Starting phenix.real_space_refine (version: dev) on Mon Dec 12 03:28:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/12_2022/7op8_13014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/12_2022/7op8_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_13014/12_2022/7op8_13014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/12_2022/7op8_13014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/12_2022/7op8_13014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op8_13014/12_2022/7op8_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 Convert atoms to be neutral 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-4807/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: 5.31, per 1000 atoms: 0.60 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 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: 1.59 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: 3.25 Time building geometry restraints manager: 3.48 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 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. 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: 1.460 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: 9.800 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.070 Process input model: 26.730 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 1.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1652 time to fit residues: 39.1754 Evaluate side-chains 120 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4441 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.6558 ------------------------------------------------------------------------------- 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: 0.7733 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 9090 Z= 0.203 Angle : 0.569 7.960 12349 Z= 0.286 Chirality : 0.044 0.196 1408 Planarity : 0.004 0.045 1546 Dihedral : 4.668 21.937 1213 Min Nonbonded Distance : 1.323 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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: 0.34 (0.25), residues: 421 sheet: -1.52 (0.45), residues: 125 loop : -1.62 (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 145 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.089 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.1716 time to fit residues: 36.0409 Evaluate side-chains 127 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0925 time to fit residues: 3.1211 ------------------------------------------------------------------------------- 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: 0.0270 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1394 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1332 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= 0.187 Angle : 0.552 8.073 12349 Z= 0.276 Chirality : 0.043 0.191 1408 Planarity : 0.004 0.042 1546 Dihedral : 4.466 19.622 1213 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1100 helix: 0.53 (0.25), residues: 421 sheet: -1.40 (0.46), residues: 119 loop : -1.55 (0.25), residues: 560 *********************** 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 139 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.122 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 0.1745 time to fit residues: 35.2933 Evaluate side-chains 124 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0864 time to fit residues: 2.6568 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- 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** A1225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1951 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= 0.300 Angle : 0.607 9.728 12349 Z= 0.307 Chirality : 0.045 0.230 1408 Planarity : 0.004 0.038 1546 Dihedral : 4.663 21.660 1213 Min Nonbonded Distance : 1.354 Molprobity Statistics. All-atom Clashscore : 10.96 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: -1.12 (0.25), residues: 1100 helix: 0.61 (0.25), residues: 413 sheet: -1.49 (0.45), residues: 125 loop : -1.62 (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: 15 poor density : 129 time to evaluate : 1.067 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 140 average time/residue: 0.1700 time to fit residues: 36.0777 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.040 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0917 time to fit residues: 3.3286 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.0030 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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: 0.7856 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9090 Z= 0.240 Angle : 0.578 9.952 12349 Z= 0.288 Chirality : 0.043 0.193 1408 Planarity : 0.004 0.040 1546 Dihedral : 4.557 21.162 1213 Min Nonbonded Distance : 1.345 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.33 % 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: 0.68 (0.26), residues: 414 sheet: -1.52 (0.45), residues: 125 loop : -1.63 (0.25), residues: 561 *********************** 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 142 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 136 average time/residue: 0.1777 time to fit residues: 35.8815 Evaluate side-chains 122 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0864 time to fit residues: 2.7068 ------------------------------------------------------------------------------- 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: 1.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 26 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7840 moved from start: 0.2106 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= 0.201 Angle : 0.565 10.294 12349 Z= 0.281 Chirality : 0.042 0.176 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.481 20.734 1213 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer Outliers : 0.72 % 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: -0.92 (0.25), residues: 1100 helix: 0.84 (0.26), residues: 411 sheet: -1.54 (0.45), residues: 125 loop : -1.51 (0.25), residues: 564 *********************** 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 135 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 128 time to evaluate : 1.077 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 132 average time/residue: 0.1809 time to fit residues: 36.2579 Evaluate side-chains 122 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0972 time to fit residues: 2.5669 ------------------------------------------------------------------------------- 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: 6.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 0.0770 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- 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** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 9090 Z= 0.403 Angle : 0.675 9.087 12349 Z= 0.342 Chirality : 0.047 0.297 1408 Planarity : 0.004 0.040 1546 Dihedral : 4.976 23.542 1213 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 2.05 % 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: -1.37 (0.25), residues: 1100 helix: 0.32 (0.25), residues: 425 sheet: -1.70 (0.45), residues: 125 loop : -1.71 (0.25), residues: 550 *********************** 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 142 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.155 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 16 residues processed: 136 average time/residue: 0.1620 time to fit residues: 33.6239 Evaluate side-chains 126 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0872 time to fit residues: 3.8697 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9090 Z= 0.213 Angle : 0.592 9.075 12349 Z= 0.296 Chirality : 0.043 0.207 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.714 21.956 1213 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer Outliers : 0.72 % 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: -1.07 (0.25), residues: 1100 helix: 0.66 (0.26), residues: 413 sheet: -1.69 (0.44), residues: 127 loop : -1.54 (0.25), residues: 560 *********************** 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 129 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.043 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 128 average time/residue: 0.1709 time to fit residues: 33.1451 Evaluate side-chains 118 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0893 time to fit residues: 2.2794 ------------------------------------------------------------------------------- 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: 0.0010 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.2592 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= 0.186 Angle : 0.585 10.932 12349 Z= 0.289 Chirality : 0.043 0.201 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.486 21.416 1213 Min Nonbonded Distance : 1.378 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.51 % 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: -0.91 (0.25), residues: 1100 helix: 0.78 (0.26), residues: 420 sheet: -1.66 (0.44), residues: 130 loop : -1.45 (0.26), residues: 550 *********************** 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 128 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 123 average time/residue: 0.1809 time to fit residues: 33.0902 Evaluate side-chains 121 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1022 time to fit residues: 2.1420 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 111 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2608 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= 0.178 Angle : 0.595 10.826 12349 Z= 0.295 Chirality : 0.043 0.189 1408 Planarity : 0.004 0.035 1546 Dihedral : 4.427 21.042 1213 Min Nonbonded Distance : 1.390 Molprobity Statistics. All-atom Clashscore : 10.62 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: -0.87 (0.25), residues: 1100 helix: 0.85 (0.26), residues: 420 sheet: -1.60 (0.44), residues: 129 loop : -1.46 (0.26), residues: 551 ********************** 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 131 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.053 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 0.1793 time to fit residues: 34.8562 Evaluate side-chains 120 residues out of total 974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1059 time to fit residues: 1.5902 ------------------------------------------------------------------------------- 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: 2.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** A 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146158 restraints weight = 12556.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.147344 restraints weight = 8435.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148699 restraints weight = 8081.104| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2657 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= 0.194 Angle : 0.618 10.728 12349 Z= 0.307 Chirality : 0.043 0.191 1408 Planarity : 0.004 0.066 1546 Dihedral : 4.402 21.030 1213 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1100 helix: 0.91 (0.26), residues: 420 sheet: -1.67 (0.44), residues: 129 loop : -1.50 (0.25), residues: 551 =============================================================================== Job complete usr+sys time: 1772.83 seconds wall clock time: 33 minutes 11.61 seconds (1991.61 seconds total)