Starting phenix.real_space_refine on Sat Nov 16 21:46:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfq_40448/11_2024/8sfq_40448.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfq_40448/11_2024/8sfq_40448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfq_40448/11_2024/8sfq_40448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfq_40448/11_2024/8sfq_40448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfq_40448/11_2024/8sfq_40448.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfq_40448/11_2024/8sfq_40448.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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: 5 Type Number sf(0) Gaussians P 91 5.49 5 S 23 5.16 5 C 7395 2.51 5 N 2050 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12045 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 7.93, per 1000 atoms: 0.66 Number of scatterers: 12045 At special positions: 0 Unit cell: (89.964, 99.96, 137.445, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 91 15.00 O 2486 8.00 N 2050 7.00 C 7395 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 - 3.00 Amino acid : True - 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: 3.22 Conformation dependent library (CDL) restraints added in 1.5 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 55.9% alpha, 10.7% beta 40 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.660A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.917A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.787A pdb=" N GLU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 4.093A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.094A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.050A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.625A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.837A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.521A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.502A pdb=" N ASN A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.567A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.934A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 429 through 452 Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.568A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.167A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.902A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.738A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.583A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.578A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.514A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 957 removed outlier: 3.663A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.662A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1014 through 1025 removed outlier: 3.831A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.609A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1088 " --> pdb=" O TRP A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1088' Processing helix chain 'A' and resid 1090 through 1100 removed outlier: 3.639A pdb=" N GLY A1100 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1205 removed outlier: 3.508A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.620A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.521A pdb=" N PHE A1253 " --> pdb=" O ASP A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1283 removed outlier: 3.626A pdb=" N GLU A1283 " --> pdb=" O ASN A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.651A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.301A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.651A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.852A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ARG A 909 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 6.651A pdb=" N PHE A1101 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS A1118 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A1112 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1162 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 523 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3172 1.34 - 1.46: 3308 1.46 - 1.58: 5799 1.58 - 1.70: 183 1.70 - 1.83: 38 Bond restraints: 12500 Sorted by residual: bond pdb=" CB ARG A 392 " pdb=" CG ARG A 392 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.38e+00 bond pdb=" CB PRO A 453 " pdb=" CG PRO A 453 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.85e+00 bond pdb=" CB PHE A 683 " pdb=" CG PHE A 683 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.30e-02 1.89e+03 5.06e+00 bond pdb=" CB GLU A 422 " pdb=" CG GLU A 422 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.28e+00 bond pdb=" CA ASP A 184 " pdb=" CB ASP A 184 " ideal model delta sigma weight residual 1.531 1.562 -0.031 1.51e-02 4.39e+03 4.17e+00 ... (remaining 12495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.19: 17165 5.19 - 10.39: 109 10.39 - 15.58: 18 15.58 - 20.77: 3 20.77 - 25.97: 1 Bond angle restraints: 17296 Sorted by residual: angle pdb=" CA PRO A 453 " pdb=" N PRO A 453 " pdb=" CD PRO A 453 " ideal model delta sigma weight residual 112.00 99.18 12.82 1.40e+00 5.10e-01 8.38e+01 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 133.97 -25.97 3.00e+00 1.11e-01 7.49e+01 angle pdb=" O3' DT C 27 " pdb=" P DA C 28 " pdb=" OP1 DA C 28 " ideal model delta sigma weight residual 108.00 125.19 -17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 103.52 16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" CA ASP A 184 " pdb=" CB ASP A 184 " pdb=" CG ASP A 184 " ideal model delta sigma weight residual 112.60 117.64 -5.04 1.00e+00 1.00e+00 2.54e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 6900 32.95 - 65.90: 497 65.90 - 98.85: 38 98.85 - 131.80: 0 131.80 - 164.75: 4 Dihedral angle restraints: 7439 sinusoidal: 3781 harmonic: 3658 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 51.52 148.48 1 1.50e+01 4.44e-03 7.90e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 68.02 131.98 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" CA ALA A1067 " pdb=" C ALA A1067 " pdb=" N PRO A1068 " pdb=" CA PRO A1068 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 7436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1878 0.149 - 0.299: 35 0.299 - 0.448: 14 0.448 - 0.597: 2 0.597 - 0.747: 1 Chirality restraints: 1930 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.35 -3.09 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" P DA C 8 " pdb=" OP1 DA C 8 " pdb=" OP2 DA C 8 " pdb=" O5' DA C 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.52 2.00e-01 2.50e+01 6.67e+00 ... (remaining 1927 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 452 " 0.087 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A 453 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 365 " -0.017 2.00e-02 2.50e+03 2.76e-02 1.34e+01 pdb=" CG PHE A 365 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 365 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 365 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 365 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 365 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 365 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1236 " 0.016 2.00e-02 2.50e+03 2.46e-02 1.22e+01 pdb=" CG TYR A1236 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A1236 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A1236 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A1236 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1236 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1236 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1236 " -0.011 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1596 2.76 - 3.29: 11600 3.29 - 3.83: 22227 3.83 - 4.36: 25046 4.36 - 4.90: 40352 Nonbonded interactions: 100821 Sorted by model distance: nonbonded pdb=" NH1 ARG A 392 " pdb=" OG SER A 425 " model vdw 2.220 3.120 nonbonded pdb=" OG SER A 236 " pdb=" OE1 GLU A 238 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 88 " pdb=" OE1 GLU A 90 " model vdw 2.268 3.040 nonbonded pdb=" O LYS A 429 " pdb=" OG SER A 432 " model vdw 2.281 3.040 nonbonded pdb=" O HIS A1280 " pdb=" OG SER A1284 " model vdw 2.287 3.040 ... (remaining 100816 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.640 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.005 0.121 12500 Z= 0.333 Angle : 1.108 25.966 17296 Z= 0.523 Chirality : 0.066 0.747 1930 Planarity : 0.006 0.122 1895 Dihedral : 20.081 164.749 5071 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.72 % Allowed : 18.77 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.23), residues: 1234 helix: 0.23 (0.20), residues: 612 sheet: -0.01 (0.45), residues: 143 loop : 0.38 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 483 HIS 0.005 0.001 HIS A 618 PHE 0.058 0.003 PHE A 365 TYR 0.057 0.003 TYR A1236 ARG 0.009 0.001 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1001 SER cc_start: 0.9511 (m) cc_final: 0.9217 (p) REVERT: A 1155 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9188 (tp) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.2916 time to fit residues: 37.8224 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 415 HIS ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12500 Z= 0.220 Angle : 0.616 13.047 17296 Z= 0.322 Chirality : 0.040 0.157 1930 Planarity : 0.004 0.044 1895 Dihedral : 19.479 176.754 2529 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.44 % Allowed : 15.79 % Favored : 81.77 % 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: 1.32 (0.24), residues: 1234 helix: 1.39 (0.21), residues: 616 sheet: -0.05 (0.45), residues: 134 loop : 0.68 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A1269 PHE 0.016 0.001 PHE A 353 TYR 0.019 0.001 TYR A 764 ARG 0.005 0.000 ARG A 392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1001 SER cc_start: 0.9513 (m) cc_final: 0.9285 (p) REVERT: A 1099 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.8974 (pt0) REVERT: A 1215 MET cc_start: 0.8793 (ptm) cc_final: 0.8585 (ptp) outliers start: 27 outliers final: 11 residues processed: 90 average time/residue: 0.2288 time to fit residues: 31.9253 Evaluate side-chains 70 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12500 Z= 0.354 Angle : 0.645 13.973 17296 Z= 0.342 Chirality : 0.041 0.166 1930 Planarity : 0.004 0.039 1895 Dihedral : 19.438 176.862 2521 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.70 % Allowed : 15.79 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1234 helix: 1.62 (0.21), residues: 619 sheet: -0.16 (0.44), residues: 144 loop : 0.84 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1258 HIS 0.005 0.001 HIS A 720 PHE 0.018 0.002 PHE A1249 TYR 0.025 0.002 TYR A1012 ARG 0.003 0.000 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 53 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 908 ASP cc_start: 0.7236 (t0) cc_final: 0.6922 (t0) REVERT: A 1001 SER cc_start: 0.9504 (m) cc_final: 0.9284 (p) REVERT: A 1127 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8348 (mtt-85) outliers start: 41 outliers final: 23 residues processed: 86 average time/residue: 0.2310 time to fit residues: 30.3521 Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 706 ASP Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12500 Z= 0.201 Angle : 0.575 12.690 17296 Z= 0.299 Chirality : 0.039 0.184 1930 Planarity : 0.003 0.037 1895 Dihedral : 19.362 173.149 2521 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.16 % Allowed : 16.34 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.25), residues: 1234 helix: 1.89 (0.21), residues: 617 sheet: 0.11 (0.46), residues: 132 loop : 0.96 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 PHE 0.014 0.001 PHE A1249 TYR 0.022 0.001 TYR A 764 ARG 0.002 0.000 ARG A1121 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LEU cc_start: 0.9470 (mt) cc_final: 0.9214 (tt) REVERT: A 908 ASP cc_start: 0.7192 (t0) cc_final: 0.6845 (t0) REVERT: A 1001 SER cc_start: 0.9488 (m) cc_final: 0.9272 (p) REVERT: A 1055 MET cc_start: 0.8515 (tmm) cc_final: 0.8228 (tmm) outliers start: 35 outliers final: 18 residues processed: 84 average time/residue: 0.2158 time to fit residues: 28.8645 Evaluate side-chains 70 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 113 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12500 Z= 0.254 Angle : 0.586 12.413 17296 Z= 0.307 Chirality : 0.040 0.162 1930 Planarity : 0.003 0.037 1895 Dihedral : 19.350 174.946 2521 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.98 % Allowed : 16.97 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.25), residues: 1234 helix: 2.03 (0.21), residues: 610 sheet: 0.11 (0.46), residues: 132 loop : 0.93 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.004 0.001 HIS A 720 PHE 0.015 0.001 PHE A1249 TYR 0.028 0.002 TYR A1012 ARG 0.002 0.000 ARG A 912 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LEU cc_start: 0.9510 (mt) cc_final: 0.9277 (tt) REVERT: A 908 ASP cc_start: 0.7331 (t0) cc_final: 0.7031 (t0) REVERT: A 1001 SER cc_start: 0.9493 (m) cc_final: 0.9247 (p) REVERT: A 1127 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8293 (mtt-85) outliers start: 33 outliers final: 21 residues processed: 78 average time/residue: 0.2413 time to fit residues: 28.9587 Evaluate side-chains 72 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12500 Z= 0.251 Angle : 0.584 10.120 17296 Z= 0.306 Chirality : 0.039 0.162 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.358 172.550 2521 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.98 % Allowed : 17.06 % Favored : 79.96 % 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: 2.06 (0.25), residues: 1234 helix: 2.04 (0.21), residues: 618 sheet: 0.18 (0.46), residues: 132 loop : 1.01 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 PHE 0.015 0.001 PHE A1249 TYR 0.019 0.001 TYR A 764 ARG 0.007 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LEU cc_start: 0.9526 (mt) cc_final: 0.9318 (tt) REVERT: A 908 ASP cc_start: 0.7326 (t0) cc_final: 0.7041 (t0) REVERT: A 1001 SER cc_start: 0.9468 (m) cc_final: 0.9231 (p) REVERT: A 1055 MET cc_start: 0.8593 (tmm) cc_final: 0.8303 (tmm) outliers start: 33 outliers final: 24 residues processed: 75 average time/residue: 0.2293 time to fit residues: 27.0988 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12500 Z= 0.213 Angle : 0.571 9.249 17296 Z= 0.298 Chirality : 0.039 0.168 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.331 172.067 2521 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.35 % Allowed : 17.42 % Favored : 80.23 % 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: 2.17 (0.25), residues: 1234 helix: 2.18 (0.21), residues: 610 sheet: 0.20 (0.46), residues: 132 loop : 1.01 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 PHE 0.014 0.001 PHE A1249 TYR 0.023 0.001 TYR A1012 ARG 0.006 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 LEU cc_start: 0.9517 (mt) cc_final: 0.9317 (tt) REVERT: A 908 ASP cc_start: 0.7354 (t0) cc_final: 0.7093 (t0) REVERT: A 1001 SER cc_start: 0.9483 (m) cc_final: 0.9240 (p) REVERT: A 1127 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8242 (mtt-85) outliers start: 26 outliers final: 21 residues processed: 78 average time/residue: 0.2430 time to fit residues: 28.9514 Evaluate side-chains 75 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 878 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: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12500 Z= 0.235 Angle : 0.589 10.668 17296 Z= 0.306 Chirality : 0.039 0.148 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.341 171.980 2521 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.53 % Allowed : 17.60 % Favored : 79.87 % 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: 2.13 (0.25), residues: 1234 helix: 2.10 (0.21), residues: 618 sheet: 0.21 (0.47), residues: 132 loop : 1.05 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 191 PHE 0.014 0.001 PHE A1249 TYR 0.017 0.001 TYR A 764 ARG 0.005 0.000 ARG A1003 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6928 (tpt) cc_final: 0.6377 (tpt) REVERT: A 481 LEU cc_start: 0.9523 (mt) cc_final: 0.9321 (tt) REVERT: A 908 ASP cc_start: 0.7439 (t0) cc_final: 0.7133 (t0) REVERT: A 949 LYS cc_start: 0.8695 (ptpp) cc_final: 0.8283 (mtmm) REVERT: A 1001 SER cc_start: 0.9472 (m) cc_final: 0.9207 (p) REVERT: A 1127 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8282 (mtt-85) outliers start: 28 outliers final: 23 residues processed: 75 average time/residue: 0.2509 time to fit residues: 29.3336 Evaluate side-chains 78 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** A1206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 12500 Z= 0.436 Angle : 0.699 11.352 17296 Z= 0.370 Chirality : 0.043 0.157 1930 Planarity : 0.004 0.035 1895 Dihedral : 19.537 172.298 2521 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.89 % Allowed : 17.51 % Favored : 79.60 % 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: 1.77 (0.25), residues: 1234 helix: 1.81 (0.21), residues: 618 sheet: 0.18 (0.47), residues: 132 loop : 0.80 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 483 HIS 0.007 0.001 HIS A 720 PHE 0.022 0.002 PHE A 769 TYR 0.025 0.002 TYR A1012 ARG 0.004 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 48 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7082 (tpt) cc_final: 0.6612 (tpt) REVERT: A 949 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8268 (mtmm) REVERT: A 1001 SER cc_start: 0.9469 (m) cc_final: 0.9249 (p) REVERT: A 1055 MET cc_start: 0.8691 (tmm) cc_final: 0.8446 (tmm) outliers start: 32 outliers final: 27 residues processed: 72 average time/residue: 0.2300 time to fit residues: 25.8455 Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 46 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1210 HIS Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12500 Z= 0.185 Angle : 0.605 10.470 17296 Z= 0.311 Chirality : 0.040 0.154 1930 Planarity : 0.003 0.035 1895 Dihedral : 19.381 167.556 2521 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.99 % Allowed : 18.59 % Favored : 79.42 % 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: 2.04 (0.25), residues: 1234 helix: 2.04 (0.21), residues: 618 sheet: 0.20 (0.47), residues: 132 loop : 0.96 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1258 HIS 0.004 0.001 HIS A 618 PHE 0.015 0.001 PHE A1249 TYR 0.019 0.001 TYR A 764 ARG 0.005 0.000 ARG A1003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6988 (tpt) cc_final: 0.6617 (tpt) REVERT: A 949 LYS cc_start: 0.8681 (ptpp) cc_final: 0.8310 (mtmm) REVERT: A 1001 SER cc_start: 0.9457 (m) cc_final: 0.9209 (p) REVERT: A 1055 MET cc_start: 0.8606 (tmm) cc_final: 0.8353 (tmm) outliers start: 22 outliers final: 21 residues processed: 73 average time/residue: 0.2577 time to fit residues: 29.4740 Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.039954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.029445 restraints weight = 78842.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.030692 restraints weight = 38722.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.031551 restraints weight = 25072.504| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12500 Z= 0.212 Angle : 0.608 13.119 17296 Z= 0.312 Chirality : 0.040 0.153 1930 Planarity : 0.003 0.035 1895 Dihedral : 19.314 170.054 2521 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.90 % Allowed : 18.77 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.25), residues: 1234 helix: 2.08 (0.21), residues: 618 sheet: 0.21 (0.47), residues: 132 loop : 1.02 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 PHE 0.013 0.001 PHE A1249 TYR 0.026 0.001 TYR A1012 ARG 0.008 0.000 ARG A 930 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.34 seconds wall clock time: 36 minutes 52.78 seconds (2212.78 seconds total)