Starting phenix.real_space_refine on Mon Mar 11 19:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/03_2024/7op8_13014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/03_2024/7op8_13014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/03_2024/7op8_13014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/03_2024/7op8_13014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/03_2024/7op8_13014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/03_2024/7op8_13014_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 53 5.16 5 Be 1 3.05 5 C 5761 2.51 5 N 1472 2.21 5 O 1581 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1078": "OE1" <-> "OE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1184": "OD1" <-> "OD2" Residue "A TYR 1246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1120, 8872 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 1118, 'undetermined': 2} Link IDs: {'PTRANS': 56, 'TRANS': 1061, None: 2} Not linked: pdbres="GLN A1394 " pdbres="BEF A1401 " Not linked: pdbres="BEF A1401 " pdbres=" MG A1402 " Chain breaks: 8 Time building chain proxies: 5.22, per 1000 atoms: 0.59 Number of scatterers: 8872 At special positions: 0 Unit cell: (83.2, 97.344, 143.104, 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) S 53 16.00 Mg 1 11.99 F 3 9.00 O 1581 8.00 N 1472 7.00 C 5761 6.00 Be 1 4.00 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 12 sheets defined 38.3% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.977A pdb=" N TYR A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.920A pdb=" N LYS A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 362 through 372 removed outlier: 4.047A pdb=" N LYS A 365 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 392 No H-bonds generated for 'chain 'A' and resid 389 through 392' Processing helix chain 'A' and resid 395 through 407 removed outlier: 4.160A pdb=" N VAL A 401 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 445 removed outlier: 3.983A pdb=" N ALA A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 518 No H-bonds generated for 'chain 'A' and resid 515 through 518' Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.821A pdb=" N HIS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 570 through 578 Processing helix chain 'A' and resid 588 through 590 No H-bonds generated for 'chain 'A' and resid 588 through 590' Processing helix chain 'A' and resid 594 through 613 removed outlier: 3.873A pdb=" N GLY A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 629 removed outlier: 4.039A pdb=" N ILE A 624 " --> pdb=" O HIS A 620 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU A 625 " --> pdb=" O TRP A 621 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 658 removed outlier: 3.729A pdb=" N THR A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 670 through 673 Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 939 through 948 Processing helix chain 'A' and resid 961 through 971 Processing helix chain 'A' and resid 1043 through 1052 removed outlier: 3.851A pdb=" N ASP A1051 " --> pdb=" O ARG A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 Processing helix chain 'A' and resid 1073 through 1085 Processing helix chain 'A' and resid 1101 through 1104 No H-bonds generated for 'chain 'A' and resid 1101 through 1104' Processing helix chain 'A' and resid 1130 through 1142 Proline residue: A1134 - end of helix removed outlier: 4.956A pdb=" N GLU A1139 " --> pdb=" O VAL A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1166 removed outlier: 3.683A pdb=" N TYR A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A1155 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A1156 " --> pdb=" O LYS A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 4.047A pdb=" N LEU A1181 " --> pdb=" O ASP A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1195 removed outlier: 3.912A pdb=" N PHE A1194 " --> pdb=" O PRO A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1242 Proline residue: A1221 - end of helix removed outlier: 3.508A pdb=" N ILE A1232 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1281 removed outlier: 3.733A pdb=" N ALA A1269 " --> pdb=" O THR A1265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A1278 " --> pdb=" O TYR A1274 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL A1279 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A1280 " --> pdb=" O LEU A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1312 Processing helix chain 'A' and resid 1317 through 1322 Processing helix chain 'A' and resid 1330 through 1351 Processing helix chain 'A' and resid 1355 through 1362 Processing helix chain 'A' and resid 1378 through 1391 Processing sheet with id= A, first strand: chain 'A' and resid 207 through 209 Processing sheet with id= B, first strand: chain 'A' and resid 223 through 225 Processing sheet with id= C, first strand: chain 'A' and resid 322 through 325 Processing sheet with id= D, first strand: chain 'A' and resid 451 through 455 Processing sheet with id= E, first strand: chain 'A' and resid 487 through 489 Processing sheet with id= F, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.156A pdb=" N ASN A 497 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU A 543 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 660 through 662 Processing sheet with id= H, first strand: chain 'A' and resid 952 through 955 Processing sheet with id= I, first strand: chain 'A' and resid 691 through 697 removed outlier: 6.897A pdb=" N ILE A 930 " --> pdb=" O LEU A 693 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE A 695 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 928 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL A 697 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL A 926 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 926 " --> pdb=" O CYS A 898 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS A 898 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N PHE A 928 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 896 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 930 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG A 894 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG A 850 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N VAL A 832 " --> pdb=" O ARG A 850 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 981 through 986 removed outlier: 4.143A pdb=" N LYS A 996 " --> pdb=" O ILE A 986 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 764 through 767 removed outlier: 3.712A pdb=" N ARG A 764 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 771 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 766 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 769 " --> pdb=" O VAL A 766 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 7.559A pdb=" N VAL A1041 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR A1068 " --> pdb=" O VAL A1041 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 837 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: 2.70 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2528 1.34 - 1.46: 1707 1.46 - 1.58: 4778 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9090 Sorted by residual: bond pdb=" BE BEF A1401 " pdb=" F2 BEF A1401 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" BE BEF A1401 " pdb=" F3 BEF A1401 " ideal model delta sigma weight residual 1.476 1.544 -0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" BE BEF A1401 " pdb=" F1 BEF A1401 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" C ASP A1010 " pdb=" N PRO A1011 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" C ARG A1285 " pdb=" N PRO A1286 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.85e+00 ... (remaining 9085 not shown) Histogram of bond angle deviations from ideal: 95.96 - 103.57: 123 103.57 - 111.19: 3484 111.19 - 118.80: 3708 118.80 - 126.41: 4873 126.41 - 134.03: 161 Bond angle restraints: 12349 Sorted by residual: angle pdb=" F2 BEF A1401 " pdb=" BE BEF A1401 " pdb=" F3 BEF A1401 " ideal model delta sigma weight residual 119.96 107.45 12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" CA LYS A1383 " pdb=" CB LYS A1383 " pdb=" CG LYS A1383 " ideal model delta sigma weight residual 114.10 121.43 -7.33 2.00e+00 2.50e-01 1.34e+01 angle pdb=" C VAL A1251 " pdb=" N ASP A1252 " pdb=" CA ASP A1252 " ideal model delta sigma weight residual 121.70 128.21 -6.51 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C GLU A 975 " pdb=" CA GLU A 975 " pdb=" CB GLU A 975 " ideal model delta sigma weight residual 109.54 116.11 -6.57 1.84e+00 2.95e-01 1.28e+01 angle pdb=" CB GLU A1078 " pdb=" CG GLU A1078 " pdb=" CD GLU A1078 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.70e+00 3.46e-01 1.20e+01 ... (remaining 12344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 4763 16.90 - 33.80: 509 33.80 - 50.70: 89 50.70 - 67.61: 10 67.61 - 84.51: 11 Dihedral angle restraints: 5382 sinusoidal: 2120 harmonic: 3262 Sorted by residual: dihedral pdb=" CA TRP A 345 " pdb=" C TRP A 345 " pdb=" N LYS A 346 " pdb=" CA LYS A 346 " ideal model delta harmonic sigma weight residual 180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA GLU A 866 " pdb=" C GLU A 866 " pdb=" N CYS A 867 " pdb=" CA CYS A 867 " ideal model delta harmonic sigma weight residual 180.00 161.27 18.73 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO A 252 " pdb=" C PRO A 252 " pdb=" N LYS A 253 " pdb=" CA LYS A 253 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 5379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1159 0.068 - 0.135: 222 0.135 - 0.203: 20 0.203 - 0.271: 5 0.271 - 0.339: 2 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CB VAL A 468 " pdb=" CA VAL A 468 " pdb=" CG1 VAL A 468 " pdb=" CG2 VAL A 468 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB THR A 429 " pdb=" CA THR A 429 " pdb=" OG1 THR A 429 " pdb=" CG2 THR A 429 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL A 472 " pdb=" CA VAL A 472 " pdb=" CG1 VAL A 472 " pdb=" CG2 VAL A 472 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1405 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 624 " -0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C ILE A 624 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE A 624 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A 625 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1339 " 0.016 2.00e-02 2.50e+03 2.29e-02 9.21e+00 pdb=" CG PHE A1339 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A1339 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A1339 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A1339 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1339 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1339 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1004 " -0.046 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO A1005 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A1005 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1005 " -0.039 5.00e-02 4.00e+02 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 72 2.54 - 3.13: 6611 3.13 - 3.72: 13896 3.72 - 4.31: 18531 4.31 - 4.90: 30807 Nonbonded interactions: 69917 Sorted by model distance: nonbonded pdb=" BE BEF A1401 " pdb="MG MG A1402 " model vdw 1.950 1.550 nonbonded pdb=" F3 BEF A1401 " pdb="MG MG A1402 " model vdw 2.002 2.120 nonbonded pdb=" F1 BEF A1401 " pdb="MG MG A1402 " model vdw 2.023 2.120 nonbonded pdb=" F2 BEF A1401 " pdb="MG MG A1402 " model vdw 2.139 2.120 nonbonded pdb=" O THR A 682 " pdb="MG MG A1402 " model vdw 2.181 2.170 ... (remaining 69912 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.120 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.930 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9090 Z= 0.291 Angle : 0.861 12.507 12349 Z= 0.432 Chirality : 0.054 0.339 1408 Planarity : 0.006 0.071 1546 Dihedral : 14.437 84.507 3270 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.73 (0.23), residues: 1100 helix: -0.34 (0.23), residues: 419 sheet: -1.50 (0.46), residues: 119 loop : -1.69 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1245 HIS 0.009 0.001 HIS A1225 PHE 0.052 0.002 PHE A1339 TYR 0.045 0.002 TYR A1088 ARG 0.006 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.991 Fit side-chains REVERT: A 221 SER cc_start: 0.6503 (t) cc_final: 0.6000 (t) REVERT: A 1129 ASP cc_start: 0.7068 (p0) cc_final: 0.6577 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1614 time to fit residues: 38.3182 Evaluate side-chains 121 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A1225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9090 Z= 0.205 Angle : 0.567 8.010 12349 Z= 0.285 Chirality : 0.044 0.199 1408 Planarity : 0.004 0.045 1546 Dihedral : 4.658 22.583 1213 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.54 % Allowed : 10.27 % Favored : 88.19 % 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: 1100 helix: 0.34 (0.25), residues: 421 sheet: -1.53 (0.45), residues: 125 loop : -1.61 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 270 HIS 0.001 0.000 HIS A1225 PHE 0.038 0.001 PHE A1339 TYR 0.019 0.001 TYR A1088 ARG 0.003 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.6868 (t) cc_final: 0.6579 (t) REVERT: A 223 PHE cc_start: 0.6762 (m-80) cc_final: 0.6379 (m-80) REVERT: A 265 PHE cc_start: 0.6887 (p90) cc_final: 0.6382 (p90) REVERT: A 530 HIS cc_start: 0.6956 (OUTLIER) cc_final: 0.6453 (t-90) REVERT: A 975 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6667 (tm-30) REVERT: A 1129 ASP cc_start: 0.7224 (p0) cc_final: 0.6659 (p0) REVERT: A 1231 MET cc_start: 0.7056 (mmm) cc_final: 0.6660 (mmm) REVERT: A 1392 TYR cc_start: 0.7014 (m-80) cc_final: 0.6568 (m-80) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 0.1628 time to fit residues: 34.5534 Evaluate side-chains 130 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 ASN A1225 HIS A1394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9090 Z= 0.266 Angle : 0.586 7.890 12349 Z= 0.294 Chirality : 0.045 0.215 1408 Planarity : 0.004 0.040 1546 Dihedral : 4.618 20.905 1213 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.67 % Allowed : 12.22 % Favored : 85.11 % 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: -1.17 (0.25), residues: 1100 helix: 0.52 (0.25), residues: 415 sheet: -1.59 (0.45), residues: 121 loop : -1.60 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 270 HIS 0.024 0.001 HIS A1225 PHE 0.026 0.001 PHE A1339 TYR 0.029 0.001 TYR A1088 ARG 0.005 0.000 ARG A 440 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.7011 (t) cc_final: 0.6711 (t) REVERT: A 223 PHE cc_start: 0.6755 (m-80) cc_final: 0.6397 (m-80) REVERT: A 530 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6509 (t-90) REVERT: A 1231 MET cc_start: 0.7154 (mmm) cc_final: 0.6753 (mmm) outliers start: 26 outliers final: 21 residues processed: 142 average time/residue: 0.1610 time to fit residues: 34.9054 Evaluate side-chains 139 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.0980 chunk 48 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9090 Z= 0.251 Angle : 0.577 9.751 12349 Z= 0.289 Chirality : 0.044 0.203 1408 Planarity : 0.004 0.043 1546 Dihedral : 4.543 20.860 1213 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.57 % Allowed : 15.20 % Favored : 82.24 % 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: -1.08 (0.25), residues: 1100 helix: 0.66 (0.25), residues: 413 sheet: -1.63 (0.45), residues: 121 loop : -1.58 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1012 HIS 0.012 0.001 HIS A1225 PHE 0.019 0.001 PHE A1339 TYR 0.029 0.001 TYR A1088 ARG 0.002 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.885 Fit side-chains REVERT: A 221 SER cc_start: 0.7045 (t) cc_final: 0.6735 (t) REVERT: A 223 PHE cc_start: 0.6787 (m-80) cc_final: 0.6422 (m-80) REVERT: A 1225 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7124 (t70) REVERT: A 1231 MET cc_start: 0.7233 (mmm) cc_final: 0.6825 (mmm) outliers start: 25 outliers final: 20 residues processed: 141 average time/residue: 0.1615 time to fit residues: 35.0473 Evaluate side-chains 139 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 overall best weight: 0.8420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9090 Z= 0.219 Angle : 0.568 9.799 12349 Z= 0.282 Chirality : 0.043 0.188 1408 Planarity : 0.004 0.042 1546 Dihedral : 4.479 20.787 1213 Min Nonbonded Distance : 1.359 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.87 % Allowed : 16.74 % Favored : 80.39 % 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: -1.02 (0.25), residues: 1100 helix: 0.73 (0.26), residues: 414 sheet: -1.46 (0.45), residues: 125 loop : -1.60 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1012 HIS 0.009 0.001 HIS A1225 PHE 0.016 0.001 PHE A1339 TYR 0.027 0.001 TYR A1088 ARG 0.003 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.7030 (t) cc_final: 0.6700 (t) REVERT: A 223 PHE cc_start: 0.6782 (m-80) cc_final: 0.6411 (m-80) REVERT: A 1225 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7076 (t70) REVERT: A 1231 MET cc_start: 0.7260 (mmm) cc_final: 0.6843 (mmm) REVERT: A 1323 MET cc_start: 0.8208 (tpp) cc_final: 0.7959 (tpt) outliers start: 28 outliers final: 23 residues processed: 146 average time/residue: 0.1664 time to fit residues: 36.5498 Evaluate side-chains 140 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9090 Z= 0.292 Angle : 0.599 9.940 12349 Z= 0.299 Chirality : 0.044 0.203 1408 Planarity : 0.004 0.040 1546 Dihedral : 4.576 21.777 1213 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.39 % Allowed : 17.86 % Favored : 78.75 % 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: -1.00 (0.25), residues: 1100 helix: 0.73 (0.26), residues: 411 sheet: -1.52 (0.46), residues: 125 loop : -1.54 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1012 HIS 0.014 0.001 HIS A1225 PHE 0.014 0.001 PHE A1339 TYR 0.035 0.001 TYR A1088 ARG 0.004 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.7128 (t) cc_final: 0.6762 (t) REVERT: A 223 PHE cc_start: 0.6846 (m-80) cc_final: 0.6458 (m-80) REVERT: A 530 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6533 (t-90) REVERT: A 1225 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7239 (t70) REVERT: A 1231 MET cc_start: 0.7320 (mmm) cc_final: 0.6886 (mmm) outliers start: 33 outliers final: 28 residues processed: 147 average time/residue: 0.1621 time to fit residues: 35.9501 Evaluate side-chains 148 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.0060 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9090 Z= 0.318 Angle : 0.623 9.241 12349 Z= 0.311 Chirality : 0.044 0.212 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.725 22.640 1213 Min Nonbonded Distance : 1.322 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.80 % Allowed : 18.99 % Favored : 77.21 % 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: -1.08 (0.25), residues: 1100 helix: 0.61 (0.25), residues: 418 sheet: -1.56 (0.46), residues: 125 loop : -1.57 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A1245 HIS 0.018 0.001 HIS A1225 PHE 0.026 0.001 PHE A1339 TYR 0.037 0.002 TYR A1088 ARG 0.003 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 221 SER cc_start: 0.7269 (t) cc_final: 0.6906 (t) REVERT: A 223 PHE cc_start: 0.6892 (m-80) cc_final: 0.6424 (m-80) REVERT: A 530 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6581 (t-90) REVERT: A 1088 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.6937 (t80) REVERT: A 1225 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7221 (t70) REVERT: A 1231 MET cc_start: 0.7396 (mmm) cc_final: 0.6976 (mmm) outliers start: 37 outliers final: 32 residues processed: 150 average time/residue: 0.1567 time to fit residues: 35.8946 Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1088 TYR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.0020 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9090 Z= 0.191 Angle : 0.591 14.439 12349 Z= 0.288 Chirality : 0.042 0.180 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.537 21.405 1213 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.08 % Allowed : 20.12 % Favored : 76.80 % 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: -0.89 (0.25), residues: 1100 helix: 0.80 (0.26), residues: 412 sheet: -1.49 (0.46), residues: 125 loop : -1.46 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1245 HIS 0.007 0.001 HIS A1225 PHE 0.024 0.001 PHE A1339 TYR 0.024 0.001 TYR A1088 ARG 0.004 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 0.988 Fit side-chains REVERT: A 221 SER cc_start: 0.7192 (t) cc_final: 0.6801 (t) REVERT: A 223 PHE cc_start: 0.6731 (m-80) cc_final: 0.6257 (m-80) REVERT: A 1225 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7113 (t70) REVERT: A 1231 MET cc_start: 0.7281 (mmm) cc_final: 0.6853 (mmm) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.1531 time to fit residues: 33.8634 Evaluate side-chains 142 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1155 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9090 Z= 0.192 Angle : 0.604 16.344 12349 Z= 0.294 Chirality : 0.043 0.200 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.500 21.237 1213 Min Nonbonded Distance : 1.369 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.39 % Allowed : 20.53 % Favored : 76.08 % 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: -0.88 (0.25), residues: 1100 helix: 0.82 (0.26), residues: 418 sheet: -1.51 (0.46), residues: 125 loop : -1.48 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1245 HIS 0.005 0.001 HIS A1225 PHE 0.019 0.001 PHE A1339 TYR 0.023 0.001 TYR A1088 ARG 0.004 0.000 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.029 Fit side-chains REVERT: A 221 SER cc_start: 0.7192 (t) cc_final: 0.6775 (t) REVERT: A 223 PHE cc_start: 0.6696 (m-80) cc_final: 0.6238 (m-80) REVERT: A 1225 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.6990 (t70) REVERT: A 1231 MET cc_start: 0.7256 (mmm) cc_final: 0.6852 (mmm) outliers start: 33 outliers final: 29 residues processed: 145 average time/residue: 0.1690 time to fit residues: 37.2242 Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 119 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 265 PHE Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9090 Z= 0.320 Angle : 0.650 10.477 12349 Z= 0.323 Chirality : 0.045 0.231 1408 Planarity : 0.004 0.033 1546 Dihedral : 4.696 22.643 1213 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.49 % Allowed : 20.53 % Favored : 75.98 % 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: -1.11 (0.25), residues: 1100 helix: 0.57 (0.25), residues: 425 sheet: -1.60 (0.46), residues: 126 loop : -1.59 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A1245 HIS 0.009 0.001 HIS A1225 PHE 0.033 0.001 PHE A1339 TYR 0.038 0.002 TYR A1088 ARG 0.003 0.000 ARG A1241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 0.951 Fit side-chains REVERT: A 221 SER cc_start: 0.7265 (t) cc_final: 0.6900 (t) REVERT: A 223 PHE cc_start: 0.6799 (m-80) cc_final: 0.6315 (m-80) REVERT: A 404 LEU cc_start: 0.7809 (mm) cc_final: 0.7608 (mm) REVERT: A 530 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6583 (t-90) REVERT: A 1088 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 1225 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7284 (t70) REVERT: A 1231 MET cc_start: 0.7386 (mmm) cc_final: 0.6999 (mmm) REVERT: A 1242 GLN cc_start: 0.8147 (pp30) cc_final: 0.7932 (mp10) REVERT: A 1322 PHE cc_start: 0.6871 (m-80) cc_final: 0.6629 (m-80) REVERT: A 1328 MET cc_start: 0.7419 (tpp) cc_final: 0.7172 (tpp) outliers start: 34 outliers final: 29 residues processed: 143 average time/residue: 0.1622 time to fit residues: 35.0326 Evaluate side-chains 149 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 414 TYR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 530 HIS Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 691 ASP Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 880 ASP Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1013 THR Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1088 TYR Chi-restraints excluded: chain A residue 1095 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1225 HIS Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.0670 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.182983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.145131 restraints weight = 13295.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.147398 restraints weight = 8288.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.147975 restraints weight = 8701.869| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9090 Z= 0.188 Angle : 0.614 10.658 12349 Z= 0.303 Chirality : 0.043 0.193 1408 Planarity : 0.004 0.034 1546 Dihedral : 4.556 21.394 1213 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.87 % Allowed : 21.25 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.25), residues: 1100 helix: 0.76 (0.26), residues: 419 sheet: -1.54 (0.46), residues: 126 loop : -1.48 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A1245 HIS 0.010 0.001 HIS A1225 PHE 0.032 0.001 PHE A1339 TYR 0.023 0.001 TYR A1088 ARG 0.003 0.000 ARG A 627 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1897.46 seconds wall clock time: 35 minutes 19.90 seconds (2119.90 seconds total)