Starting phenix.real_space_refine on Sat Mar 16 17:00:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyt_23601/03_2024/7lyt_23601_updated.pdb" } resolution = 2.9 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= 0.298 sd= 1.017 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 899 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 94 5.49 5 Mg 2 5.21 5 S 24 5.16 5 C 4475 2.51 5 N 1392 2.21 5 O 1644 1.98 5 H 6722 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 53": "OE1" <-> "OE2" Residue "A ASP 72": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 97": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 240": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 285": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 288": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ARG 348": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 359": "OD1" <-> "OD2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 532": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A ARG 595": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A ASP 646": "OD1" <-> "OD2" Residue "A ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A ASP 679": "OD1" <-> "OD2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A ASP 697": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14354 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 11358 Classifications: {'peptide': 712} Link IDs: {'PTRANS': 41, 'TRANS': 670} Chain: "B" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 1259 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 1045 Classifications: {'DNA': 33} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 689 Unusual residues: {' SC': 3} Classifications: {'DNA': 20, 'undetermined': 3} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 19, None: 3} Not linked: pdbres=" DA D 10 " pdbres=" SC D 11 " Not linked: pdbres=" SC D 11 " pdbres=" SC D 12 " Not linked: pdbres=" SC D 12 " pdbres=" SC D 13 " Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10645 SG CYS A 667 19.951 34.452 36.126 1.00 74.36 S ATOM 10691 SG CYS A 670 19.371 30.891 34.874 1.00 74.35 S ATOM 10893 SG CYS A 685 20.918 33.488 32.615 1.00 72.22 S ATOM 10933 SG CYS A 688 17.233 33.644 33.534 1.00 73.11 S Time building chain proxies: 7.36, per 1000 atoms: 0.51 Number of scatterers: 14354 At special positions: 0 Unit cell: (88.085, 98.12, 124.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 24 16.00 P 94 15.00 Mg 2 11.99 O 1644 8.00 N 1392 7.00 C 4475 6.00 H 6722 1.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.45 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 685 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 670 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 688 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 667 " Number of angles added : 6 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 4 sheets defined 39.2% alpha, 7.7% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 9.00 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 25 through 38 Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 44 through 47 No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 126 through 168 removed outlier: 3.882A pdb=" N LEU A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 253 through 256 No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.513A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 372 through 382 removed outlier: 3.513A pdb=" N THR A 375 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.901A pdb=" N GLU A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 468 Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 550 through 565 Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.751A pdb=" N VAL A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.686A pdb=" N ARG A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 Processing sheet with id= A, first strand: chain 'A' and resid 197 through 199 removed outlier: 3.583A pdb=" N HIS A 65 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 310 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS A 69 " --> pdb=" O TRP A 308 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TRP A 308 " --> pdb=" O LYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.705A pdb=" N ALA A 261 " --> pdb=" O VAL A 270 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 388 through 395 removed outlier: 6.163A pdb=" N ARG A 407 " --> pdb=" O PRO A 419 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 606 211 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 12.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 6711 1.09 - 1.35: 2334 1.35 - 1.61: 5600 1.61 - 1.86: 55 1.86 - 2.12: 3 Bond restraints: 14703 Sorted by residual: bond pdb=" P SC D 11 " pdb=" S2P SC D 11 " ideal model delta sigma weight residual 1.882 2.120 -0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" P SC D 13 " pdb=" S2P SC D 13 " ideal model delta sigma weight residual 1.882 2.119 -0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" P SC D 12 " pdb=" S2P SC D 12 " ideal model delta sigma weight residual 1.882 2.118 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C2 SC D 12 " pdb=" N3 SC D 12 " ideal model delta sigma weight residual 1.504 1.317 0.187 2.00e-02 2.50e+03 8.75e+01 bond pdb=" C2 SC D 13 " pdb=" N3 SC D 13 " ideal model delta sigma weight residual 1.504 1.317 0.187 2.00e-02 2.50e+03 8.73e+01 ... (remaining 14698 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.92: 805 106.92 - 113.70: 16705 113.70 - 120.48: 5273 120.48 - 127.25: 3564 127.25 - 134.03: 227 Bond angle restraints: 26574 Sorted by residual: angle pdb=" C3' DG D -8 " pdb=" C2' DG D -8 " pdb=" C1' DG D -8 " ideal model delta sigma weight residual 101.60 104.87 -3.27 1.50e+00 4.44e-01 4.75e+00 angle pdb=" C3' DC C -6 " pdb=" C2' DC C -6 " pdb=" C1' DC C -6 " ideal model delta sigma weight residual 101.60 104.48 -2.88 1.50e+00 4.44e-01 3.69e+00 angle pdb=" N ALA A 74 " pdb=" CA ALA A 74 " pdb=" C ALA A 74 " ideal model delta sigma weight residual 113.29 109.54 3.75 2.00e+00 2.50e-01 3.52e+00 angle pdb=" C LYS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 120.53 125.13 -4.60 2.52e+00 1.57e-01 3.33e+00 angle pdb=" N THR A 409 " pdb=" CA THR A 409 " pdb=" C THR A 409 " ideal model delta sigma weight residual 109.81 107.07 2.74 1.53e+00 4.27e-01 3.20e+00 ... (remaining 26569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.33: 6253 34.33 - 68.65: 456 68.65 - 102.98: 37 102.98 - 137.30: 0 137.30 - 171.63: 2 Dihedral angle restraints: 6748 sinusoidal: 4361 harmonic: 2387 Sorted by residual: dihedral pdb=" O4' G B -20 " pdb=" C1' G B -20 " pdb=" N9 G B -20 " pdb=" C4 G B -20 " ideal model delta sinusoidal sigma weight residual 68.00 144.05 -76.05 1 1.70e+01 3.46e-03 2.52e+01 dihedral pdb=" CA GLN A 410 " pdb=" C GLN A 410 " pdb=" N GLU A 411 " pdb=" CA GLU A 411 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C4' DG D -8 " pdb=" C3' DG D -8 " pdb=" O3' DG D -8 " pdb=" P DC D -7 " ideal model delta sinusoidal sigma weight residual 220.00 48.37 171.63 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 757 0.026 - 0.051: 333 0.051 - 0.077: 101 0.077 - 0.102: 46 0.102 - 0.128: 23 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE A 330 " pdb=" N ILE A 330 " pdb=" C ILE A 330 " pdb=" CB ILE A 330 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 351 " pdb=" N ILE A 351 " pdb=" C ILE A 351 " pdb=" CB ILE A 351 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL A 601 " pdb=" N VAL A 601 " pdb=" C VAL A 601 " pdb=" CB VAL A 601 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 1257 not shown) Planarity restraints: 1857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' SC D 11 " 0.174 2.00e-02 2.50e+03 5.96e-01 7.11e+03 pdb=" C2' SC D 11 " -1.038 2.00e-02 2.50e+03 pdb=" C3' SC D 11 " -0.424 2.00e-02 2.50e+03 pdb=" C4' SC D 11 " 0.418 2.00e-02 2.50e+03 pdb=" C5' SC D 11 " -0.352 2.00e-02 2.50e+03 pdb=" N1 SC D 11 " -0.159 2.00e-02 2.50e+03 pdb=" O3' SC D 11 " 0.314 2.00e-02 2.50e+03 pdb=" O4' SC D 11 " 1.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC D 13 " 0.291 2.00e-02 2.50e+03 5.42e-01 5.88e+03 pdb=" C2' SC D 13 " -0.901 2.00e-02 2.50e+03 pdb=" C3' SC D 13 " -0.390 2.00e-02 2.50e+03 pdb=" C4' SC D 13 " 0.366 2.00e-02 2.50e+03 pdb=" C5' SC D 13 " -0.448 2.00e-02 2.50e+03 pdb=" N1 SC D 13 " -0.206 2.00e-02 2.50e+03 pdb=" O3' SC D 13 " 0.426 2.00e-02 2.50e+03 pdb=" O4' SC D 13 " 0.863 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SC D 12 " 0.404 2.00e-02 2.50e+03 3.54e-01 2.51e+03 pdb=" C2' SC D 12 " -0.337 2.00e-02 2.50e+03 pdb=" C3' SC D 12 " -0.358 2.00e-02 2.50e+03 pdb=" C4' SC D 12 " 0.330 2.00e-02 2.50e+03 pdb=" C5' SC D 12 " -0.401 2.00e-02 2.50e+03 pdb=" N1 SC D 12 " -0.311 2.00e-02 2.50e+03 pdb=" O3' SC D 12 " 0.284 2.00e-02 2.50e+03 pdb=" O4' SC D 12 " 0.388 2.00e-02 2.50e+03 ... (remaining 1854 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 681 2.17 - 2.78: 26188 2.78 - 3.39: 38073 3.39 - 3.99: 50273 3.99 - 4.60: 76154 Nonbonded interactions: 191369 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 146 " pdb=" O2 DC C -5 " model vdw 1.565 1.850 nonbonded pdb="HH22 ARG A 542 " pdb=" O6 DG C -18 " model vdw 1.569 1.850 nonbonded pdb=" OE1 GLU A 7 " pdb=" H GLU A 7 " model vdw 1.604 1.850 nonbonded pdb=" HG1 THR A 340 " pdb=" OP2 DT C 0 " model vdw 1.607 1.850 nonbonded pdb=" O LEU A 14 " pdb=" H PHE A 18 " model vdw 1.625 1.850 ... (remaining 191364 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.190 Extract box with map and model: 2.610 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 59.960 Find NCS groups from input model: 0.280 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.009 0.238 7981 Z= 0.453 Angle : 0.550 7.501 11217 Z= 0.312 Chirality : 0.036 0.128 1260 Planarity : 0.027 0.596 1116 Dihedral : 20.715 171.627 3416 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.33 % Allowed : 4.79 % Favored : 94.88 % 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: -1.59 (0.29), residues: 710 helix: -0.04 (0.30), residues: 281 sheet: -1.48 (0.64), residues: 62 loop : -1.83 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.002 0.001 HIS A 641 PHE 0.010 0.001 PHE A 354 TYR 0.008 0.001 TYR A 221 ARG 0.005 0.001 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 PHE cc_start: 0.8309 (t80) cc_final: 0.7614 (t80) outliers start: 2 outliers final: 1 residues processed: 117 average time/residue: 2.1626 time to fit residues: 268.9354 Evaluate side-chains 83 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 495 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7981 Z= 0.230 Angle : 0.864 20.899 11217 Z= 0.386 Chirality : 0.039 0.129 1260 Planarity : 0.004 0.036 1116 Dihedral : 22.296 172.209 2001 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.82 % Allowed : 13.86 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.30), residues: 710 helix: 0.65 (0.30), residues: 286 sheet: -1.19 (0.66), residues: 62 loop : -1.45 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.003 0.001 HIS A 701 PHE 0.010 0.001 PHE A 354 TYR 0.008 0.001 TYR A 570 ARG 0.003 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 1.9124 time to fit residues: 179.1764 Evaluate side-chains 85 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7981 Z= 0.253 Angle : 0.831 17.511 11217 Z= 0.373 Chirality : 0.039 0.134 1260 Planarity : 0.004 0.030 1116 Dihedral : 22.313 171.852 2001 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.47 % Allowed : 13.86 % Favored : 82.67 % 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: -0.73 (0.30), residues: 710 helix: 0.79 (0.30), residues: 289 sheet: -1.21 (0.67), residues: 60 loop : -1.43 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 308 HIS 0.004 0.001 HIS A 701 PHE 0.011 0.001 PHE A 656 TYR 0.009 0.001 TYR A 570 ARG 0.002 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 79 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8135 (ptt90) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 1.8643 time to fit residues: 182.7464 Evaluate side-chains 88 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 692 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7981 Z= 0.188 Angle : 0.804 16.886 11217 Z= 0.357 Chirality : 0.038 0.131 1260 Planarity : 0.004 0.034 1116 Dihedral : 22.159 170.163 2001 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.48 % Allowed : 16.17 % Favored : 81.35 % 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: -0.40 (0.31), residues: 710 helix: 1.09 (0.31), residues: 289 sheet: -1.22 (0.66), residues: 60 loop : -1.24 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 308 HIS 0.002 0.001 HIS A 65 PHE 0.011 0.001 PHE A 354 TYR 0.010 0.001 TYR A 570 ARG 0.002 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 1.9053 time to fit residues: 182.6863 Evaluate side-chains 86 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 692 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7981 Z= 0.240 Angle : 0.817 17.011 11217 Z= 0.365 Chirality : 0.039 0.130 1260 Planarity : 0.004 0.036 1116 Dihedral : 22.156 169.269 2001 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.30 % Allowed : 16.67 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.31), residues: 710 helix: 1.13 (0.31), residues: 291 sheet: -1.22 (0.65), residues: 60 loop : -1.29 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 308 HIS 0.003 0.001 HIS A 701 PHE 0.009 0.001 PHE A 354 TYR 0.009 0.001 TYR A 570 ARG 0.002 0.000 ARG A 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8145 (ptt90) outliers start: 20 outliers final: 10 residues processed: 94 average time/residue: 1.9713 time to fit residues: 199.1245 Evaluate side-chains 88 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 692 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7981 Z= 0.281 Angle : 0.831 17.090 11217 Z= 0.374 Chirality : 0.040 0.129 1260 Planarity : 0.004 0.035 1116 Dihedral : 22.197 168.366 2001 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.30 % Allowed : 17.82 % Favored : 78.88 % 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: -0.59 (0.31), residues: 710 helix: 0.91 (0.30), residues: 293 sheet: -1.20 (0.64), residues: 60 loop : -1.38 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 623 HIS 0.004 0.001 HIS A 701 PHE 0.009 0.001 PHE A 683 TYR 0.009 0.001 TYR A 570 ARG 0.003 0.000 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8132 (ptt90) REVERT: A 284 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7995 (mtm180) REVERT: A 311 ILE cc_start: 0.9058 (pt) cc_final: 0.8800 (pt) REVERT: A 508 ASN cc_start: 0.5905 (OUTLIER) cc_final: 0.5041 (m-40) outliers start: 20 outliers final: 12 residues processed: 93 average time/residue: 1.9467 time to fit residues: 194.7028 Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 517 PHE Chi-restraints excluded: chain A residue 608 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7981 Z= 0.158 Angle : 0.795 16.342 11217 Z= 0.351 Chirality : 0.037 0.125 1260 Planarity : 0.004 0.037 1116 Dihedral : 22.040 169.297 2001 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.15 % Allowed : 19.47 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.32), residues: 710 helix: 1.42 (0.31), residues: 292 sheet: -1.37 (0.61), residues: 66 loop : -1.14 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 491 HIS 0.002 0.001 HIS A 65 PHE 0.012 0.001 PHE A 354 TYR 0.010 0.001 TYR A 570 ARG 0.003 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 SER cc_start: 0.8490 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 311 ILE cc_start: 0.9035 (pt) cc_final: 0.8780 (pt) REVERT: A 337 ASP cc_start: 0.7504 (m-30) cc_final: 0.7270 (m-30) REVERT: A 508 ASN cc_start: 0.5869 (OUTLIER) cc_final: 0.5091 (m-40) outliers start: 13 outliers final: 7 residues processed: 96 average time/residue: 2.0858 time to fit residues: 214.4062 Evaluate side-chains 92 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 692 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7981 Z= 0.162 Angle : 0.791 16.107 11217 Z= 0.349 Chirality : 0.037 0.126 1260 Planarity : 0.004 0.036 1116 Dihedral : 21.930 168.845 2000 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.15 % Allowed : 20.13 % Favored : 77.72 % 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: 0.05 (0.32), residues: 710 helix: 1.57 (0.32), residues: 292 sheet: -1.29 (0.60), residues: 66 loop : -1.04 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 491 HIS 0.002 0.001 HIS A 614 PHE 0.010 0.001 PHE A 354 TYR 0.009 0.001 TYR A 570 ARG 0.003 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ILE cc_start: 0.9027 (pt) cc_final: 0.8787 (pt) REVERT: A 508 ASN cc_start: 0.5857 (OUTLIER) cc_final: 0.5107 (m-40) outliers start: 13 outliers final: 10 residues processed: 93 average time/residue: 1.9601 time to fit residues: 198.0861 Evaluate side-chains 94 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 692 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7981 Z= 0.329 Angle : 0.845 17.074 11217 Z= 0.383 Chirality : 0.041 0.136 1260 Planarity : 0.005 0.036 1116 Dihedral : 22.124 167.482 2000 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.15 % Allowed : 20.30 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.31), residues: 710 helix: 1.07 (0.31), residues: 287 sheet: -1.15 (0.62), residues: 62 loop : -1.36 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 491 HIS 0.004 0.001 HIS A 701 PHE 0.010 0.001 PHE A 683 TYR 0.011 0.002 TYR A 221 ARG 0.005 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7478 (tm130) REVERT: A 508 ASN cc_start: 0.5959 (OUTLIER) cc_final: 0.5049 (m-40) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 1.9494 time to fit residues: 190.6331 Evaluate side-chains 93 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 586 ASN Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 6 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7981 Z= 0.165 Angle : 0.799 16.353 11217 Z= 0.354 Chirality : 0.037 0.123 1260 Planarity : 0.004 0.037 1116 Dihedral : 22.006 168.498 2000 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.98 % Allowed : 20.46 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.32), residues: 710 helix: 1.42 (0.32), residues: 292 sheet: -1.24 (0.60), residues: 66 loop : -1.13 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 491 HIS 0.002 0.001 HIS A 65 PHE 0.011 0.001 PHE A 354 TYR 0.010 0.001 TYR A 123 ARG 0.003 0.000 ARG A 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 508 ASN cc_start: 0.5859 (OUTLIER) cc_final: 0.5011 (m-40) outliers start: 12 outliers final: 8 residues processed: 92 average time/residue: 1.9272 time to fit residues: 191.4740 Evaluate side-chains 90 residues out of total 606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 608 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.081842 restraints weight = 46766.373| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.61 r_work: 0.3146 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7981 Z= 0.283 Angle : 0.830 16.938 11217 Z= 0.373 Chirality : 0.040 0.128 1260 Planarity : 0.004 0.036 1116 Dihedral : 22.078 167.592 2000 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.15 % Allowed : 20.30 % Favored : 77.56 % 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: -0.38 (0.32), residues: 710 helix: 1.21 (0.31), residues: 287 sheet: -1.22 (0.59), residues: 66 loop : -1.30 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 491 HIS 0.003 0.001 HIS A 701 PHE 0.009 0.001 PHE A 683 TYR 0.012 0.002 TYR A 123 ARG 0.006 0.000 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.18 seconds wall clock time: 91 minutes 27.03 seconds (5487.03 seconds total)