Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:54:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/04_2023/8e28_27828.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/04_2023/8e28_27828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/04_2023/8e28_27828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/04_2023/8e28_27828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/04_2023/8e28_27828.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e28_27828/04_2023/8e28_27828.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 31 5.16 5 C 3638 2.51 5 N 976 2.21 5 O 1129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ASP 620": "OD1" <-> "OD2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A ASP 651": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ASP 682": "OD1" <-> "OD2" Residue "A PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 815": "OE1" <-> "OE2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A GLU 826": "OE1" <-> "OE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 847": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5789 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5489 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 41, 'TRANS': 648} Chain breaks: 2 Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 300 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 8} Time building chain proxies: 3.68, per 1000 atoms: 0.64 Number of scatterers: 5789 At special positions: 0 Unit cell: (79.86, 86.46, 93.06, 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 31 16.00 P 15 15.00 O 1129 8.00 N 976 7.00 C 3638 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: 2.07 Conformation dependent library (CDL) restraints added in 808.6 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1318 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 10 sheets defined 32.0% alpha, 23.2% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 292 through 297 removed outlier: 4.438A pdb=" N ASP A 295 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 297 " --> pdb=" O LYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.889A pdb=" N TYR A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.765A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 503 Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.771A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 521 through 547 removed outlier: 3.846A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.598A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 627 removed outlier: 3.674A pdb=" N SER A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 646 Processing helix chain 'A' and resid 653 through 666 Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.636A pdb=" N GLN A 685 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 687 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 764 removed outlier: 3.557A pdb=" N LEU A 732 " --> pdb=" O ALA A 728 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 7.253A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS A 114 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 235 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252 removed outlier: 6.783A pdb=" N LEU A 319 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR A 299 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU A 251 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 374 removed outlier: 4.424A pdb=" N ARG A 487 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.481A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.430A pdb=" N ALA A 557 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS A 570 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 559 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796 removed outlier: 3.715A pdb=" N GLY A 776 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 785 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL A 774 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 802 through 809 removed outlier: 6.713A pdb=" N VAL A 819 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A 805 " --> pdb=" O THR A 817 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 817 " --> pdb=" O HIS A 805 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N PHE A 807 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 815 " --> pdb=" O PHE A 807 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 612 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1626 1.34 - 1.45: 952 1.45 - 1.57: 3283 1.57 - 1.69: 29 1.69 - 1.81: 47 Bond restraints: 5937 Sorted by residual: bond pdb=" C LEU A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.57e+00 bond pdb=" C GLU A 330 " pdb=" N PRO A 331 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.76e+00 bond pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.47e+00 bond pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.87e+00 ... (remaining 5932 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.72: 265 106.72 - 113.54: 3187 113.54 - 120.36: 2283 120.36 - 127.18: 2298 127.18 - 134.00: 64 Bond angle restraints: 8097 Sorted by residual: angle pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " ideal model delta sigma weight residual 112.00 120.35 -8.35 2.20e+00 2.07e-01 1.44e+01 angle pdb=" CB GLU A 495 " pdb=" CG GLU A 495 " pdb=" CD GLU A 495 " ideal model delta sigma weight residual 112.60 118.96 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" N ASN A 391 " pdb=" CA ASN A 391 " pdb=" C ASN A 391 " ideal model delta sigma weight residual 113.17 117.74 -4.57 1.26e+00 6.30e-01 1.31e+01 angle pdb=" CA LYS A 283 " pdb=" CB LYS A 283 " pdb=" CG LYS A 283 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" N GLY A 482 " pdb=" CA GLY A 482 " pdb=" C GLY A 482 " ideal model delta sigma weight residual 111.37 115.62 -4.25 1.29e+00 6.01e-01 1.09e+01 ... (remaining 8092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 3040 16.13 - 32.25: 423 32.25 - 48.38: 123 48.38 - 64.51: 24 64.51 - 80.63: 11 Dihedral angle restraints: 3621 sinusoidal: 1597 harmonic: 2024 Sorted by residual: dihedral pdb=" CA PHE A 464 " pdb=" C PHE A 464 " pdb=" N SER A 465 " pdb=" CA SER A 465 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 158.88 21.12 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 3618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 633 0.043 - 0.086: 212 0.086 - 0.129: 65 0.129 - 0.172: 16 0.172 - 0.215: 2 Chirality restraints: 928 Sorted by residual: chirality pdb=" CB ILE A 856 " pdb=" CA ILE A 856 " pdb=" CG1 ILE A 856 " pdb=" CG2 ILE A 856 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 99 " pdb=" N VAL A 99 " pdb=" C VAL A 99 " pdb=" CB VAL A 99 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 925 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 444 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO A 445 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 97 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" CG ASP A 97 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 97 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 728 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 729 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.033 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1725 2.83 - 3.35: 4525 3.35 - 3.87: 8908 3.87 - 4.38: 10327 4.38 - 4.90: 18495 Nonbonded interactions: 43980 Sorted by model distance: nonbonded pdb=" OH TYR A 575 " pdb=" OE1 GLU A 583 " model vdw 2.316 2.440 nonbonded pdb=" OH TYR A 696 " pdb=" OP1 U C 13 " model vdw 2.334 2.440 nonbonded pdb=" OD1 ASP A 288 " pdb=" OH TYR A 296 " model vdw 2.348 2.440 nonbonded pdb=" NH2 ARG A 543 " pdb=" OE2 GLU A 584 " model vdw 2.374 2.520 nonbonded pdb=" NE2 GLN A 827 " pdb=" O GLU A 828 " model vdw 2.379 2.520 ... (remaining 43975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 6.200 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.050 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 5937 Z= 0.257 Angle : 0.832 10.320 8097 Z= 0.443 Chirality : 0.049 0.215 928 Planarity : 0.007 0.062 997 Dihedral : 16.454 80.633 2303 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.30), residues: 684 helix: -1.10 (0.32), residues: 210 sheet: -0.21 (0.42), residues: 163 loop : -1.62 (0.31), residues: 311 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.700 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1766 time to fit residues: 14.5636 Evaluate side-chains 48 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.0570 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 5937 Z= 0.292 Angle : 0.558 5.896 8097 Z= 0.289 Chirality : 0.044 0.150 928 Planarity : 0.006 0.051 997 Dihedral : 7.912 72.112 924 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.31), residues: 684 helix: 0.03 (0.36), residues: 204 sheet: 0.01 (0.43), residues: 153 loop : -1.55 (0.30), residues: 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.620 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 54 average time/residue: 0.2194 time to fit residues: 15.5608 Evaluate side-chains 53 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.802 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0582 time to fit residues: 1.0585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.0020 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5937 Z= 0.121 Angle : 0.465 5.275 8097 Z= 0.240 Chirality : 0.040 0.142 928 Planarity : 0.004 0.035 997 Dihedral : 7.678 70.807 924 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.32), residues: 684 helix: 0.50 (0.37), residues: 210 sheet: -0.00 (0.42), residues: 167 loop : -1.27 (0.33), residues: 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.687 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 0.2357 time to fit residues: 18.6872 Evaluate side-chains 56 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.684 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0551 time to fit residues: 1.1345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 5937 Z= 0.232 Angle : 0.511 5.351 8097 Z= 0.262 Chirality : 0.042 0.140 928 Planarity : 0.004 0.036 997 Dihedral : 7.645 70.551 924 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.98 % 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: -0.42 (0.32), residues: 684 helix: 0.70 (0.37), residues: 204 sheet: 0.30 (0.42), residues: 164 loop : -1.24 (0.33), residues: 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.709 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 59 average time/residue: 0.1916 time to fit residues: 15.2631 Evaluate side-chains 61 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.690 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0642 time to fit residues: 1.7878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 34 optimal weight: 0.0980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 579 ASN ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5937 Z= 0.120 Angle : 0.453 5.178 8097 Z= 0.233 Chirality : 0.040 0.139 928 Planarity : 0.004 0.030 997 Dihedral : 7.518 70.494 924 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.33), residues: 684 helix: 0.89 (0.37), residues: 210 sheet: 0.43 (0.43), residues: 163 loop : -1.14 (0.34), residues: 311 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.689 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.2088 time to fit residues: 16.2861 Evaluate side-chains 51 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.692 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0548 time to fit residues: 1.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5937 Z= 0.242 Angle : 0.512 5.292 8097 Z= 0.260 Chirality : 0.042 0.139 928 Planarity : 0.004 0.034 997 Dihedral : 7.558 70.306 924 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.66 % 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: -0.16 (0.33), residues: 684 helix: 0.93 (0.37), residues: 204 sheet: 0.49 (0.44), residues: 158 loop : -1.09 (0.34), residues: 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.700 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 55 average time/residue: 0.2350 time to fit residues: 16.7153 Evaluate side-chains 51 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 5937 Z= 0.144 Angle : 0.466 5.163 8097 Z= 0.237 Chirality : 0.040 0.134 928 Planarity : 0.004 0.030 997 Dihedral : 7.471 70.161 924 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.33), residues: 684 helix: 0.98 (0.37), residues: 210 sheet: 0.70 (0.44), residues: 154 loop : -1.08 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.696 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.2482 time to fit residues: 17.7021 Evaluate side-chains 53 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0605 time to fit residues: 1.2927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 5937 Z= 0.317 Angle : 0.555 5.644 8097 Z= 0.281 Chirality : 0.044 0.143 928 Planarity : 0.004 0.036 997 Dihedral : 7.646 69.810 924 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.33), residues: 684 helix: 0.85 (0.37), residues: 204 sheet: 0.30 (0.44), residues: 160 loop : -1.09 (0.34), residues: 320 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.716 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 57 average time/residue: 0.2107 time to fit residues: 15.8690 Evaluate side-chains 54 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0657 time to fit residues: 1.2977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.0570 chunk 49 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 41 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.128 Angle : 0.463 5.153 8097 Z= 0.237 Chirality : 0.040 0.140 928 Planarity : 0.004 0.031 997 Dihedral : 7.472 69.717 924 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.33), residues: 684 helix: 1.19 (0.37), residues: 204 sheet: 0.68 (0.44), residues: 153 loop : -0.97 (0.34), residues: 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.690 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.2257 time to fit residues: 15.0917 Evaluate side-chains 51 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 44 optimal weight: 0.0970 chunk 59 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 5937 Z= 0.110 Angle : 0.439 5.225 8097 Z= 0.224 Chirality : 0.039 0.131 928 Planarity : 0.004 0.030 997 Dihedral : 7.347 69.403 924 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.33), residues: 684 helix: 1.24 (0.37), residues: 210 sheet: 0.68 (0.43), residues: 150 loop : -0.94 (0.35), residues: 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.691 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2225 time to fit residues: 15.7688 Evaluate side-chains 54 residues out of total 607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.0070 chunk 48 optimal weight: 0.0270 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109684 restraints weight = 7055.693| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.83 r_work: 0.3107 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5937 Z= 0.114 Angle : 0.440 5.233 8097 Z= 0.223 Chirality : 0.039 0.133 928 Planarity : 0.004 0.030 997 Dihedral : 7.195 68.770 924 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 0.33 % 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: 0.26 (0.33), residues: 684 helix: 1.38 (0.38), residues: 210 sheet: 0.69 (0.43), residues: 150 loop : -0.88 (0.35), residues: 324 =============================================================================== Job complete usr+sys time: 1474.22 seconds wall clock time: 27 minutes 15.31 seconds (1635.31 seconds total)