.65 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: 0.700 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: 0.000 Extract box with map and model: 3.230 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.090 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.005 0.107 8271 Z= 0.338 Angle : 0.509 11.713 11279 Z= 0.242 Chirality : 0.040 0.273 1308 Planarity : 0.002 0.021 1413 Dihedral : 12.600 87.216 2931 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 0.23 % Allowed : 7.58 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.24), residues: 1023 helix: -0.38 (0.29), residues: 255 sheet: -1.90 (0.25), residues: 333 loop : -1.36 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 330 HIS 0.001 0.000 HIS B 30 PHE 0.004 0.000 PHE A 147 TYR 0.004 0.000 TYR L 92 ARG 0.001 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 303 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASN cc_start: 0.7881 (m-40) cc_final: 0.7569 (m-40) REVERT: A 121 ASP cc_start: 0.8282 (t0) cc_final: 0.8066 (t0) REVERT: A 154 THR cc_start: 0.8467 (m) cc_final: 0.8072 (p) REVERT: A 182 TRP cc_start: 0.7354 (p-90) cc_final: 0.6972 (p-90) REVERT: A 192 CYS cc_start: 0.4226 (t) cc_final: 0.3700 (t) REVERT: A 204 ASN cc_start: 0.7277 (p0) cc_final: 0.6898 (p0) REVERT: A 217 TYR cc_start: 0.7651 (m-80) cc_final: 0.7390 (m-80) REVERT: A 221 LEU cc_start: 0.8424 (tp) cc_final: 0.8158 (tt) REVERT: A 235 LYS cc_start: 0.7549 (mttt) cc_final: 0.7322 (mtpp) REVERT: A 325 PHE cc_start: 0.8508 (t80) cc_final: 0.8230 (t80) REVERT: A 339 ASN cc_start: 0.8419 (m-40) cc_final: 0.8104 (m110) REVERT: B 29 ASP cc_start: 0.7763 (t0) cc_final: 0.7501 (t0) REVERT: H 111 ASP cc_start: 0.7495 (m-30) cc_final: 0.6562 (m-30) REVERT: L 3 ILE cc_start: 0.7294 (mt) cc_final: 0.7026 (mp) REVERT: L 80 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7661 (mp10) REVERT: L 91 GLN cc_start: 0.8215 (pp30) cc_final: 0.7818 (pp30) REVERT: L 178 SER cc_start: 0.8134 (t) cc_final: 0.7860 (t) REVERT: L 195 CYS cc_start: 0.4880 (m) cc_final: 0.4225 (m) outliers start: 2 outliers final: 1 residues processed: 305 average time/residue: 0.2070 time to fit residues: 83.9439 Evaluate side-chains 195 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN B 85 GLN B 162 ASN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN L 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8271 Z= 0.271 Angle : 0.588 9.971 11279 Z= 0.293 Chirality : 0.042 0.159 1308 Planarity : 0.004 0.050 1413 Dihedral : 6.965 82.160 1164 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.03 % Allowed : 14.70 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: -0.60 (0.25), residues: 1023 helix: 1.38 (0.32), residues: 250 sheet: -1.23 (0.28), residues: 323 loop : -0.63 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.003 0.001 HIS L 190 PHE 0.023 0.002 PHE B 87 TYR 0.017 0.002 TYR A 193 ARG 0.005 0.001 ARG B 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8589 (tpp) cc_final: 0.8329 (mmm) REVERT: A 192 CYS cc_start: 0.3998 (t) cc_final: 0.3596 (t) REVERT: A 204 ASN cc_start: 0.7576 (p0) cc_final: 0.7266 (p0) REVERT: A 213 ILE cc_start: 0.8468 (mm) cc_final: 0.8247 (mm) REVERT: A 221 LEU cc_start: 0.8439 (tp) cc_final: 0.8159 (tt) REVERT: A 235 LYS cc_start: 0.7718 (mttt) cc_final: 0.7392 (mtpp) REVERT: A 339 ASN cc_start: 0.8571 (m-40) cc_final: 0.8279 (m110) REVERT: H 68 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7953 (ttpp) REVERT: H 83 TYR cc_start: 0.7747 (m-80) cc_final: 0.7449 (m-80) REVERT: H 120 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8388 (m) REVERT: H 220 LYS cc_start: 0.8530 (pptt) cc_final: 0.8308 (pptt) REVERT: L 71 ASP cc_start: 0.7948 (m-30) cc_final: 0.7617 (m-30) REVERT: L 91 GLN cc_start: 0.8592 (pp30) cc_final: 0.7969 (pp30) REVERT: L 178 SER cc_start: 0.7933 (t) cc_final: 0.7280 (t) REVERT: L 195 CYS cc_start: 0.4618 (m) cc_final: 0.2813 (m) outliers start: 26 outliers final: 17 residues processed: 223 average time/residue: 0.1906 time to fit residues: 57.8741 Evaluate side-chains 203 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 164 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 94 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8271 Z= 0.277 Angle : 0.581 7.639 11279 Z= 0.290 Chirality : 0.042 0.188 1308 Planarity : 0.004 0.031 1413 Dihedral : 6.821 85.572 1163 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.27 % Allowed : 16.80 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: -0.20 (0.26), residues: 1023 helix: 1.71 (0.32), residues: 256 sheet: -1.02 (0.27), residues: 342 loop : -0.33 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 149 HIS 0.006 0.001 HIS L 190 PHE 0.021 0.002 PHE H 132 TYR 0.016 0.002 TYR B 173 ARG 0.006 0.001 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.7553 (p0) cc_final: 0.7288 (p0) REVERT: A 235 LYS cc_start: 0.7720 (mttt) cc_final: 0.7359 (mtpp) REVERT: A 325 PHE cc_start: 0.8277 (t80) cc_final: 0.8059 (t80) REVERT: A 339 ASN cc_start: 0.8405 (m-40) cc_final: 0.8095 (m110) REVERT: B 58 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8250 (t) REVERT: H 62 TYR cc_start: 0.8465 (m-80) cc_final: 0.8203 (m-80) REVERT: H 68 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8009 (ttpp) REVERT: H 83 TYR cc_start: 0.7852 (m-80) cc_final: 0.7591 (m-80) REVERT: H 119 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7247 (m) REVERT: L 91 GLN cc_start: 0.8692 (pp30) cc_final: 0.8130 (pp30) REVERT: L 177 SER cc_start: 0.8629 (m) cc_final: 0.8197 (m) outliers start: 28 outliers final: 17 residues processed: 215 average time/residue: 0.1769 time to fit residues: 52.9731 Evaluate side-chains 201 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8271 Z= 0.342 Angle : 0.626 9.364 11279 Z= 0.312 Chirality : 0.042 0.150 1308 Planarity : 0.004 0.035 1413 Dihedral : 6.866 86.681 1163 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.50 % Allowed : 19.25 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: -0.11 (0.26), residues: 1023 helix: 1.66 (0.32), residues: 255 sheet: -0.99 (0.28), residues: 346 loop : -0.17 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 149 HIS 0.006 0.001 HIS L 190 PHE 0.025 0.002 PHE H 132 TYR 0.019 0.002 TYR L 187 ARG 0.005 0.001 ARG L 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8661 (tpp) cc_final: 0.8372 (mmm) REVERT: A 203 THR cc_start: 0.7928 (p) cc_final: 0.7712 (p) REVERT: A 235 LYS cc_start: 0.7768 (mttt) cc_final: 0.7491 (mtpp) REVERT: A 325 PHE cc_start: 0.8270 (t80) cc_final: 0.8038 (t80) REVERT: A 339 ASN cc_start: 0.8322 (m-40) cc_final: 0.8011 (m110) REVERT: B 248 GLN cc_start: 0.7933 (mt0) cc_final: 0.7715 (tt0) REVERT: H 68 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8090 (ttpp) REVERT: L 91 GLN cc_start: 0.8748 (pp30) cc_final: 0.8081 (pp30) REVERT: L 109 ARG cc_start: 0.7335 (ptm160) cc_final: 0.7073 (ptm160) REVERT: L 177 SER cc_start: 0.8678 (m) cc_final: 0.8281 (m) outliers start: 30 outliers final: 24 residues processed: 216 average time/residue: 0.1769 time to fit residues: 53.3682 Evaluate side-chains 207 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN L 80 GLN ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8271 Z= 0.228 Angle : 0.600 9.881 11279 Z= 0.295 Chirality : 0.042 0.213 1308 Planarity : 0.004 0.032 1413 Dihedral : 6.779 84.155 1163 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.27 % Allowed : 21.00 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: -0.12 (0.26), residues: 1023 helix: 1.81 (0.32), residues: 251 sheet: -1.00 (0.28), residues: 335 loop : -0.28 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 149 HIS 0.005 0.001 HIS L 190 PHE 0.024 0.002 PHE H 132 TYR 0.020 0.002 TYR L 193 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 200 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 TYR cc_start: 0.7442 (m-10) cc_final: 0.7174 (m-80) REVERT: A 235 LYS cc_start: 0.7748 (mttt) cc_final: 0.7465 (mtpp) REVERT: A 325 PHE cc_start: 0.8267 (t80) cc_final: 0.8022 (t80) REVERT: A 339 ASN cc_start: 0.8356 (m-40) cc_final: 0.8037 (m110) REVERT: B 346 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6975 (mt-10) REVERT: H 119 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.6985 (t) REVERT: H 155 TYR cc_start: 0.8226 (p90) cc_final: 0.7587 (p90) REVERT: L 91 GLN cc_start: 0.8652 (pp30) cc_final: 0.8164 (pp30) REVERT: L 109 ARG cc_start: 0.7186 (ptm160) cc_final: 0.6845 (ptm160) REVERT: L 177 SER cc_start: 0.8635 (m) cc_final: 0.8170 (m) REVERT: L 196 GLU cc_start: 0.7429 (tt0) cc_final: 0.7011 (pt0) outliers start: 28 outliers final: 24 residues processed: 218 average time/residue: 0.1701 time to fit residues: 52.0288 Evaluate side-chains 207 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 0.0050 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8271 Z= 0.183 Angle : 0.599 9.618 11279 Z= 0.290 Chirality : 0.042 0.192 1308 Planarity : 0.004 0.034 1413 Dihedral : 6.669 85.653 1163 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.80 % Allowed : 21.94 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: 0.02 (0.27), residues: 1023 helix: 1.93 (0.32), residues: 252 sheet: -0.93 (0.29), residues: 334 loop : -0.20 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 149 HIS 0.005 0.001 HIS L 190 PHE 0.028 0.002 PHE H 132 TYR 0.023 0.001 TYR B 113 ARG 0.005 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.7290 (p0) cc_final: 0.6980 (p0) REVERT: A 235 LYS cc_start: 0.7705 (mttt) cc_final: 0.7441 (mtpp) REVERT: A 339 ASN cc_start: 0.8397 (m-40) cc_final: 0.8067 (m110) REVERT: B 346 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6925 (mt-10) REVERT: H 68 LYS cc_start: 0.8258 (ttpp) cc_final: 0.8035 (ttpp) REVERT: H 79 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7413 (pttt) REVERT: H 85 GLN cc_start: 0.7803 (tp40) cc_final: 0.7534 (tp40) REVERT: H 90 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7464 (mtt-85) REVERT: H 119 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.6708 (t) REVERT: L 91 GLN cc_start: 0.8537 (pp30) cc_final: 0.8064 (pp30) REVERT: L 109 ARG cc_start: 0.7091 (ptm160) cc_final: 0.6781 (ptm160) REVERT: L 170 LYS cc_start: 0.8153 (tmmt) cc_final: 0.7742 (tmmt) REVERT: L 177 SER cc_start: 0.8526 (m) cc_final: 0.8117 (m) REVERT: L 196 GLU cc_start: 0.7328 (tt0) cc_final: 0.6799 (pt0) outliers start: 24 outliers final: 20 residues processed: 210 average time/residue: 0.1764 time to fit residues: 51.6671 Evaluate side-chains 203 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 56 optimal weight: 0.4980 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 59 optimal weight: 0.0060 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8271 Z= 0.180 Angle : 0.606 9.207 11279 Z= 0.292 Chirality : 0.042 0.193 1308 Planarity : 0.004 0.034 1413 Dihedral : 6.576 86.099 1163 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.22 % Allowed : 22.87 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: 0.01 (0.27), residues: 1023 helix: 1.79 (0.32), residues: 252 sheet: -0.85 (0.29), residues: 337 loop : -0.19 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 149 HIS 0.007 0.001 HIS L 190 PHE 0.026 0.002 PHE H 132 TYR 0.027 0.002 TYR L 141 ARG 0.005 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.8648 (tpp) cc_final: 0.8265 (mmm) REVERT: A 181 TRP cc_start: 0.7865 (m-90) cc_final: 0.7620 (m-90) REVERT: A 184 ASP cc_start: 0.6011 (m-30) cc_final: 0.5674 (m-30) REVERT: A 204 ASN cc_start: 0.7468 (p0) cc_final: 0.7013 (p0) REVERT: A 214 ILE cc_start: 0.8315 (tt) cc_final: 0.8069 (tp) REVERT: A 235 LYS cc_start: 0.7706 (mttt) cc_final: 0.7437 (mtpp) REVERT: A 339 ASN cc_start: 0.8357 (m-40) cc_final: 0.8027 (m110) REVERT: H 79 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7410 (pttt) REVERT: H 119 VAL cc_start: 0.7396 (OUTLIER) cc_final: 0.6595 (t) REVERT: L 91 GLN cc_start: 0.8483 (pp30) cc_final: 0.8073 (pp30) REVERT: L 177 SER cc_start: 0.8508 (m) cc_final: 0.8115 (m) REVERT: L 196 GLU cc_start: 0.7257 (tt0) cc_final: 0.6720 (pt0) outliers start: 19 outliers final: 14 residues processed: 201 average time/residue: 0.1726 time to fit residues: 48.6639 Evaluate side-chains 198 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 91 optimal weight: 0.0970 chunk 96 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 93 optimal weight: 4.9990 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8271 Z= 0.187 Angle : 0.605 9.299 11279 Z= 0.293 Chirality : 0.042 0.198 1308 Planarity : 0.004 0.098 1413 Dihedral : 6.473 86.077 1163 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.45 % Allowed : 23.69 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: 0.07 (0.26), residues: 1023 helix: 1.79 (0.32), residues: 253 sheet: -0.82 (0.29), residues: 335 loop : -0.12 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP L 149 HIS 0.006 0.001 HIS L 190 PHE 0.029 0.002 PHE H 132 TYR 0.033 0.002 TYR A 193 ARG 0.005 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8751 (tpp) cc_final: 0.8386 (mmm) REVERT: A 184 ASP cc_start: 0.6248 (OUTLIER) cc_final: 0.5809 (m-30) REVERT: A 204 ASN cc_start: 0.7310 (p0) cc_final: 0.6948 (p0) REVERT: A 214 ILE cc_start: 0.8293 (tt) cc_final: 0.8044 (tp) REVERT: A 235 LYS cc_start: 0.7692 (mttt) cc_final: 0.7427 (mtpp) REVERT: A 339 ASN cc_start: 0.8372 (m-40) cc_final: 0.8019 (m110) REVERT: B 202 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8076 (t) REVERT: H 79 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7398 (pttt) REVERT: H 119 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.6555 (t) REVERT: L 30 VAL cc_start: 0.7051 (t) cc_final: 0.6213 (m) REVERT: L 91 GLN cc_start: 0.8610 (pp30) cc_final: 0.8064 (pp30) REVERT: L 177 SER cc_start: 0.8459 (m) cc_final: 0.7995 (m) REVERT: L 196 GLU cc_start: 0.7245 (tt0) cc_final: 0.6686 (pt0) outliers start: 21 outliers final: 17 residues processed: 206 average time/residue: 0.1742 time to fit residues: 50.5913 Evaluate side-chains 203 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 183 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 135 CYS Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8271 Z= 0.221 Angle : 0.619 9.387 11279 Z= 0.302 Chirality : 0.042 0.203 1308 Planarity : 0.004 0.091 1413 Dihedral : 6.465 85.663 1163 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.33 % Allowed : 24.39 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: 0.05 (0.26), residues: 1023 helix: 1.73 (0.32), residues: 253 sheet: -0.81 (0.29), residues: 335 loop : -0.13 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP L 149 HIS 0.007 0.001 HIS L 190 PHE 0.028 0.002 PHE H 132 TYR 0.021 0.002 TYR L 141 ARG 0.004 0.000 ARG L 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 184 ASP cc_start: 0.6376 (OUTLIER) cc_final: 0.5787 (m-30) REVERT: A 193 TYR cc_start: 0.7201 (m-80) cc_final: 0.6912 (m-80) REVERT: A 204 ASN cc_start: 0.7302 (p0) cc_final: 0.6920 (p0) REVERT: A 235 LYS cc_start: 0.7694 (mttt) cc_final: 0.7427 (mtpp) REVERT: A 339 ASN cc_start: 0.8349 (m-40) cc_final: 0.8000 (m110) REVERT: B 202 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8112 (t) REVERT: H 68 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8073 (ttpp) REVERT: H 79 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7442 (pttt) REVERT: H 119 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.6561 (t) REVERT: L 91 GLN cc_start: 0.8660 (pp30) cc_final: 0.8065 (pp30) REVERT: L 177 SER cc_start: 0.8457 (m) cc_final: 0.7972 (m) REVERT: L 196 GLU cc_start: 0.7283 (tt0) cc_final: 0.6733 (pt0) outliers start: 20 outliers final: 16 residues processed: 198 average time/residue: 0.1784 time to fit residues: 49.3941 Evaluate side-chains 198 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 179 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8271 Z= 0.224 Angle : 0.638 9.289 11279 Z= 0.309 Chirality : 0.043 0.200 1308 Planarity : 0.004 0.087 1413 Dihedral : 6.451 85.875 1163 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.45 % Allowed : 24.15 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: 0.07 (0.26), residues: 1023 helix: 1.75 (0.32), residues: 253 sheet: -0.80 (0.29), residues: 335 loop : -0.11 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 149 HIS 0.007 0.001 HIS L 190 PHE 0.028 0.002 PHE H 132 TYR 0.027 0.002 TYR L 141 ARG 0.002 0.000 ARG B 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 184 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5671 (m-30) REVERT: A 204 ASN cc_start: 0.7305 (p0) cc_final: 0.6964 (p0) REVERT: A 214 ILE cc_start: 0.8156 (tt) cc_final: 0.7913 (tp) REVERT: A 235 LYS cc_start: 0.7690 (mttt) cc_final: 0.7426 (mtpp) REVERT: A 339 ASN cc_start: 0.8345 (m-40) cc_final: 0.8008 (m110) REVERT: B 202 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.8117 (t) REVERT: H 68 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8075 (ttpp) REVERT: H 79 LYS cc_start: 0.7878 (mtmm) cc_final: 0.7508 (pttt) REVERT: H 127 LYS cc_start: 0.8144 (mptt) cc_final: 0.7855 (mmtt) REVERT: L 91 GLN cc_start: 0.8658 (pp30) cc_final: 0.8051 (pp30) REVERT: L 177 SER cc_start: 0.8539 (m) cc_final: 0.8054 (m) REVERT: L 196 GLU cc_start: 0.7310 (tt0) cc_final: 0.6748 (pt0) outliers start: 21 outliers final: 16 residues processed: 195 average time/residue: 0.1866 time to fit residues: 51.2889 Evaluate side-chains 199 residues out of total 911 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 164 VAL Chi-restraints excluded: chain L residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.167068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.121684 restraints weight = 11155.830| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.59 r_work: 0.3406 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8271 Z= 0.234 Angle : 0.649 10.391 11279 Z= 0.314 Chirality : 0.043 0.205 1308 Planarity : 0.004 0.084 1413 Dihedral : 6.410 85.957 1163 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.33 % Allowed : 24.85 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.10 % 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: 0.09 (0.27), residues: 1023 helix: 1.76 (0.32), residues: 253 sheet: -0.83 (0.29), residues: 335 loop : -0.06 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 149 HIS 0.007 0.001 HIS L 190 PHE 0.030 0.002 PHE H 132 TYR 0.025 0.002 TYR L 141 ARG 0.002 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2173.42 seconds wall clock time: 40 minutes 6.25 seconds (2406.25 seconds total)