Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:26:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/04_2023/7op8_13014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/04_2023/7op8_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_13014/04_2023/7op8_13014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/04_2023/7op8_13014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/04_2023/7op8_13014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/04_2023/7op8_13014_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 5.06, per 1000 atoms: 0.57 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: 3.34 Conformation dependent library (CDL) restraints added in 1.4 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: 1.67 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: 3.07 Time building geometry restraints manager: 3.61 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: 2.010 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: 10.490 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.060 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.770 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.075 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1688 time to fit residues: 39.9000 Evaluate side-chains 120 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4205 ------------------------------------------------------------------------------- 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: 0.7552 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9090 Z= 0.201 Angle : 0.565 7.912 12349 Z= 0.284 Chirality : 0.044 0.202 1408 Planarity : 0.004 0.046 1546 Dihedral : 4.669 22.888 1213 Min Nonbonded Distance : 1.307 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer Outliers : 1.54 % 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: 0.33 (0.25), residues: 421 sheet: -1.52 (0.45), residues: 125 loop : -1.61 (0.25), residues: 554 *********************** 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 144 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 1.060 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.1682 time to fit residues: 35.0873 Evaluate side-chains 128 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0942 time to fit residues: 3.1669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS A 613 ASN ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 9090 Z= 0.300 Angle : 0.616 7.861 12349 Z= 0.310 Chirality : 0.046 0.233 1408 Planarity : 0.004 0.040 1546 Dihedral : 4.738 21.777 1213 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 1.54 % 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: -1.19 (0.25), residues: 1100 helix: 0.48 (0.25), residues: 416 sheet: -1.47 (0.46), residues: 125 loop : -1.63 (0.25), residues: 559 *********************** 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 146 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.054 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 139 average time/residue: 0.1720 time to fit residues: 36.3191 Evaluate side-chains 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0884 time to fit residues: 2.9832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2079 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= 0.286 Angle : 0.587 7.212 12349 Z= 0.298 Chirality : 0.044 0.211 1408 Planarity : 0.004 0.038 1546 Dihedral : 4.696 21.973 1213 Min Nonbonded Distance : 1.338 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 1.85 % 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: -1.12 (0.25), residues: 1100 helix: 0.62 (0.25), residues: 413 sheet: -1.50 (0.46), residues: 125 loop : -1.63 (0.25), residues: 562 *********************** 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 144 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 138 average time/residue: 0.1872 time to fit residues: 38.5464 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.087 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1006 time to fit residues: 3.5475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0040 chunk 1 optimal weight: 0.0970 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.3388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 9090 Z= 0.157 Angle : 0.540 8.995 12349 Z= 0.268 Chirality : 0.042 0.174 1408 Planarity : 0.004 0.037 1546 Dihedral : 4.410 20.282 1213 Min Nonbonded Distance : 1.409 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.92 % 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: -0.94 (0.25), residues: 1100 helix: 0.80 (0.26), residues: 415 sheet: -1.45 (0.46), residues: 123 loop : -1.55 (0.25), residues: 562 *********************** 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 146 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 143 average time/residue: 0.1726 time to fit residues: 37.0625 Evaluate side-chains 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0875 time to fit residues: 2.8860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 26 optimal weight: 0.0870 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- 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: 0.7760 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 9090 Z= 0.374 Angle : 0.641 8.392 12349 Z= 0.327 Chirality : 0.046 0.287 1408 Planarity : 0.004 0.033 1546 Dihedral : 4.796 22.968 1213 Min Nonbonded Distance : 1.340 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer Outliers : 1.75 % 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: -1.13 (0.25), residues: 1100 helix: 0.53 (0.25), residues: 418 sheet: -1.62 (0.46), residues: 125 loop : -1.55 (0.26), residues: 557 *********************** 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 146 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 139 average time/residue: 0.1786 time to fit residues: 36.9206 Evaluate side-chains 127 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0953 time to fit residues: 3.2243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.0070 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.0470 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 0.4074 ------------------------------------------------------------------------------- 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** ** A1098 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9090 Z= 0.168 Angle : 0.558 7.458 12349 Z= 0.279 Chirality : 0.042 0.185 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.503 20.544 1213 Min Nonbonded Distance : 1.400 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer Outliers : 0.62 % 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: -0.84 (0.25), residues: 1100 helix: 0.87 (0.26), residues: 413 sheet: -1.65 (0.44), residues: 127 loop : -1.40 (0.26), residues: 560 *********************** 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 137 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.006 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 135 average time/residue: 0.1800 time to fit residues: 35.8747 Evaluate side-chains 119 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0834 time to fit residues: 1.6841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 103 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 ** A1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2439 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= 0.190 Angle : 0.566 7.582 12349 Z= 0.283 Chirality : 0.042 0.197 1408 Planarity : 0.004 0.041 1546 Dihedral : 4.427 20.797 1213 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 1.75 % 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: -0.80 (0.25), residues: 1100 helix: 0.96 (0.26), residues: 412 sheet: -1.62 (0.44), residues: 127 loop : -1.42 (0.26), residues: 561 *********************** 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 140 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 13 residues processed: 134 average time/residue: 0.1829 time to fit residues: 36.2663 Evaluate side-chains 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1231 time to fit residues: 4.1169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0670 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9090 Z= 0.168 Angle : 0.573 9.568 12349 Z= 0.285 Chirality : 0.042 0.182 1408 Planarity : 0.004 0.051 1546 Dihedral : 4.353 20.153 1213 Min Nonbonded Distance : 1.403 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.62 % 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 (0.25), residues: 1100 helix: 1.03 (0.26), residues: 413 sheet: -1.57 (0.44), residues: 127 loop : -1.42 (0.26), residues: 560 *********************** 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 133 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 129 average time/residue: 0.1880 time to fit residues: 35.5469 Evaluate side-chains 122 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0833 time to fit residues: 1.9472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 73 optimal weight: 0.0270 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 0.0000 chunk 70 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 overall best weight: 0.3820 ------------------------------------------------------------------------------- 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: 0.7607 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9090 Z= 0.169 Angle : 0.581 8.549 12349 Z= 0.287 Chirality : 0.042 0.183 1408 Planarity : 0.004 0.045 1546 Dihedral : 4.280 19.793 1213 Min Nonbonded Distance : 1.400 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.31 % 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: -0.68 (0.25), residues: 1100 helix: 1.08 (0.26), residues: 417 sheet: -1.51 (0.45), residues: 127 loop : -1.41 (0.26), residues: 556 ********************** 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 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 127 average time/residue: 0.1953 time to fit residues: 36.3865 Evaluate side-chains 123 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 121 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1216 time to fit residues: 1.8842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0170 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5220 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.195356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.157986 restraints weight = 13307.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.159695 restraints weight = 7956.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.160525 restraints weight = 8587.576| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2463 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= 0.184 Angle : 0.581 8.369 12349 Z= 0.288 Chirality : 0.042 0.186 1408 Planarity : 0.004 0.046 1546 Dihedral : 4.260 19.938 1213 Min Nonbonded Distance : 1.389 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.31 % 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: -0.75 (0.25), residues: 1100 helix: 1.06 (0.26), residues: 418 sheet: -1.70 (0.42), residues: 135 loop : -1.43 (0.26), residues: 547 =============================================================================== Job complete usr+sys time: 1845.87 seconds wall clock time: 34 minutes 31.49 seconds (2071.49 seconds total)