Starting phenix.real_space_refine (version: dev) on Mon Apr 4 16:37:07 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/04_2022/7n4x_24180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/04_2022/7n4x_24180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/04_2022/7n4x_24180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/04_2022/7n4x_24180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/04_2022/7n4x_24180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n4x_24180/04_2022/7n4x_24180_updated.pdb" } resolution = 3.33 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= 0.003 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 PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A ASP 478": "OD1" <-> "OD2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 534": "OD1" <-> "OD2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ASP 632": "OD1" <-> "OD2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 902": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 913": "OE1" <-> "OE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1067": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A GLU 1091": "OE1" <-> "OE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1187": "NH1" <-> "NH2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A GLU 1282": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 7647 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7423 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Unusual residues: {'NAG': 4, 'CLR': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.88, per 1000 atoms: 0.64 Number of scatterers: 7647 At special positions: 0 Unit cell: (134.113, 93.296, 79.135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1392 8.00 N 1218 7.00 C 4992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.02 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 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 Atom "HETATM 7561 O5 NAG A1404 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A 506 " " NAG A1404 " - " ASN A1075 " " NAG B 1 " - " ASN A 497 " " NAG C 1 " - " ASN A 909 " " NAG D 1 " - " ASN A1037 " Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 7 sheets defined 55.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 352 through 372 Proline residue: A 362 - end of helix removed outlier: 4.834A pdb=" N GLY A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 438 through 452 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 552 through 555 No H-bonds generated for 'chain 'A' and resid 552 through 555' Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 586 through 606 Processing helix chain 'A' and resid 620 through 629 removed outlier: 3.618A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.903A pdb=" N SER A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 663 No H-bonds generated for 'chain 'A' and resid 660 through 663' Processing helix chain 'A' and resid 666 through 689 Processing helix chain 'A' and resid 702 through 723 removed outlier: 4.671A pdb=" N ASP A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 714 " --> pdb=" O GLY A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 763 Proline residue: A 745 - end of helix removed outlier: 4.595A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 803 removed outlier: 3.563A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 843 through 866 removed outlier: 4.618A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N CYS A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N HIS A 866 " --> pdb=" O TYR A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 892 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 930 through 939 Processing helix chain 'A' and resid 953 through 960 Processing helix chain 'A' and resid 1005 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1028 through 1031 No H-bonds generated for 'chain 'A' and resid 1028 through 1031' Processing helix chain 'A' and resid 1059 through 1082 removed outlier: 3.549A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1106 No H-bonds generated for 'chain 'A' and resid 1104 through 1106' Processing helix chain 'A' and resid 1109 through 1129 Proline residue: A1122 - end of helix Processing helix chain 'A' and resid 1135 through 1159 Processing helix chain 'A' and resid 1165 through 1190 removed outlier: 4.328A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1224 removed outlier: 4.195A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1227 through 1229 No H-bonds generated for 'chain 'A' and resid 1227 through 1229' Processing helix chain 'A' and resid 1233 through 1238 Processing helix chain 'A' and resid 1241 through 1265 removed outlier: 6.350A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1271 through 1275 Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 4.103A pdb=" N GLU A1281 " --> pdb=" O LYS A1278 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 406 through 408 Processing sheet with id= B, first strand: chain 'A' and resid 614 through 616 Processing sheet with id= C, first strand: chain 'A' and resid 420 through 423 Processing sheet with id= D, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.779A pdb=" N ARG A 463 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 505 through 509 Processing sheet with id= F, first strand: chain 'A' and resid 1050 through 1052 Processing sheet with id= G, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.786A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1372 1.33 - 1.45: 1956 1.45 - 1.58: 4441 1.58 - 1.70: 0 1.70 - 1.82: 69 Bond restraints: 7838 Sorted by residual: bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.98e+01 bond pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.68e+01 bond pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta sigma weight residual 1.456 1.491 -0.036 8.70e-03 1.32e+04 1.67e+01 bond pdb=" N LEU A1109 " pdb=" CA LEU A1109 " ideal model delta sigma weight residual 1.463 1.491 -0.028 6.90e-03 2.10e+04 1.63e+01 bond pdb=" N LEU A1221 " pdb=" CA LEU A1221 " ideal model delta sigma weight residual 1.462 1.493 -0.032 8.50e-03 1.38e+04 1.38e+01 ... (remaining 7833 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.74: 265 106.74 - 113.95: 4384 113.95 - 121.17: 3638 121.17 - 128.38: 2365 128.38 - 135.59: 40 Bond angle restraints: 10692 Sorted by residual: angle pdb=" C3 NAG A1402 " pdb=" C2 NAG A1402 " pdb=" N2 NAG A1402 " ideal model delta sigma weight residual 110.58 116.09 -5.51 9.20e-01 1.18e+00 3.58e+01 angle pdb=" N VAL A 813 " pdb=" CA VAL A 813 " pdb=" C VAL A 813 " ideal model delta sigma weight residual 113.10 108.53 4.57 9.70e-01 1.06e+00 2.22e+01 angle pdb=" C ARG A 846 " pdb=" N GLY A 847 " pdb=" CA GLY A 847 " ideal model delta sigma weight residual 119.94 124.95 -5.01 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C MET A 684 " pdb=" N GLY A 685 " pdb=" CA GLY A 685 " ideal model delta sigma weight residual 119.94 124.94 -5.00 1.11e+00 8.12e-01 2.03e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 124.91 -4.93 1.11e+00 8.12e-01 1.97e+01 ... (remaining 10687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 4313 23.41 - 46.82: 260 46.82 - 70.22: 27 70.22 - 93.63: 10 93.63 - 117.04: 2 Dihedral angle restraints: 4612 sinusoidal: 1836 harmonic: 2776 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" C3 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sinusoidal sigma weight residual -50.00 67.04 -117.04 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" C3 NAG A1404 " pdb=" C1 NAG A1404 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sinusoidal sigma weight residual -50.00 67.00 -117.00 1 2.00e+01 2.50e-03 3.49e+01 ... (remaining 4609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.938: 1269 0.938 - 1.875: 2 1.875 - 2.813: 1 2.813 - 3.750: 0 3.750 - 4.688: 2 Chirality restraints: 1274 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.29 -4.69 2.00e-02 2.50e+03 5.49e+04 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 1.70 -4.10 2.00e-01 2.50e+01 4.21e+02 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A 506 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 -0.48 -1.92 2.00e-01 2.50e+01 9.20e+01 ... (remaining 1271 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.247 2.00e-02 2.50e+03 2.05e-01 5.28e+02 pdb=" C7 NAG B 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.341 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 431 " -0.115 2.00e-02 2.50e+03 1.88e-01 4.41e+02 pdb=" CG ASN A 431 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 431 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 431 " 0.336 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 909 " -0.149 2.00e-02 2.50e+03 1.66e-01 3.45e+02 pdb=" CG ASN A 909 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 909 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 909 " 0.265 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.202 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 125 2.69 - 3.24: 7117 3.24 - 3.79: 11743 3.79 - 4.35: 15672 4.35 - 4.90: 27233 Nonbonded interactions: 61890 Sorted by model distance: nonbonded pdb=" OG SER A 912 " pdb=" O5 NAG C 1 " model vdw 2.134 2.440 nonbonded pdb=" OG SER A 912 " pdb=" O6 NAG C 1 " model vdw 2.148 2.440 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.315 2.440 nonbonded pdb=" O GLY A 710 " pdb=" NE2 GLN A 787 " model vdw 2.323 2.520 nonbonded pdb=" O THR A 629 " pdb=" NE2 GLN A 700 " model vdw 2.384 2.520 ... (remaining 61885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 4992 2.51 5 N 1218 2.21 5 O 1392 1.98 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 individual isotropic 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: 1.020 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: 5.400 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.070 Process input model: 24.330 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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 : 0.014 0.050 7838 Z= 0.911 Angle : 1.758 7.704 10692 Z= 1.328 Chirality : 0.210 4.688 1274 Planarity : 0.009 0.205 1321 Dihedral : 15.231 117.038 2804 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % 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: -3.15 (0.23), residues: 951 helix: -1.73 (0.18), residues: 516 sheet: -2.85 (0.54), residues: 62 loop : -2.28 (0.29), residues: 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.855 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 109 average time/residue: 0.1636 time to fit residues: 25.6972 Evaluate side-chains 74 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.897 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.0726 time to fit residues: 2.1266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 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 339 GLN A 397 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 943 GLN A1253 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 7838 Z= 0.217 Angle : 0.602 6.768 10692 Z= 0.308 Chirality : 0.042 0.306 1274 Planarity : 0.004 0.031 1321 Dihedral : 7.801 92.023 1113 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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: -1.05 (0.27), residues: 951 helix: 0.09 (0.23), residues: 550 sheet: -1.83 (0.56), residues: 63 loop : -1.68 (0.32), residues: 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.867 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 0.1615 time to fit residues: 22.6530 Evaluate side-chains 70 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.893 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0793 time to fit residues: 1.9738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 7838 Z= 0.304 Angle : 0.596 7.334 10692 Z= 0.304 Chirality : 0.042 0.284 1274 Planarity : 0.005 0.101 1321 Dihedral : 8.477 106.702 1113 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % 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: -0.78 (0.27), residues: 951 helix: 0.29 (0.23), residues: 543 sheet: -1.35 (0.58), residues: 63 loop : -1.55 (0.32), residues: 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.837 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 82 average time/residue: 0.1430 time to fit residues: 18.6270 Evaluate side-chains 76 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.832 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.0701 time to fit residues: 2.2694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 7838 Z= 0.201 Angle : 0.520 7.268 10692 Z= 0.264 Chirality : 0.039 0.312 1274 Planarity : 0.005 0.100 1321 Dihedral : 8.344 105.987 1113 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.99 % 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: -0.46 (0.27), residues: 951 helix: 0.51 (0.23), residues: 544 sheet: -0.99 (0.59), residues: 63 loop : -1.41 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.833 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 87 average time/residue: 0.1299 time to fit residues: 18.0153 Evaluate side-chains 75 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.848 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0672 time to fit residues: 1.6163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.0050 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 7838 Z= 0.199 Angle : 0.518 8.560 10692 Z= 0.265 Chirality : 0.038 0.190 1274 Planarity : 0.005 0.105 1321 Dihedral : 8.277 106.651 1113 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.86 % 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: -0.25 (0.27), residues: 951 helix: 0.65 (0.23), residues: 544 sheet: -0.69 (0.61), residues: 63 loop : -1.31 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.039 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.1374 time to fit residues: 18.1701 Evaluate side-chains 77 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0832 time to fit residues: 1.8087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.097 7838 Z= 0.213 Angle : 0.522 8.735 10692 Z= 0.268 Chirality : 0.038 0.205 1274 Planarity : 0.005 0.107 1321 Dihedral : 8.241 106.666 1113 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.37 % 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: -0.13 (0.27), residues: 951 helix: 0.73 (0.23), residues: 543 sheet: -0.67 (0.59), residues: 63 loop : -1.20 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.869 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 83 average time/residue: 0.1415 time to fit residues: 18.5599 Evaluate side-chains 77 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.903 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0774 time to fit residues: 1.7040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 0.0670 chunk 77 optimal weight: 0.0270 chunk 51 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 7838 Z= 0.200 Angle : 0.522 9.567 10692 Z= 0.270 Chirality : 0.038 0.201 1274 Planarity : 0.006 0.109 1321 Dihedral : 8.212 106.052 1113 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.28), residues: 951 helix: 0.93 (0.23), residues: 544 sheet: -0.89 (0.61), residues: 63 loop : -1.08 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.777 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 81 average time/residue: 0.1427 time to fit residues: 18.3483 Evaluate side-chains 79 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.898 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.0805 time to fit residues: 2.1050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 71 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.168 7838 Z= 0.226 Angle : 0.529 10.873 10692 Z= 0.275 Chirality : 0.038 0.179 1274 Planarity : 0.005 0.110 1321 Dihedral : 8.131 106.326 1113 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 951 helix: 0.97 (0.23), residues: 544 sheet: -0.80 (0.62), residues: 63 loop : -1.02 (0.33), residues: 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.889 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 0.1370 time to fit residues: 17.0967 Evaluate side-chains 73 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.866 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0737 time to fit residues: 1.5826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.0270 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.258 7838 Z= 0.273 Angle : 0.556 14.926 10692 Z= 0.297 Chirality : 0.038 0.180 1274 Planarity : 0.006 0.117 1321 Dihedral : 8.124 106.488 1113 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.12 % 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: 0.12 (0.28), residues: 951 helix: 0.92 (0.23), residues: 547 sheet: -0.79 (0.62), residues: 63 loop : -1.06 (0.34), residues: 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.852 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.1385 time to fit residues: 17.3988 Evaluate side-chains 73 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.844 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0717 time to fit residues: 1.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 94 optimal weight: 0.0470 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.562 7838 Z= 0.540 Angle : 0.971 72.938 10692 Z= 0.424 Chirality : 0.037 0.176 1274 Planarity : 0.005 0.125 1321 Dihedral : 8.100 106.155 1113 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.25 % 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: 0.19 (0.28), residues: 951 helix: 0.99 (0.23), residues: 547 sheet: -0.80 (0.59), residues: 69 loop : -1.02 (0.34), residues: 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.891 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.1408 time to fit residues: 16.5428 Evaluate side-chains 74 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.889 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0751 time to fit residues: 1.5126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 ASN ** 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 = 0.3351 r_free = 0.3351 target = 0.126226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.103704 restraints weight = 9010.085| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.46 r_work: 0.3059 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 1.30 restraints_weight: 0.2500 r_work: 0.3030 rms_B_bonded: 1.40 restraints_weight: 0.1250 r_work: 0.3011 rms_B_bonded: 1.58 restraints_weight: 0.0625 r_work: 0.2988 rms_B_bonded: 1.86 restraints_weight: 0.0312 r_work: 0.2958 rms_B_bonded: 2.26 restraints_weight: 0.0156 r_work: 0.2921 rms_B_bonded: 2.82 restraints_weight: 0.0078 r_work: 0.2872 rms_B_bonded: 3.59 restraints_weight: 0.0039 r_work: 0.2808 rms_B_bonded: 4.70 restraints_weight: 0.0020 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.141 7838 Z= 0.261 Angle : 0.550 14.204 10692 Z= 0.297 Chirality : 0.038 0.210 1274 Planarity : 0.006 0.123 1321 Dihedral : 8.103 106.293 1113 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.25 % 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: 0.17 (0.28), residues: 951 helix: 1.00 (0.23), residues: 545 sheet: -0.80 (0.62), residues: 63 loop : -1.07 (0.34), residues: 343 =============================================================================== Job complete usr+sys time: 1530.61 seconds wall clock time: 28 minutes 41.74 seconds (1721.74 seconds total)