Starting phenix.real_space_refine on Sun Jul 21 13:07:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/07_2024/8pjb_17703_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/07_2024/8pjb_17703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/07_2024/8pjb_17703.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/07_2024/8pjb_17703.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/07_2024/8pjb_17703_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjb_17703/07_2024/8pjb_17703_neut.cif" } resolution = 3.62 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= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7765 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 4933 2.51 5 N 1357 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A ARG 905": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7840 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7632 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 962, 7621 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 962, 7621 Classifications: {'peptide': 962} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 915} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7754 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.40, per 1000 atoms: 1.07 Number of scatterers: 7840 At special positions: 0 Unit cell: (87.132, 96.174, 104.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 11 15.00 Mg 1 11.99 O 1490 8.00 N 1357 7.00 C 4933 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: 3.20 Conformation dependent library (CDL) restraints added in 2.7 seconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 7 sheets defined 52.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.812A pdb=" N ASN A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.085A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 removed outlier: 3.581A pdb=" N ALA A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.702A pdb=" N ARG A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 400 removed outlier: 4.132A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.281A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.589A pdb=" N ARG A 512 " --> pdb=" O ILE A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.567A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 583 through 590 Processing helix chain 'A' and resid 610 through 614 removed outlier: 3.554A pdb=" N LYS A 613 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 3.614A pdb=" N LEU A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 651 removed outlier: 3.587A pdb=" N ASN A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 676 removed outlier: 3.705A pdb=" N THR A 676 " --> pdb=" O PHE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 701 Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 758 through 768 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 843 Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 880 through 890 Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.881A pdb=" N LEU A 914 " --> pdb=" O HIS A 910 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 915' Processing helix chain 'A' and resid 916 through 919 Processing helix chain 'A' and resid 920 through 939 removed outlier: 3.505A pdb=" N ARG A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 951 Processing helix chain 'A' and resid 953 through 975 removed outlier: 3.639A pdb=" N GLY A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 4.125A pdb=" N ILE A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.822A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1078 Processing helix chain 'A' and resid 1086 through 1088 No H-bonds generated for 'chain 'A' and resid 1086 through 1088' Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 4.088A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.870A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 202 removed outlier: 3.545A pdb=" N PHE A 200 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 221 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 5.911A pdb=" N TYR A 263 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 329 removed outlier: 4.206A pdb=" N ALA A 329 " --> pdb=" O LEU A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 removed outlier: 3.986A pdb=" N THR A 486 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE A 436 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N CYS A 485 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL A 438 " --> pdb=" O CYS A 485 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP A 507 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 439 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 504 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N MET A 538 " --> pdb=" O ILE A 504 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL A 506 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 407 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.504A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 655 " --> pdb=" O PHE A 731 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE A 733 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 657 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744 Processing sheet with id=AA7, first strand: chain 'A' and resid 1054 through 1056 removed outlier: 8.236A pdb=" N CYS A1063 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU A1030 " --> pdb=" O CYS A1063 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU A1017 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A1022 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N HIS A1015 " --> pdb=" O LEU A1022 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1017 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: 2.73 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1295 1.30 - 1.43: 1991 1.43 - 1.56: 4627 1.56 - 1.69: 20 1.69 - 1.81: 73 Bond restraints: 8006 Sorted by residual: bond pdb=" CA SER A 222 " pdb=" CB SER A 222 " ideal model delta sigma weight residual 1.533 1.458 0.075 1.60e-02 3.91e+03 2.17e+01 bond pdb=" CA SER A 892 " pdb=" CB SER A 892 " ideal model delta sigma weight residual 1.530 1.453 0.077 1.69e-02 3.50e+03 2.08e+01 bond pdb=" C PRO A 191 " pdb=" O PRO A 191 " ideal model delta sigma weight residual 1.233 1.177 0.056 1.24e-02 6.50e+03 2.06e+01 bond pdb=" CA ALA A 202 " pdb=" CB ALA A 202 " ideal model delta sigma weight residual 1.533 1.455 0.078 1.72e-02 3.38e+03 2.03e+01 bond pdb=" CA SER A 891 " pdb=" CB SER A 891 " ideal model delta sigma weight residual 1.528 1.469 0.058 1.35e-02 5.49e+03 1.85e+01 ... (remaining 8001 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.89: 148 103.89 - 111.96: 3933 111.96 - 120.03: 3401 120.03 - 128.10: 3350 128.10 - 136.16: 49 Bond angle restraints: 10881 Sorted by residual: angle pdb=" C3' U C 9 " pdb=" O3' U C 9 " pdb=" P U C 10 " ideal model delta sigma weight residual 120.20 103.40 16.80 1.50e+00 4.44e-01 1.25e+02 angle pdb=" C3' U C 3 " pdb=" O3' U C 3 " pdb=" P C C 4 " ideal model delta sigma weight residual 120.20 107.33 12.87 1.50e+00 4.44e-01 7.36e+01 angle pdb=" C3' C C 2 " pdb=" O3' C C 2 " pdb=" P U C 3 " ideal model delta sigma weight residual 120.20 108.63 11.57 1.50e+00 4.44e-01 5.95e+01 angle pdb=" N ARG A1059 " pdb=" CA ARG A1059 " pdb=" C ARG A1059 " ideal model delta sigma weight residual 112.72 104.35 8.37 1.14e+00 7.69e-01 5.39e+01 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N SER A 222 " ideal model delta sigma weight residual 114.58 120.82 -6.24 8.60e-01 1.35e+00 5.26e+01 ... (remaining 10876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.73: 4197 18.73 - 37.45: 521 37.45 - 56.18: 163 56.18 - 74.91: 48 74.91 - 93.63: 8 Dihedral angle restraints: 4937 sinusoidal: 2111 harmonic: 2826 Sorted by residual: dihedral pdb=" CD ARG A 905 " pdb=" NE ARG A 905 " pdb=" CZ ARG A 905 " pdb=" NH1 ARG A 905 " ideal model delta sinusoidal sigma weight residual 0.00 -77.76 77.76 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CD ARG A 590 " pdb=" NE ARG A 590 " pdb=" CZ ARG A 590 " pdb=" NH1 ARG A 590 " ideal model delta sinusoidal sigma weight residual 0.00 -64.26 64.26 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " pdb=" CZ ARG A 198 " pdb=" NH1 ARG A 198 " ideal model delta sinusoidal sigma weight residual 0.00 -53.38 53.38 1 1.00e+01 1.00e-02 3.87e+01 ... (remaining 4934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1171 0.112 - 0.224: 64 0.224 - 0.336: 11 0.336 - 0.448: 4 0.448 - 0.561: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" P C C 2 " pdb=" OP1 C C 2 " pdb=" OP2 C C 2 " pdb=" O5' C C 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.86e+00 chirality pdb=" P C C 4 " pdb=" OP1 C C 4 " pdb=" OP2 C C 4 " pdb=" O5' C C 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" P U C 3 " pdb=" OP1 U C 3 " pdb=" OP2 U C 3 " pdb=" O5' U C 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.77 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1248 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 905 " 1.064 9.50e-02 1.11e+02 4.77e-01 1.37e+02 pdb=" NE ARG A 905 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 905 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 905 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 905 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 590 " -0.989 9.50e-02 1.11e+02 4.43e-01 1.19e+02 pdb=" NE ARG A 590 " 0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A 590 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 590 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 590 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 198 " -0.881 9.50e-02 1.11e+02 3.95e-01 9.45e+01 pdb=" NE ARG A 198 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 198 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 198 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 198 " -0.024 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 168 2.66 - 3.22: 7370 3.22 - 3.78: 12253 3.78 - 4.34: 16148 4.34 - 4.90: 26440 Nonbonded interactions: 62379 Sorted by model distance: nonbonded pdb=" OG1 THR A 414 " pdb=" OD2 ASP A 507 " model vdw 2.096 2.440 nonbonded pdb=" OE1 GLN A 621 " pdb=" NH2 ARG A 624 " model vdw 2.266 2.520 nonbonded pdb=" O GLN A 332 " pdb=" OH TYR A 479 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLN A 440 " pdb=" OG SER A 445 " model vdw 2.296 2.440 nonbonded pdb=" OG ASER A1070 " pdb=" NE2 GLN A1073 " model vdw 2.316 2.520 ... (remaining 62374 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=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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 30.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.006 0.078 8006 Z= 0.353 Angle : 0.985 16.796 10881 Z= 0.618 Chirality : 0.063 0.561 1251 Planarity : 0.026 0.477 1371 Dihedral : 18.757 93.633 3097 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 1.15 % Allowed : 5.65 % Favored : 93.20 % Rotamer: Outliers : 4.25 % Allowed : 22.67 % Favored : 73.08 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 958 helix: 1.03 (0.25), residues: 443 sheet: -0.98 (0.43), residues: 148 loop : -1.08 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.007 0.001 HIS A 910 PHE 0.029 0.002 PHE A 240 TYR 0.015 0.002 TYR A 550 ARG 0.008 0.001 ARG A 867 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 10 residues processed: 194 average time/residue: 0.2138 time to fit residues: 55.4705 Evaluate side-chains 123 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 980 CYS Chi-restraints excluded: chain A residue 1057 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.0040 chunk 87 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A1037 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8006 Z= 0.202 Angle : 0.775 14.603 10881 Z= 0.371 Chirality : 0.045 0.261 1251 Planarity : 0.006 0.133 1371 Dihedral : 10.213 82.819 1225 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.33 % Favored : 94.25 % Rotamer: Outliers : 3.54 % Allowed : 27.04 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.06 (0.27), residues: 958 helix: 0.95 (0.24), residues: 457 sheet: -0.66 (0.46), residues: 138 loop : -0.75 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 328 HIS 0.004 0.001 HIS A 910 PHE 0.036 0.001 PHE A 155 TYR 0.028 0.002 TYR A 420 ARG 0.010 0.001 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8626 (p) REVERT: A 253 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7728 (mmmt) REVERT: A 1131 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7513 (ptp-110) outliers start: 29 outliers final: 17 residues processed: 144 average time/residue: 0.1796 time to fit residues: 36.3316 Evaluate side-chains 129 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 892 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 664 ASN ** A1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8006 Z= 0.197 Angle : 0.726 11.758 10881 Z= 0.348 Chirality : 0.043 0.220 1251 Planarity : 0.005 0.113 1371 Dihedral : 9.657 78.147 1211 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.39 % Favored : 95.29 % Rotamer: Outliers : 4.25 % Allowed : 25.15 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.27), residues: 958 helix: 1.06 (0.24), residues: 457 sheet: -0.37 (0.46), residues: 134 loop : -0.82 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 949 HIS 0.007 0.001 HIS A1032 PHE 0.025 0.001 PHE A 155 TYR 0.035 0.002 TYR A 420 ARG 0.007 0.001 ARG A1057 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 119 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 MET cc_start: 0.7099 (tmm) cc_final: 0.6706 (ttp) REVERT: A 891 SER cc_start: 0.7985 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 981 MET cc_start: 0.6318 (ptm) cc_final: 0.6038 (ptm) REVERT: A 1064 LYS cc_start: 0.7406 (tppp) cc_final: 0.7018 (tppt) outliers start: 35 outliers final: 19 residues processed: 145 average time/residue: 0.1591 time to fit residues: 33.4590 Evaluate side-chains 124 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 104 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 0.0030 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8006 Z= 0.187 Angle : 0.726 11.268 10881 Z= 0.350 Chirality : 0.043 0.208 1251 Planarity : 0.005 0.103 1371 Dihedral : 9.334 78.043 1207 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.39 % Favored : 95.29 % Rotamer: Outliers : 3.31 % Allowed : 26.56 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 958 helix: 1.12 (0.24), residues: 454 sheet: -0.25 (0.45), residues: 144 loop : -0.82 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 328 HIS 0.003 0.001 HIS A 646 PHE 0.016 0.001 PHE A1045 TYR 0.031 0.001 TYR A 420 ARG 0.009 0.001 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 MET cc_start: 0.6358 (ptm) cc_final: 0.6052 (ptm) outliers start: 27 outliers final: 21 residues processed: 129 average time/residue: 0.1627 time to fit residues: 30.7024 Evaluate side-chains 120 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1035 SER Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8006 Z= 0.301 Angle : 0.747 10.652 10881 Z= 0.361 Chirality : 0.044 0.203 1251 Planarity : 0.005 0.099 1371 Dihedral : 9.358 79.362 1206 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.50 % Favored : 95.19 % Rotamer: Outliers : 3.90 % Allowed : 25.62 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.28 (0.27), residues: 958 helix: 1.17 (0.24), residues: 456 sheet: -0.24 (0.44), residues: 144 loop : -0.84 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 328 HIS 0.005 0.001 HIS A 510 PHE 0.019 0.001 PHE A1045 TYR 0.009 0.001 TYR A 752 ARG 0.005 0.001 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 MET cc_start: 0.7067 (tmm) cc_final: 0.6760 (ttp) outliers start: 32 outliers final: 26 residues processed: 121 average time/residue: 0.1644 time to fit residues: 28.9385 Evaluate side-chains 124 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8006 Z= 0.179 Angle : 0.714 10.820 10881 Z= 0.340 Chirality : 0.043 0.203 1251 Planarity : 0.005 0.096 1371 Dihedral : 9.104 76.639 1204 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.08 % Favored : 95.71 % Rotamer: Outliers : 3.54 % Allowed : 25.86 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.36 (0.27), residues: 958 helix: 1.25 (0.24), residues: 455 sheet: -0.24 (0.44), residues: 146 loop : -0.81 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 338 HIS 0.005 0.001 HIS A 922 PHE 0.009 0.001 PHE A 518 TYR 0.015 0.001 TYR A 550 ARG 0.004 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 MET cc_start: 0.6981 (tmm) cc_final: 0.6712 (ttt) outliers start: 29 outliers final: 22 residues processed: 131 average time/residue: 0.1732 time to fit residues: 32.6209 Evaluate side-chains 125 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1094 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A1094 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8006 Z= 0.234 Angle : 0.730 11.794 10881 Z= 0.347 Chirality : 0.044 0.201 1251 Planarity : 0.005 0.095 1371 Dihedral : 9.100 77.192 1204 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.71 % Favored : 95.08 % Rotamer: Outliers : 3.07 % Allowed : 26.80 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.49 (0.27), residues: 958 helix: 1.40 (0.24), residues: 455 sheet: -0.18 (0.44), residues: 146 loop : -0.80 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 338 HIS 0.006 0.001 HIS A 910 PHE 0.033 0.001 PHE A 155 TYR 0.009 0.001 TYR A 420 ARG 0.004 0.000 ARG A1080 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 871 MET cc_start: 0.7005 (tmm) cc_final: 0.6749 (ttt) outliers start: 25 outliers final: 22 residues processed: 120 average time/residue: 0.1655 time to fit residues: 29.0182 Evaluate side-chains 121 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 99 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 966 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8006 Z= 0.201 Angle : 0.731 10.874 10881 Z= 0.342 Chirality : 0.043 0.202 1251 Planarity : 0.005 0.093 1371 Dihedral : 9.039 76.057 1204 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.29 % Favored : 95.50 % Rotamer: Outliers : 3.54 % Allowed : 25.97 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.66 (0.27), residues: 958 helix: 1.58 (0.24), residues: 448 sheet: -0.03 (0.45), residues: 146 loop : -0.76 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 338 HIS 0.006 0.001 HIS A 910 PHE 0.033 0.001 PHE A 155 TYR 0.019 0.001 TYR A 550 ARG 0.003 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 871 MET cc_start: 0.7025 (tmm) cc_final: 0.6794 (ttt) outliers start: 29 outliers final: 25 residues processed: 126 average time/residue: 0.1790 time to fit residues: 31.9868 Evaluate side-chains 127 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 253 LYS Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.0030 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 966 GLN A1037 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8006 Z= 0.189 Angle : 0.734 10.984 10881 Z= 0.346 Chirality : 0.043 0.201 1251 Planarity : 0.005 0.093 1371 Dihedral : 9.016 73.561 1204 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.39 % Favored : 95.40 % Rotamer: Outliers : 3.42 % Allowed : 26.33 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 958 helix: 1.69 (0.24), residues: 447 sheet: -0.01 (0.45), residues: 147 loop : -0.77 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 338 HIS 0.008 0.001 HIS A 910 PHE 0.032 0.001 PHE A 155 TYR 0.008 0.001 TYR A 420 ARG 0.008 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 25 residues processed: 122 average time/residue: 0.1903 time to fit residues: 33.0015 Evaluate side-chains 126 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 95 optimal weight: 0.0010 chunk 88 optimal weight: 0.0870 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN A 910 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8006 Z= 0.184 Angle : 0.756 11.050 10881 Z= 0.355 Chirality : 0.043 0.203 1251 Planarity : 0.005 0.091 1371 Dihedral : 8.867 73.516 1200 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.18 % Favored : 95.61 % Rotamer: Outliers : 3.19 % Allowed : 26.92 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.81 (0.28), residues: 958 helix: 1.69 (0.24), residues: 447 sheet: 0.37 (0.46), residues: 140 loop : -0.81 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP A 663 HIS 0.008 0.001 HIS A 910 PHE 0.031 0.001 PHE A 155 TYR 0.016 0.001 TYR A 550 ARG 0.007 0.000 ARG A 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 981 MET cc_start: 0.6558 (ptm) cc_final: 0.6343 (ptm) outliers start: 26 outliers final: 21 residues processed: 129 average time/residue: 0.1692 time to fit residues: 31.4056 Evaluate side-chains 126 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 711 THR Chi-restraints excluded: chain A residue 722 THR Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1056 ILE Chi-restraints excluded: chain A residue 1072 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.071692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055589 restraints weight = 61412.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058467 restraints weight = 25174.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.060479 restraints weight = 14813.622| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8006 Z= 0.218 Angle : 0.759 10.497 10881 Z= 0.358 Chirality : 0.044 0.200 1251 Planarity : 0.005 0.090 1371 Dihedral : 8.879 73.459 1200 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.29 % Favored : 95.50 % Rotamer: Outliers : 2.83 % Allowed : 27.63 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.73 (0.28), residues: 958 helix: 1.67 (0.25), residues: 448 sheet: 0.06 (0.42), residues: 159 loop : -0.82 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 663 HIS 0.007 0.001 HIS A 746 PHE 0.016 0.001 PHE A 155 TYR 0.017 0.001 TYR A 420 ARG 0.008 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.41 seconds wall clock time: 33 minutes 41.90 seconds (2021.90 seconds total)