Starting phenix.real_space_refine on Wed Feb 14 16:17:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/02_2024/6r4o_4721_updated.pdb" } resolution = 4.2 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= -0.005 sd= 0.435 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Mn 2 7.51 5 P 6 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 6170 2.51 5 N 1605 2.21 5 O 1749 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1026": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1148": "NH1" <-> "NH2" Residue "A ARG 1206": "NH1" <-> "NH2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 9602 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6687 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 20, 'TRANS': 820} Chain breaks: 6 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2809 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' MN': 2, 'FOK': 1, 'ONM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.76, per 1000 atoms: 0.60 Number of scatterers: 9602 At special positions: 0 Unit cell: (166.608, 105.091, 115.344, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 2 24.99 S 69 16.00 P 6 15.00 Mg 1 11.99 O 1749 8.00 N 1605 7.00 C 6170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 8 sheets defined 53.9% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.634A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 Processing helix chain 'A' and resid 144 through 164 Proline residue: A 148 - end of helix removed outlier: 4.298A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 190 Processing helix chain 'A' and resid 220 through 237 removed outlier: 3.876A pdb=" N VAL A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 261 Processing helix chain 'A' and resid 281 through 336 removed outlier: 3.932A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 414 through 433 Processing helix chain 'A' and resid 458 through 480 Processing helix chain 'A' and resid 512 through 522 Processing helix chain 'A' and resid 533 through 536 No H-bonds generated for 'chain 'A' and resid 533 through 536' Processing helix chain 'A' and resid 783 through 807 removed outlier: 3.870A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 842 Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 862 through 883 removed outlier: 3.802A pdb=" N HIS A 866 " --> pdb=" O TRP A 862 " (cutoff:3.500A) Proline residue: A 876 - end of helix removed outlier: 5.180A pdb=" N HIS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 910 removed outlier: 4.455A pdb=" N VAL A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLN A 908 " --> pdb=" O THR A 904 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 909 " --> pdb=" O ALA A 905 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N CYS A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 927 Processing helix chain 'A' and resid 930 through 936 Processing helix chain 'A' and resid 980 through 1036 removed outlier: 4.362A pdb=" N ALA A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1045 Processing helix chain 'A' and resid 1080 through 1098 removed outlier: 3.851A pdb=" N LEU A1097 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER A1098 " --> pdb=" O ASP A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1134 through 1156 Processing helix chain 'A' and resid 1190 through 1200 Processing helix chain 'A' and resid 1211 through 1217 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 90 through 110 Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.532A pdb=" N GLN B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 129 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 132 " --> pdb=" O ASP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.938A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.898A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.903A pdb=" N ALA B 351 " --> pdb=" O ARG B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 387 Processing sheet with id= A, first strand: chain 'A' and resid 387 through 390 Processing sheet with id= B, first strand: chain 'A' and resid 486 through 493 removed outlier: 3.861A pdb=" N SER A 394 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 446 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 439 " --> pdb=" O TYR A 446 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL A 448 " --> pdb=" O LYS A 437 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS A 437 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 529 through 531 removed outlier: 4.338A pdb=" N THR A 568 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1052 through 1055 Processing sheet with id= E, first strand: chain 'A' and resid 1164 through 1171 removed outlier: 3.822A pdb=" N ALA A1117 " --> pdb=" O ILE A1061 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1225 through 1232 removed outlier: 6.712A pdb=" N THR A1240 " --> pdb=" O ARG A1227 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR A1229 " --> pdb=" O MET A1238 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N MET A1238 " --> pdb=" O THR A1229 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN A1231 " --> pdb=" O GLY A1236 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A1236 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 42 through 45 removed outlier: 7.074A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 244 through 249 removed outlier: 3.570A pdb=" N VAL B 248 " --> pdb=" O PHE B 290 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1479 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: 3.58 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1541 1.30 - 1.43: 2617 1.43 - 1.55: 5531 1.55 - 1.68: 16 1.68 - 1.81: 106 Bond restraints: 9811 Sorted by residual: bond pdb=" C21 FOK A2001 " pdb=" O4 FOK A2001 " ideal model delta sigma weight residual 1.335 1.452 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C PHE A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.24e-02 6.50e+03 1.35e+01 bond pdb=" C PRO B 326 " pdb=" N GLU B 327 " ideal model delta sigma weight residual 1.329 1.286 0.043 1.35e-02 5.49e+03 9.94e+00 bond pdb=" C CYS A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.20e-02 6.94e+03 8.11e+00 bond pdb=" CA ONM A2000 " pdb=" O3' ONM A2000 " ideal model delta sigma weight residual 1.452 1.399 0.053 2.00e-02 2.50e+03 6.95e+00 ... (remaining 9806 not shown) Histogram of bond angle deviations from ideal: 97.74 - 108.68: 628 108.68 - 119.62: 7876 119.62 - 130.56: 4725 130.56 - 141.50: 64 141.50 - 152.44: 1 Bond angle restraints: 13294 Sorted by residual: angle pdb=" C1' ONM A2000 " pdb=" N9 ONM A2000 " pdb=" C4 ONM A2000 " ideal model delta sigma weight residual 135.98 152.44 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.13 -9.59 1.91e+00 2.74e-01 2.52e+01 angle pdb=" N GLU A1073 " pdb=" CA GLU A1073 " pdb=" C GLU A1073 " ideal model delta sigma weight residual 110.42 117.67 -7.25 1.46e+00 4.69e-01 2.46e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" CA LEU A 807 " pdb=" CB LEU A 807 " pdb=" CG LEU A 807 " ideal model delta sigma weight residual 116.30 133.34 -17.04 3.50e+00 8.16e-02 2.37e+01 ... (remaining 13289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 5324 15.43 - 30.86: 396 30.86 - 46.29: 130 46.29 - 61.72: 12 61.72 - 77.15: 11 Dihedral angle restraints: 5873 sinusoidal: 2415 harmonic: 3458 Sorted by residual: dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual -180.00 -147.36 -32.64 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA GLN A 191 " pdb=" C GLN A 191 " pdb=" N PHE A 192 " pdb=" CA PHE A 192 " ideal model delta harmonic sigma weight residual -180.00 -148.26 -31.74 0 5.00e+00 4.00e-02 4.03e+01 dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 150.33 29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1449 0.136 - 0.273: 44 0.273 - 0.409: 2 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C9 FOK A2001 " pdb=" C10 FOK A2001 " pdb=" C11 FOK A2001 " pdb=" C8 FOK A2001 " both_signs ideal model delta sigma weight residual False -2.58 -1.90 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C5 FOK A2001 " pdb=" C10 FOK A2001 " pdb=" C4 FOK A2001 " pdb=" C6 FOK A2001 " both_signs ideal model delta sigma weight residual False 2.11 1.73 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CB VAL B 114 " pdb=" CA VAL B 114 " pdb=" CG1 VAL B 114 " pdb=" CG2 VAL B 114 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1493 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1037 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO A1038 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1038 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1038 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 240 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.65e+00 pdb=" N PRO A 241 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 995 " 0.017 2.00e-02 2.50e+03 1.45e-02 5.26e+00 pdb=" CG TRP A 995 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 995 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 995 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 995 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 995 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 995 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 995 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 995 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 995 " 0.003 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 43 2.40 - 3.02: 5150 3.02 - 3.65: 15221 3.65 - 4.27: 21459 4.27 - 4.90: 33208 Nonbonded interactions: 75081 Sorted by model distance: nonbonded pdb=" O ILE A 400 " pdb="MN MN A2003 " model vdw 1.774 2.320 nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.066 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.103 2.170 nonbonded pdb=" O3B GSP B 501 " pdb="MG MG B 502 " model vdw 2.129 2.170 nonbonded pdb=" O2 FOK A2001 " pdb=" O6 FOK A2001 " model vdw 2.202 2.440 ... (remaining 75076 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: 4.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 14.980 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 30.600 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 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 : 0.006 0.117 9811 Z= 0.415 Angle : 1.210 17.035 13294 Z= 0.634 Chirality : 0.064 0.681 1496 Planarity : 0.007 0.066 1660 Dihedral : 12.712 77.146 3635 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.48 % Allowed : 7.30 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.19), residues: 1164 helix: -2.92 (0.14), residues: 670 sheet: -1.26 (0.42), residues: 130 loop : -3.24 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 995 HIS 0.011 0.003 HIS A 866 PHE 0.032 0.003 PHE A 152 TYR 0.030 0.004 TYR A 235 ARG 0.010 0.001 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 258 time to evaluate : 1.131 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.8370 (t80) cc_final: 0.7633 (m-80) REVERT: A 177 LEU cc_start: 0.8052 (tt) cc_final: 0.7797 (mt) REVERT: A 228 ILE cc_start: 0.8643 (mm) cc_final: 0.8390 (mm) REVERT: A 256 PHE cc_start: 0.8179 (t80) cc_final: 0.7914 (t80) REVERT: A 318 MET cc_start: 0.8096 (mmm) cc_final: 0.7660 (mmt) REVERT: A 999 ARG cc_start: 0.6864 (tmt90) cc_final: 0.6575 (ttt180) REVERT: A 1075 ASN cc_start: 0.8726 (m110) cc_final: 0.8394 (t0) REVERT: A 1088 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7781 (tm-30) REVERT: A 1096 LEU cc_start: 0.9012 (mt) cc_final: 0.8638 (mt) REVERT: A 1142 PHE cc_start: 0.8241 (t80) cc_final: 0.7324 (t80) REVERT: A 1146 MET cc_start: 0.8973 (ptm) cc_final: 0.8671 (ptm) REVERT: A 1186 ASP cc_start: 0.8806 (t0) cc_final: 0.8561 (t70) REVERT: B 50 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8529 (mm-30) REVERT: B 63 LEU cc_start: 0.8097 (mt) cc_final: 0.7892 (mt) REVERT: B 101 GLU cc_start: 0.9301 (tt0) cc_final: 0.8928 (pt0) REVERT: B 245 ILE cc_start: 0.8961 (mt) cc_final: 0.8656 (mp) REVERT: B 315 PHE cc_start: 0.9237 (t80) cc_final: 0.8724 (t80) outliers start: 5 outliers final: 1 residues processed: 261 average time/residue: 0.2418 time to fit residues: 84.9524 Evaluate side-chains 160 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.1980 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 239 HIS A 303 GLN A 908 GLN A1008 HIS A1122 ASN A1155 ASN A1170 HIS ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 213 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 HIS B 371 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9811 Z= 0.173 Angle : 0.703 10.414 13294 Z= 0.356 Chirality : 0.043 0.212 1496 Planarity : 0.005 0.051 1660 Dihedral : 7.323 61.007 1383 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.29 % Allowed : 4.13 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.22), residues: 1164 helix: -0.86 (0.18), residues: 694 sheet: -0.80 (0.43), residues: 133 loop : -3.12 (0.29), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 130 HIS 0.008 0.001 HIS A 866 PHE 0.039 0.002 PHE A 152 TYR 0.014 0.002 TYR A 118 ARG 0.006 0.001 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 214 time to evaluate : 1.043 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 PHE cc_start: 0.8434 (t80) cc_final: 0.7876 (m-80) REVERT: A 177 LEU cc_start: 0.8161 (tt) cc_final: 0.7934 (mt) REVERT: A 183 VAL cc_start: 0.8869 (t) cc_final: 0.8651 (t) REVERT: A 224 PHE cc_start: 0.8511 (t80) cc_final: 0.8276 (t80) REVERT: A 228 ILE cc_start: 0.8401 (mm) cc_final: 0.8052 (mm) REVERT: A 256 PHE cc_start: 0.8010 (t80) cc_final: 0.7585 (t80) REVERT: A 397 PHE cc_start: 0.8322 (m-10) cc_final: 0.8014 (m-10) REVERT: A 910 CYS cc_start: 0.7768 (m) cc_final: 0.7258 (t) REVERT: A 992 LEU cc_start: 0.9454 (mt) cc_final: 0.9242 (mt) REVERT: A 1075 ASN cc_start: 0.8647 (m110) cc_final: 0.8334 (t0) REVERT: A 1142 PHE cc_start: 0.8111 (t80) cc_final: 0.7632 (t80) REVERT: A 1146 MET cc_start: 0.9129 (ptm) cc_final: 0.8768 (ptm) REVERT: A 1152 ASP cc_start: 0.8989 (m-30) cc_final: 0.8764 (m-30) REVERT: A 1184 LEU cc_start: 0.8514 (tt) cc_final: 0.8143 (mp) REVERT: A 1186 ASP cc_start: 0.8786 (t0) cc_final: 0.8460 (t70) REVERT: B 98 ASN cc_start: 0.8744 (m-40) cc_final: 0.8428 (m-40) REVERT: B 101 GLU cc_start: 0.9260 (tt0) cc_final: 0.8980 (pt0) REVERT: B 255 MET cc_start: 0.7587 (ptp) cc_final: 0.7355 (ptp) REVERT: B 315 PHE cc_start: 0.9098 (t80) cc_final: 0.8425 (t80) outliers start: 3 outliers final: 1 residues processed: 216 average time/residue: 0.2295 time to fit residues: 69.2414 Evaluate side-chains 157 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 389 GLN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9811 Z= 0.188 Angle : 0.683 12.643 13294 Z= 0.344 Chirality : 0.043 0.194 1496 Planarity : 0.004 0.060 1660 Dihedral : 6.875 58.492 1383 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1164 helix: -0.03 (0.19), residues: 685 sheet: -0.67 (0.43), residues: 136 loop : -2.81 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 130 HIS 0.006 0.001 HIS A 866 PHE 0.058 0.002 PHE A 121 TYR 0.015 0.002 TYR A 118 ARG 0.011 0.001 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.083 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8119 (m-10) cc_final: 0.7272 (m-10) REVERT: A 177 LEU cc_start: 0.8203 (tt) cc_final: 0.7985 (mt) REVERT: A 183 VAL cc_start: 0.8881 (t) cc_final: 0.8662 (t) REVERT: A 224 PHE cc_start: 0.8520 (t80) cc_final: 0.8257 (t80) REVERT: A 228 ILE cc_start: 0.8469 (mm) cc_final: 0.8213 (mm) REVERT: A 256 PHE cc_start: 0.7954 (t80) cc_final: 0.7594 (t80) REVERT: A 305 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8112 (ttp80) REVERT: A 338 MET cc_start: 0.7478 (ttt) cc_final: 0.7154 (tmm) REVERT: A 397 PHE cc_start: 0.8455 (m-10) cc_final: 0.8077 (m-10) REVERT: A 490 VAL cc_start: 0.8779 (t) cc_final: 0.8537 (t) REVERT: A 896 MET cc_start: 0.8605 (tpt) cc_final: 0.8130 (tpp) REVERT: A 992 LEU cc_start: 0.9354 (mt) cc_final: 0.9106 (mt) REVERT: A 1030 ASP cc_start: 0.8057 (t70) cc_final: 0.7798 (t70) REVERT: A 1075 ASN cc_start: 0.8599 (m110) cc_final: 0.8363 (t0) REVERT: A 1142 PHE cc_start: 0.8435 (t80) cc_final: 0.7692 (t80) REVERT: A 1146 MET cc_start: 0.9100 (ptm) cc_final: 0.8709 (ptm) REVERT: A 1148 ARG cc_start: 0.8965 (ttm110) cc_final: 0.8687 (tpp80) REVERT: A 1152 ASP cc_start: 0.9032 (m-30) cc_final: 0.8798 (m-30) REVERT: A 1186 ASP cc_start: 0.8805 (t0) cc_final: 0.8488 (t70) REVERT: B 98 ASN cc_start: 0.8616 (m-40) cc_final: 0.8313 (m-40) REVERT: B 101 GLU cc_start: 0.9294 (tt0) cc_final: 0.9013 (pt0) REVERT: B 315 PHE cc_start: 0.9138 (t80) cc_final: 0.8517 (t80) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2214 time to fit residues: 62.5696 Evaluate side-chains 146 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 0.0370 chunk 56 optimal weight: 0.0070 chunk 102 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9811 Z= 0.161 Angle : 0.648 9.823 13294 Z= 0.321 Chirality : 0.042 0.191 1496 Planarity : 0.004 0.053 1660 Dihedral : 6.464 59.992 1383 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.24), residues: 1164 helix: 0.57 (0.20), residues: 680 sheet: -0.46 (0.44), residues: 126 loop : -2.57 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 281 HIS 0.006 0.001 HIS A 866 PHE 0.044 0.002 PHE A 152 TYR 0.017 0.001 TYR A1076 ARG 0.006 0.000 ARG A1215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.068 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7822 (m-10) cc_final: 0.7066 (m-10) REVERT: A 183 VAL cc_start: 0.8757 (t) cc_final: 0.8517 (t) REVERT: A 224 PHE cc_start: 0.8468 (t80) cc_final: 0.8194 (t80) REVERT: A 228 ILE cc_start: 0.8493 (mm) cc_final: 0.8205 (mm) REVERT: A 256 PHE cc_start: 0.7932 (t80) cc_final: 0.7565 (t80) REVERT: A 347 MET cc_start: 0.7606 (tmm) cc_final: 0.6701 (ptm) REVERT: A 397 PHE cc_start: 0.8430 (m-10) cc_final: 0.8106 (m-10) REVERT: A 483 MET cc_start: 0.9009 (pmm) cc_final: 0.8797 (pmm) REVERT: A 793 LEU cc_start: 0.8522 (tt) cc_final: 0.8187 (tt) REVERT: A 896 MET cc_start: 0.8639 (tpt) cc_final: 0.8051 (tpp) REVERT: A 904 THR cc_start: 0.8990 (m) cc_final: 0.8595 (m) REVERT: A 992 LEU cc_start: 0.9347 (mt) cc_final: 0.9075 (mt) REVERT: A 1030 ASP cc_start: 0.8033 (t70) cc_final: 0.7796 (t70) REVERT: A 1075 ASN cc_start: 0.8516 (m110) cc_final: 0.8312 (t0) REVERT: A 1142 PHE cc_start: 0.8493 (t80) cc_final: 0.7546 (t80) REVERT: A 1146 MET cc_start: 0.9078 (ptm) cc_final: 0.8741 (ptm) REVERT: A 1148 ARG cc_start: 0.8920 (ttm110) cc_final: 0.8681 (tpp80) REVERT: A 1152 ASP cc_start: 0.9032 (m-30) cc_final: 0.8774 (m-30) REVERT: A 1186 ASP cc_start: 0.8742 (t0) cc_final: 0.8502 (t70) REVERT: B 98 ASN cc_start: 0.8494 (m-40) cc_final: 0.8114 (m-40) REVERT: B 101 GLU cc_start: 0.9260 (tt0) cc_final: 0.8953 (pt0) REVERT: B 135 MET cc_start: 0.8447 (ptm) cc_final: 0.8169 (ptt) REVERT: B 255 MET cc_start: 0.7463 (ptp) cc_final: 0.7245 (ptp) REVERT: B 315 PHE cc_start: 0.9078 (t80) cc_final: 0.8476 (t80) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.2115 time to fit residues: 60.4716 Evaluate side-chains 146 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 97 optimal weight: 0.0010 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 262 HIS A 389 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9811 Z= 0.178 Angle : 0.661 11.731 13294 Z= 0.329 Chirality : 0.042 0.192 1496 Planarity : 0.004 0.051 1660 Dihedral : 6.343 59.632 1383 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1164 helix: 0.84 (0.20), residues: 686 sheet: -0.19 (0.46), residues: 121 loop : -2.42 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 130 HIS 0.005 0.001 HIS A 866 PHE 0.037 0.002 PHE A 121 TYR 0.014 0.001 TYR A1076 ARG 0.010 0.001 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.172 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 VAL cc_start: 0.8774 (t) cc_final: 0.8542 (t) REVERT: A 224 PHE cc_start: 0.8459 (t80) cc_final: 0.8159 (t80) REVERT: A 228 ILE cc_start: 0.8536 (mm) cc_final: 0.7976 (mm) REVERT: A 256 PHE cc_start: 0.7953 (t80) cc_final: 0.7564 (t80) REVERT: A 338 MET cc_start: 0.6861 (tmm) cc_final: 0.6511 (tmm) REVERT: A 793 LEU cc_start: 0.8488 (tt) cc_final: 0.8205 (tt) REVERT: A 896 MET cc_start: 0.8775 (tpt) cc_final: 0.8170 (tpp) REVERT: A 910 CYS cc_start: 0.8095 (m) cc_final: 0.7743 (t) REVERT: A 992 LEU cc_start: 0.9339 (mt) cc_final: 0.9112 (mt) REVERT: A 1030 ASP cc_start: 0.7983 (t70) cc_final: 0.7727 (t0) REVERT: A 1142 PHE cc_start: 0.8468 (t80) cc_final: 0.7837 (t80) REVERT: A 1146 MET cc_start: 0.9088 (ptm) cc_final: 0.8517 (ptm) REVERT: A 1148 ARG cc_start: 0.8950 (ttm110) cc_final: 0.8726 (tpp80) REVERT: A 1152 ASP cc_start: 0.9042 (m-30) cc_final: 0.8805 (m-30) REVERT: A 1186 ASP cc_start: 0.8769 (t0) cc_final: 0.8506 (t70) REVERT: B 50 GLU cc_start: 0.8956 (mp0) cc_final: 0.8704 (mm-30) REVERT: B 255 MET cc_start: 0.7574 (ptp) cc_final: 0.7319 (ptp) REVERT: B 315 PHE cc_start: 0.9088 (t80) cc_final: 0.8520 (t80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2029 time to fit residues: 54.1336 Evaluate side-chains 138 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 0.0770 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 0.0270 chunk 28 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS A 389 GLN A 420 ASN A1122 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 371 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9811 Z= 0.150 Angle : 0.636 9.475 13294 Z= 0.314 Chirality : 0.042 0.193 1496 Planarity : 0.004 0.043 1660 Dihedral : 6.082 57.189 1383 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1164 helix: 1.01 (0.20), residues: 692 sheet: 0.13 (0.47), residues: 111 loop : -2.44 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 918 HIS 0.005 0.001 HIS A 866 PHE 0.040 0.001 PHE A 987 TYR 0.012 0.001 TYR A1076 ARG 0.005 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.242 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8402 (t80) cc_final: 0.8170 (t80) REVERT: A 256 PHE cc_start: 0.8035 (t80) cc_final: 0.7685 (t80) REVERT: A 397 PHE cc_start: 0.8592 (m-10) cc_final: 0.8229 (m-10) REVERT: A 896 MET cc_start: 0.8777 (tpt) cc_final: 0.8127 (tpp) REVERT: A 904 THR cc_start: 0.8970 (m) cc_final: 0.8703 (m) REVERT: A 992 LEU cc_start: 0.9345 (mt) cc_final: 0.9112 (mt) REVERT: A 1030 ASP cc_start: 0.7898 (t70) cc_final: 0.7615 (t0) REVERT: A 1142 PHE cc_start: 0.8482 (t80) cc_final: 0.7864 (t80) REVERT: A 1146 MET cc_start: 0.9099 (ptm) cc_final: 0.8548 (ptm) REVERT: A 1152 ASP cc_start: 0.9023 (m-30) cc_final: 0.8783 (m-30) REVERT: A 1186 ASP cc_start: 0.8840 (t0) cc_final: 0.8554 (t70) REVERT: B 255 MET cc_start: 0.7479 (ptp) cc_final: 0.7201 (ptp) REVERT: B 279 ASN cc_start: 0.8387 (t0) cc_final: 0.8079 (p0) REVERT: B 315 PHE cc_start: 0.9062 (t80) cc_final: 0.8485 (t80) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2022 time to fit residues: 54.3676 Evaluate side-chains 141 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 64 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 389 GLN A1155 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9811 Z= 0.145 Angle : 0.629 9.746 13294 Z= 0.304 Chirality : 0.042 0.193 1496 Planarity : 0.004 0.048 1660 Dihedral : 5.872 56.108 1383 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.25), residues: 1164 helix: 1.23 (0.20), residues: 691 sheet: 0.58 (0.49), residues: 95 loop : -2.33 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 918 HIS 0.004 0.001 HIS A 239 PHE 0.029 0.001 PHE A 121 TYR 0.011 0.001 TYR A1039 ARG 0.005 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.054 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: symmetry clash REVERT: A 121 PHE cc_start: 0.8410 (t80) cc_final: 0.7960 (t80) REVERT: A 224 PHE cc_start: 0.8538 (t80) cc_final: 0.8310 (t80) REVERT: A 233 LEU cc_start: 0.9557 (mt) cc_final: 0.9303 (mt) REVERT: A 256 PHE cc_start: 0.7917 (t80) cc_final: 0.7458 (t80) REVERT: A 397 PHE cc_start: 0.8578 (m-10) cc_final: 0.8167 (m-10) REVERT: A 793 LEU cc_start: 0.8463 (tt) cc_final: 0.8164 (tt) REVERT: A 896 MET cc_start: 0.8798 (tpt) cc_final: 0.8189 (tpp) REVERT: A 992 LEU cc_start: 0.9323 (mt) cc_final: 0.9079 (mt) REVERT: A 1030 ASP cc_start: 0.7877 (t70) cc_final: 0.7623 (t0) REVERT: A 1142 PHE cc_start: 0.8447 (t80) cc_final: 0.7685 (t80) REVERT: A 1145 GLU cc_start: 0.8499 (pp20) cc_final: 0.8231 (pp20) REVERT: A 1146 MET cc_start: 0.9064 (ptm) cc_final: 0.8479 (ptm) REVERT: A 1152 ASP cc_start: 0.9012 (m-30) cc_final: 0.8751 (m-30) REVERT: A 1186 ASP cc_start: 0.8904 (t0) cc_final: 0.8591 (t70) REVERT: B 255 MET cc_start: 0.7523 (ptp) cc_final: 0.7255 (ptp) REVERT: B 279 ASN cc_start: 0.8391 (t0) cc_final: 0.8067 (p0) REVERT: B 315 PHE cc_start: 0.9039 (t80) cc_final: 0.8464 (t80) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2042 time to fit residues: 54.4041 Evaluate side-chains 141 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 0.0570 chunk 72 optimal weight: 0.0370 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 389 GLN A1155 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9811 Z= 0.177 Angle : 0.671 10.084 13294 Z= 0.327 Chirality : 0.043 0.201 1496 Planarity : 0.004 0.042 1660 Dihedral : 5.995 56.713 1383 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1164 helix: 1.13 (0.20), residues: 692 sheet: 0.06 (0.47), residues: 104 loop : -2.24 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 130 HIS 0.003 0.001 HIS B 220 PHE 0.036 0.001 PHE A 121 TYR 0.011 0.001 TYR A1039 ARG 0.006 0.000 ARG A 808 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.183 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: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8318 (mpp) cc_final: 0.8117 (mpp) REVERT: A 121 PHE cc_start: 0.8473 (t80) cc_final: 0.8230 (t80) REVERT: A 221 VAL cc_start: 0.8952 (m) cc_final: 0.8657 (t) REVERT: A 223 SER cc_start: 0.8656 (m) cc_final: 0.8149 (p) REVERT: A 256 PHE cc_start: 0.7974 (t80) cc_final: 0.7526 (t80) REVERT: A 397 PHE cc_start: 0.8614 (m-10) cc_final: 0.8140 (m-10) REVERT: A 793 LEU cc_start: 0.8438 (tt) cc_final: 0.8137 (tt) REVERT: A 896 MET cc_start: 0.8895 (tpt) cc_final: 0.8344 (tpp) REVERT: A 992 LEU cc_start: 0.9321 (mt) cc_final: 0.9065 (mt) REVERT: A 1030 ASP cc_start: 0.7887 (t70) cc_final: 0.7603 (t0) REVERT: A 1142 PHE cc_start: 0.8495 (t80) cc_final: 0.7604 (t80) REVERT: A 1145 GLU cc_start: 0.8559 (pp20) cc_final: 0.8336 (pp20) REVERT: A 1146 MET cc_start: 0.9085 (ptm) cc_final: 0.8411 (ptm) REVERT: A 1186 ASP cc_start: 0.8930 (t0) cc_final: 0.8598 (t70) REVERT: B 255 MET cc_start: 0.7610 (ptp) cc_final: 0.7345 (ptp) REVERT: B 279 ASN cc_start: 0.8499 (t0) cc_final: 0.8013 (p0) REVERT: B 315 PHE cc_start: 0.9068 (t80) cc_final: 0.8506 (t80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2029 time to fit residues: 53.2658 Evaluate side-chains 140 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS A 389 GLN A 458 HIS A 883 HIS ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9811 Z= 0.165 Angle : 0.660 9.632 13294 Z= 0.321 Chirality : 0.043 0.194 1496 Planarity : 0.004 0.040 1660 Dihedral : 5.990 57.096 1383 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1164 helix: 1.15 (0.20), residues: 693 sheet: 0.07 (0.47), residues: 104 loop : -2.31 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 918 HIS 0.003 0.001 HIS A 866 PHE 0.037 0.002 PHE A 987 TYR 0.012 0.001 TYR B 318 ARG 0.005 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.137 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: symmetry clash revert: symmetry clash REVERT: A 221 VAL cc_start: 0.8972 (m) cc_final: 0.8707 (t) REVERT: A 223 SER cc_start: 0.8600 (m) cc_final: 0.8082 (p) REVERT: A 238 MET cc_start: 0.7695 (mpp) cc_final: 0.7197 (mpp) REVERT: A 256 PHE cc_start: 0.7999 (t80) cc_final: 0.7554 (t80) REVERT: A 397 PHE cc_start: 0.8637 (m-10) cc_final: 0.8152 (m-10) REVERT: A 793 LEU cc_start: 0.8427 (tt) cc_final: 0.8146 (tt) REVERT: A 896 MET cc_start: 0.8828 (tpt) cc_final: 0.8316 (tpp) REVERT: A 1030 ASP cc_start: 0.7823 (t70) cc_final: 0.7545 (t0) REVERT: A 1142 PHE cc_start: 0.8447 (t80) cc_final: 0.7595 (t80) REVERT: A 1146 MET cc_start: 0.9057 (ptm) cc_final: 0.8402 (ptm) REVERT: A 1186 ASP cc_start: 0.8937 (t0) cc_final: 0.8595 (t70) REVERT: B 255 MET cc_start: 0.7670 (ptp) cc_final: 0.7386 (ptp) REVERT: B 279 ASN cc_start: 0.8436 (t0) cc_final: 0.8084 (p0) REVERT: B 315 PHE cc_start: 0.9126 (t80) cc_final: 0.8014 (t80) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1983 time to fit residues: 51.0063 Evaluate side-chains 141 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A1155 ASN ** B 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9811 Z= 0.149 Angle : 0.654 9.538 13294 Z= 0.314 Chirality : 0.042 0.193 1496 Planarity : 0.004 0.041 1660 Dihedral : 5.857 55.977 1383 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1164 helix: 1.41 (0.20), residues: 687 sheet: 0.05 (0.47), residues: 100 loop : -2.23 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 918 HIS 0.003 0.001 HIS A 866 PHE 0.027 0.001 PHE A 987 TYR 0.010 0.001 TYR A1039 ARG 0.005 0.000 ARG B 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.340 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 VAL cc_start: 0.8929 (m) cc_final: 0.8584 (t) REVERT: A 223 SER cc_start: 0.8553 (m) cc_final: 0.8076 (p) REVERT: A 238 MET cc_start: 0.7727 (mpp) cc_final: 0.7323 (mpp) REVERT: A 256 PHE cc_start: 0.7908 (t80) cc_final: 0.7494 (t80) REVERT: A 395 ILE cc_start: 0.8700 (mp) cc_final: 0.8428 (pt) REVERT: A 397 PHE cc_start: 0.8572 (m-10) cc_final: 0.8248 (m-10) REVERT: A 896 MET cc_start: 0.8810 (tpt) cc_final: 0.8351 (tpp) REVERT: A 1030 ASP cc_start: 0.7811 (t70) cc_final: 0.7543 (t0) REVERT: A 1142 PHE cc_start: 0.8410 (t80) cc_final: 0.7919 (t80) REVERT: A 1146 MET cc_start: 0.9022 (ptm) cc_final: 0.8510 (ptm) REVERT: A 1186 ASP cc_start: 0.8974 (t0) cc_final: 0.8620 (t70) REVERT: B 255 MET cc_start: 0.7531 (ptp) cc_final: 0.7262 (ptp) REVERT: B 279 ASN cc_start: 0.8429 (t0) cc_final: 0.7985 (p0) REVERT: B 315 PHE cc_start: 0.9048 (t80) cc_final: 0.7933 (t80) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1937 time to fit residues: 51.1673 Evaluate side-chains 145 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A1122 ASN A1155 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.091454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077500 restraints weight = 58363.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079083 restraints weight = 40551.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.080233 restraints weight = 30814.879| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9811 Z= 0.206 Angle : 0.693 9.877 13294 Z= 0.341 Chirality : 0.043 0.197 1496 Planarity : 0.004 0.040 1660 Dihedral : 6.198 59.999 1383 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1164 helix: 1.10 (0.20), residues: 693 sheet: 0.03 (0.47), residues: 105 loop : -2.30 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 130 HIS 0.003 0.001 HIS A 866 PHE 0.054 0.002 PHE A 184 TYR 0.012 0.002 TYR A 118 ARG 0.004 0.001 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2260.13 seconds wall clock time: 42 minutes 13.59 seconds (2533.59 seconds total)