Starting phenix.real_space_refine on Tue Nov 14 13:05:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/11_2023/7op1_13011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/11_2023/7op1_13011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/11_2023/7op1_13011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/11_2023/7op1_13011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/11_2023/7op1_13011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op1_13011/11_2023/7op1_13011_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 5683 2.51 5 N 1452 2.21 5 O 1550 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 227": "NH1" <-> "NH2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 292": "NH1" <-> "NH2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A ARG 696": "NH1" <-> "NH2" Residue "A GLU 707": "OE1" <-> "OE2" Residue "A TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 843": "NH1" <-> "NH2" Residue "A ARG 844": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A GLU 870": "OE1" <-> "OE2" Residue "A ARG 873": "NH1" <-> "NH2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 902": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 916": "NH1" <-> "NH2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A PHE 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A TYR 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 992": "OD1" <-> "OD2" Residue "A GLU 1000": "OE1" <-> "OE2" Residue "A ASP 1010": "OD1" <-> "OD2" Residue "A ARG 1060": "NH1" <-> "NH2" Residue "A TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1074": "OD1" <-> "OD2" Residue "A GLU 1116": "OE1" <-> "OE2" Residue "A PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1212": "OD1" <-> "OD2" Residue "A GLU 1254": "OE1" <-> "OE2" Residue "A GLU 1259": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A TYR 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "A PHE 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 8744 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8744 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 1} Classifications: {'peptide': 1098, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 1043, None: 3} Not linked: pdbres="PHE A1393 " pdbres=" MG A1401 " Not linked: pdbres=" MG A1401 " pdbres="ALF A1402 " Not linked: pdbres="ALF A1402 " pdbres="SPM A1403 " Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.04, per 1000 atoms: 0.58 Number of scatterers: 8744 At special positions: 0 Unit cell: (86.17, 101.681, 143.904, 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 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1550 8.00 N 1452 7.00 C 5683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.7 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 10 sheets defined 43.6% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 229 through 240 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 252 through 259 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 353 through 357 Processing helix chain 'A' and resid 362 through 372 removed outlier: 3.831A pdb=" N HIS A 367 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 372 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 Processing helix chain 'A' and resid 395 through 410 Processing helix chain 'A' and resid 413 through 441 Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 530 through 535 removed outlier: 5.027A 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 589 through 616 removed outlier: 3.787A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.980A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 657 removed outlier: 4.059A pdb=" N GLN A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 654 " --> pdb=" O PHE A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 673 removed outlier: 4.014A pdb=" N ASN A 669 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 716 No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 749 through 759 Processing helix chain 'A' and resid 774 through 783 removed outlier: 3.736A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 868 No H-bonds generated for 'chain 'A' and resid 865 through 868' Processing helix chain 'A' and resid 881 through 891 Processing helix chain 'A' and resid 910 through 913 No H-bonds generated for 'chain 'A' and resid 910 through 913' Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 939 through 948 removed outlier: 3.682A pdb=" N LYS A 944 " --> pdb=" O THR A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 1044 through 1052 removed outlier: 3.810A pdb=" N TRP A1048 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1064 Processing helix chain 'A' and resid 1073 through 1086 removed outlier: 3.835A pdb=" N ILE A1086 " --> pdb=" O LYS A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1105 removed outlier: 4.881A pdb=" N ALA A1101 " --> pdb=" O ASN A1098 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A1105 " --> pdb=" O ALA A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1171 removed outlier: 3.947A pdb=" N VAL A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1186 Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.811A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1242 Proline residue: A1221 - end of helix removed outlier: 3.642A pdb=" N SER A1224 " --> pdb=" O VAL A1220 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS A1225 " --> pdb=" O PRO A1221 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 3.844A pdb=" N ILE A1275 " --> pdb=" O CYS A1271 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A1276 " --> pdb=" O PHE A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1295 through 1313 Processing helix chain 'A' and resid 1317 through 1320 No H-bonds generated for 'chain 'A' and resid 1317 through 1320' Processing helix chain 'A' and resid 1330 through 1352 removed outlier: 4.030A pdb=" N ILE A1334 " --> pdb=" O TRP A1330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A1335 " --> pdb=" O THR A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1370 Processing helix chain 'A' and resid 1378 through 1392 Processing sheet with id= A, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.947A pdb=" N TRP A 270 " --> pdb=" O PHE A 223 " (cutoff:3.500A) 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 450 through 453 Processing sheet with id= E, first strand: chain 'A' and resid 472 through 474 removed outlier: 7.241A pdb=" N ASP A 486 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 508 through 511 removed outlier: 7.029A pdb=" N ASN A 497 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 543 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 695 through 697 removed outlier: 6.649A pdb=" N CYS A 898 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE A 928 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 896 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 930 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 894 " --> pdb=" O ILE A 930 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ARG A 850 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL A 832 " --> pdb=" O ARG A 850 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 764 through 766 Processing sheet with id= I, first strand: chain 'A' and resid 981 through 985 Processing sheet with id= J, first strand: chain 'A' and resid 1091 through 1094 removed outlier: 6.965A pdb=" N VAL A1108 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N GLY A1094 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A1110 " --> pdb=" O GLY A1094 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 356 hydrogen bonds defined for protein. 999 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: 2.88 Time building geometry restraints manager: 3.70 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: 2717 1.34 - 1.46: 1444 1.46 - 1.57: 4714 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8956 Sorted by residual: bond pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" F3 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" F4 ALF A1402 " pdb="AL ALF A1402 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" CG GLN A 653 " pdb=" CD GLN A 653 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.12e+00 ... (remaining 8951 not shown) Histogram of bond angle deviations from ideal: 89.03 - 107.17: 289 107.17 - 125.31: 11714 125.31 - 143.44: 154 143.44 - 161.58: 0 161.58 - 179.72: 2 Bond angle restraints: 12159 Sorted by residual: angle pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " pdb=" F2 ALF A1402 " ideal model delta sigma weight residual 108.68 179.72 -71.04 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 109.63 179.59 -69.96 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " pdb=" F3 ALF A1402 " ideal model delta sigma weight residual 109.59 89.03 20.56 3.00e+00 1.11e-01 4.70e+01 angle pdb=" F1 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 109.02 89.10 19.92 3.00e+00 1.11e-01 4.41e+01 angle pdb=" F2 ALF A1402 " pdb="AL ALF A1402 " pdb=" F4 ALF A1402 " ideal model delta sigma weight residual 110.21 90.77 19.44 3.00e+00 1.11e-01 4.20e+01 ... (remaining 12154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 4766 17.45 - 34.89: 463 34.89 - 52.34: 68 52.34 - 69.78: 10 69.78 - 87.23: 6 Dihedral angle restraints: 5313 sinusoidal: 2103 harmonic: 3210 Sorted by residual: dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N TYR A 328 " pdb=" CA TYR A 328 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TYR A 413 " pdb=" C TYR A 413 " pdb=" N TYR A 414 " pdb=" CA TYR A 414 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP A 347 " pdb=" C ASP A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 768 0.029 - 0.059: 403 0.059 - 0.088: 120 0.088 - 0.117: 76 0.117 - 0.147: 20 Chirality restraints: 1387 Sorted by residual: chirality pdb=" CA PRO A 348 " pdb=" N PRO A 348 " pdb=" C PRO A 348 " pdb=" CB PRO A 348 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA VAL A 580 " pdb=" N VAL A 580 " pdb=" C VAL A 580 " pdb=" CB VAL A 580 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 495 " pdb=" N ILE A 495 " pdb=" C ILE A 495 " pdb=" CB ILE A 495 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1384 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 347 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" CG ASP A 347 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP A 347 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A 347 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 982 " -0.031 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 983 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 983 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 983 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 877 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 878 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 878 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 878 " 0.026 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 34 2.46 - 3.07: 5769 3.07 - 3.68: 12313 3.68 - 4.29: 17685 4.29 - 4.90: 30056 Nonbonded interactions: 65857 Sorted by model distance: nonbonded pdb="MG MG A1401 " pdb=" F3 ALF A1402 " model vdw 1.848 2.120 nonbonded pdb="MG MG A1401 " pdb=" F2 ALF A1402 " model vdw 1.971 2.120 nonbonded pdb=" OD2 ASP A 680 " pdb=" F2 ALF A1402 " model vdw 2.069 2.390 nonbonded pdb=" OD2 ASP A 680 " pdb="MG MG A1401 " model vdw 2.081 2.170 nonbonded pdb=" OG SER A1290 " pdb=" OE1 GLU A1293 " model vdw 2.135 2.440 ... (remaining 65852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.900 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: 0.020 Extract box with map and model: 7.490 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 0.099 8956 Z= 0.276 Angle : 1.157 71.036 12159 Z= 0.482 Chirality : 0.043 0.147 1387 Planarity : 0.004 0.048 1516 Dihedral : 13.672 87.230 3235 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: -0.69 (0.26), residues: 1082 helix: 0.90 (0.24), residues: 485 sheet: -1.18 (0.51), residues: 114 loop : -1.71 (0.27), residues: 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 1.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1930 time to fit residues: 24.5902 Evaluate side-chains 69 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.147 Angle : 0.498 6.749 12159 Z= 0.260 Chirality : 0.040 0.152 1387 Planarity : 0.004 0.037 1516 Dihedral : 5.511 58.955 1206 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.63 % Allowed : 5.11 % Favored : 94.26 % 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: -0.11 (0.27), residues: 1082 helix: 1.42 (0.25), residues: 486 sheet: -1.06 (0.45), residues: 141 loop : -1.40 (0.29), residues: 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.970 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 0.1915 time to fit residues: 23.2465 Evaluate side-chains 77 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0849 time to fit residues: 2.3973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8956 Z= 0.156 Angle : 0.489 9.429 12159 Z= 0.252 Chirality : 0.040 0.144 1387 Planarity : 0.004 0.038 1516 Dihedral : 5.232 59.324 1206 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 1082 helix: 1.57 (0.25), residues: 486 sheet: -0.89 (0.46), residues: 141 loop : -1.33 (0.30), residues: 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1943 time to fit residues: 23.0394 Evaluate side-chains 68 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 0.0870 chunk 47 optimal weight: 0.0570 chunk 67 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8956 Z= 0.119 Angle : 0.454 6.060 12159 Z= 0.235 Chirality : 0.039 0.155 1387 Planarity : 0.003 0.039 1516 Dihedral : 4.860 59.509 1206 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.83 % Allowed : 9.07 % Favored : 90.09 % 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: 0.30 (0.27), residues: 1082 helix: 1.73 (0.25), residues: 490 sheet: -0.74 (0.45), residues: 151 loop : -1.23 (0.30), residues: 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.022 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 80 average time/residue: 0.1810 time to fit residues: 22.0625 Evaluate side-chains 72 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 69 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0811 time to fit residues: 1.8713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8956 Z= 0.297 Angle : 0.539 6.573 12159 Z= 0.281 Chirality : 0.043 0.151 1387 Planarity : 0.004 0.040 1516 Dihedral : 5.257 59.198 1206 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.73 % Allowed : 10.95 % Favored : 88.32 % 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: 0.15 (0.27), residues: 1082 helix: 1.53 (0.25), residues: 480 sheet: -0.69 (0.47), residues: 141 loop : -1.19 (0.30), residues: 461 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 1.000 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 80 average time/residue: 0.1854 time to fit residues: 22.1230 Evaluate side-chains 72 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.976 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0845 time to fit residues: 1.7349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 20.0000 chunk 8 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8956 Z= 0.150 Angle : 0.476 6.754 12159 Z= 0.245 Chirality : 0.040 0.139 1387 Planarity : 0.003 0.035 1516 Dihedral : 4.900 59.988 1206 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.94 % Allowed : 11.99 % Favored : 87.07 % 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: 0.31 (0.27), residues: 1082 helix: 1.73 (0.25), residues: 485 sheet: -0.69 (0.45), residues: 151 loop : -1.18 (0.30), residues: 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 1.006 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.2032 time to fit residues: 24.0181 Evaluate side-chains 76 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0863 time to fit residues: 2.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8956 Z= 0.250 Angle : 0.519 5.654 12159 Z= 0.269 Chirality : 0.042 0.140 1387 Planarity : 0.004 0.043 1516 Dihedral : 5.082 57.741 1206 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.52 % Allowed : 12.51 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.27), residues: 1082 helix: 1.60 (0.25), residues: 479 sheet: -0.69 (0.45), residues: 151 loop : -1.22 (0.30), residues: 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.001 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 0.2035 time to fit residues: 23.6836 Evaluate side-chains 69 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0827 time to fit residues: 1.5242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 92 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8956 Z= 0.142 Angle : 0.481 7.701 12159 Z= 0.246 Chirality : 0.040 0.139 1387 Planarity : 0.003 0.040 1516 Dihedral : 4.720 58.804 1206 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % 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: 0.41 (0.27), residues: 1082 helix: 1.80 (0.25), residues: 481 sheet: -0.58 (0.45), residues: 153 loop : -1.13 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.980 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1845 time to fit residues: 21.1839 Evaluate side-chains 69 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8956 Z= 0.187 Angle : 0.499 6.160 12159 Z= 0.257 Chirality : 0.041 0.148 1387 Planarity : 0.003 0.038 1516 Dihedral : 4.754 59.791 1206 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.21 % Allowed : 13.76 % Favored : 86.03 % 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: 0.39 (0.27), residues: 1082 helix: 1.76 (0.24), residues: 481 sheet: -0.53 (0.44), residues: 153 loop : -1.13 (0.30), residues: 448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.053 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.1947 time to fit residues: 21.2543 Evaluate side-chains 70 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0844 time to fit residues: 1.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 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 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8956 Z= 0.152 Angle : 0.492 7.823 12159 Z= 0.250 Chirality : 0.040 0.138 1387 Planarity : 0.003 0.037 1516 Dihedral : 4.588 59.494 1206 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % 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: 0.50 (0.27), residues: 1082 helix: 1.87 (0.25), residues: 480 sheet: -0.48 (0.44), residues: 154 loop : -1.08 (0.30), residues: 448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1971 time to fit residues: 20.9811 Evaluate side-chains 70 residues out of total 960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120798 restraints weight = 11488.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117998 restraints weight = 15476.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.119318 restraints weight = 13914.565| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8956 Z= 0.188 Angle : 0.503 7.735 12159 Z= 0.256 Chirality : 0.040 0.138 1387 Planarity : 0.003 0.037 1516 Dihedral : 4.633 58.298 1206 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.10 % Allowed : 14.08 % Favored : 85.82 % 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: 0.47 (0.27), residues: 1082 helix: 1.80 (0.24), residues: 481 sheet: -0.45 (0.44), residues: 154 loop : -1.06 (0.30), residues: 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.33 seconds wall clock time: 32 minutes 7.82 seconds (1927.82 seconds total)