Starting phenix.real_space_refine on Tue Nov 14 21:43:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_4721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_4721.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_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_4721/11_2023/6r4o_4721_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_4721_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_4721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_4721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_4721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r4o_4721/11_2023/6r4o_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-1.21rc1-5144/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: 5.54, per 1000 atoms: 0.58 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: 3.99 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: 2.43 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: 2.97 Time building geometry restraints manager: 4.25 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: 5271 15.43 - 30.86: 379 30.86 - 46.29: 128 46.29 - 61.72: 12 61.72 - 77.15: 11 Dihedral angle restraints: 5801 sinusoidal: 2343 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 5798 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: 9.540 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: 13.900 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 30.590 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- 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 : 12.704 77.146 3563 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 *********************** 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 : 1.072 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 outliers start: 5 outliers final: 1 residues processed: 261 average time/residue: 0.2470 time to fit residues: 87.9290 Evaluate side-chains 153 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1070 time to fit residues: 1.6993 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 0.9990 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: 8.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 389 GLN A 908 GLN A1008 HIS A1075 ASN A1122 ASN A1155 ASN A1170 HIS B 31 GLN B 35 GLN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3251 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= 0.171 Angle : 0.693 10.137 13294 Z= 0.350 Chirality : 0.043 0.245 1496 Planarity : 0.005 0.050 1660 Dihedral : 7.095 60.296 1311 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.48 % Allowed : 4.03 % Favored : 95.49 % 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: -2.23 (0.23), residues: 1164 helix: -0.78 (0.18), residues: 687 sheet: -0.90 (0.42), residues: 143 loop : -3.02 (0.30), residues: 334 *********************** 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 223 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 1.152 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 outliers start: 5 outliers final: 1 residues processed: 222 average time/residue: 0.2442 time to fit residues: 74.6307 Evaluate side-chains 142 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1466 time to fit residues: 2.0370 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 0.0570 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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 A1075 ASN A1122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9811 Z= 0.170 Angle : 0.666 12.542 13294 Z= 0.331 Chirality : 0.042 0.209 1496 Planarity : 0.004 0.059 1660 Dihedral : 6.632 59.086 1311 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -1.27 (0.24), residues: 1164 helix: 0.13 (0.19), residues: 679 sheet: -0.73 (0.42), residues: 142 loop : -2.78 (0.31), residues: 343 *********************** 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 200 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.277 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 outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2286 time to fit residues: 63.3236 Evaluate side-chains 137 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7331 ------------------------------------------------------------------------------- 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: 0.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 0.0570 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 A 458 HIS A 883 HIS A 914 GLN A1122 ASN B 124 ASN B 218 ASN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9811 Z= 0.280 Angle : 0.773 10.398 13294 Z= 0.394 Chirality : 0.045 0.194 1496 Planarity : 0.005 0.054 1660 Dihedral : 6.875 58.068 1311 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1164 helix: 0.13 (0.19), residues: 681 sheet: -0.76 (0.45), residues: 122 loop : -2.98 (0.28), residues: 361 *********************** 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 167 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.109 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 outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2080 time to fit residues: 49.6189 Evaluate side-chains 119 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3979 ------------------------------------------------------------------------------- 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: 3.9990 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 0.0470 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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 914 GLN B 254 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9811 Z= 0.160 Angle : 0.665 10.313 13294 Z= 0.331 Chirality : 0.043 0.204 1496 Planarity : 0.004 0.046 1660 Dihedral : 6.465 59.987 1311 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.10 % Allowed : 2.88 % Favored : 97.02 % 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: 0.67 (0.20), residues: 686 sheet: -0.70 (0.46), residues: 118 loop : -2.70 (0.29), residues: 360 *********************** 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 183 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 1.116 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 outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2094 time to fit residues: 54.4424 Evaluate side-chains 130 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4832 ------------------------------------------------------------------------------- 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: 0.0020 chunk 102 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 0.0870 chunk 59 optimal weight: 0.8980 overall best weight: 0.5768 ------------------------------------------------------------------------------- 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 914 GLN A1122 ASN B 254 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9811 Z= 0.151 Angle : 0.645 9.417 13294 Z= 0.316 Chirality : 0.042 0.205 1496 Planarity : 0.004 0.049 1660 Dihedral : 6.104 59.768 1311 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.10 % Allowed : 2.21 % 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: -0.28 (0.25), residues: 1164 helix: 1.00 (0.20), residues: 678 sheet: -0.51 (0.45), residues: 119 loop : -2.35 (0.31), residues: 367 *********************** 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 179 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 1.108 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 outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.1987 time to fit residues: 51.7821 Evaluate side-chains 128 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4737 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 220 HIS B 254 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9811 Z= 0.157 Angle : 0.645 9.491 13294 Z= 0.316 Chirality : 0.042 0.196 1496 Planarity : 0.004 0.044 1660 Dihedral : 5.992 58.862 1311 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.41 % 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: -0.18 (0.25), residues: 1164 helix: 1.08 (0.20), residues: 678 sheet: -0.31 (0.44), residues: 118 loop : -2.38 (0.31), residues: 368 *********************** 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 171 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 1.139 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 outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1973 time to fit residues: 49.8892 Evaluate side-chains 129 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6156 ------------------------------------------------------------------------------- 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: 0.7980 chunk 45 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 HIS ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A1155 ASN B 220 HIS B 254 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.5863 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= 0.149 Angle : 0.651 9.901 13294 Z= 0.318 Chirality : 0.043 0.198 1496 Planarity : 0.004 0.045 1660 Dihedral : 5.923 59.762 1311 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.04 % 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: -0.02 (0.25), residues: 1164 helix: 1.20 (0.20), residues: 684 sheet: -0.60 (0.46), residues: 109 loop : -2.17 (0.32), residues: 371 *********************** 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 173 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.130 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 outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.1933 time to fit residues: 49.0954 Evaluate side-chains 124 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5421 ------------------------------------------------------------------------------- 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: 6.9990 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.0030 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- 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 A1122 ASN A1155 ASN B 220 HIS B 254 ASN B 271 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9811 Z= 0.225 Angle : 0.731 10.862 13294 Z= 0.364 Chirality : 0.044 0.198 1496 Planarity : 0.004 0.042 1660 Dihedral : 6.222 58.876 1311 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1164 helix: 0.93 (0.20), residues: 682 sheet: -0.74 (0.45), residues: 119 loop : -2.38 (0.30), residues: 363 *********************** 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 166 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.376 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 outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1929 time to fit residues: 47.1998 Evaluate side-chains 121 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5031 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.0980 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A1155 ASN B 254 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6147 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= 0.148 Angle : 0.678 10.649 13294 Z= 0.326 Chirality : 0.043 0.199 1496 Planarity : 0.003 0.042 1660 Dihedral : 5.983 57.196 1311 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.19 % Allowed : 0.29 % Favored : 99.52 % 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: -0.08 (0.25), residues: 1164 helix: 1.16 (0.20), residues: 686 sheet: -0.62 (0.47), residues: 105 loop : -2.21 (0.30), residues: 373 ********************** 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 171 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.132 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 outliers start: 2 outliers final: 0 residues processed: 171 average time/residue: 0.1994 time to fit residues: 49.9012 Evaluate side-chains 126 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3683 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A1155 ASN B 220 HIS B 254 ASN B 371 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.092242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.078647 restraints weight = 59222.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.080284 restraints weight = 40913.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.081511 restraints weight = 31004.414| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.6169 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= 0.195 Angle : 0.700 10.898 13294 Z= 0.346 Chirality : 0.044 0.200 1496 Planarity : 0.004 0.042 1660 Dihedral : 6.108 59.262 1311 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.10 % Allowed : 0.38 % Favored : 99.52 % 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: -0.14 (0.25), residues: 1164 helix: 1.12 (0.20), residues: 685 sheet: -0.60 (0.48), residues: 105 loop : -2.26 (0.30), residues: 374 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.06 seconds wall clock time: 44 minutes 16.52 seconds (2656.52 seconds total)