Starting phenix.real_space_refine on Fri Feb 16 22:36:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/02_2024/7vyv_32215.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/02_2024/7vyv_32215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/02_2024/7vyv_32215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/02_2024/7vyv_32215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/02_2024/7vyv_32215.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vyv_32215/02_2024/7vyv_32215.pdb" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 10572 2.51 5 N 2817 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 252": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ASP 658": "OD1" <-> "OD2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B TYR 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 799": "NH1" <-> "NH2" Residue "B PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C GLU 421": "OE1" <-> "OE2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 620": "OE1" <-> "OE2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 783": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16698 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5566 Classifications: {'peptide': 720} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689} Chain: "B" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5566 Classifications: {'peptide': 720} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689} Chain: "C" Number of atoms: 5566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5566 Classifications: {'peptide': 720} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 689} Time building chain proxies: 8.78, per 1000 atoms: 0.53 Number of scatterers: 16698 At special positions: 0 Unit cell: (93.482, 92.395, 180.442, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 3243 8.00 N 2817 7.00 C 10572 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: 6.58 Conformation dependent library (CDL) restraints added in 3.3 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 20 sheets defined 17.2% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 643 through 646 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 886 through 902 Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 823 through 827 Processing helix chain 'B' and resid 828 through 832 Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 886 through 902 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 301 through 316 Processing helix chain 'C' and resid 354 through 357 Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 662 through 665 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 784 through 788 Processing helix chain 'C' and resid 823 through 827 Processing helix chain 'C' and resid 828 through 832 Processing helix chain 'C' and resid 862 through 867 Processing helix chain 'C' and resid 886 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 225 removed outlier: 5.674A pdb=" N SER A 225 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY A 239 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 263 " --> pdb=" O GLY A 260 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.498A pdb=" N PHE A 274 " --> pdb=" O ASN A 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 318 through 320 current: chain 'A' and resid 375 through 382 removed outlier: 7.150A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 428 through 431 current: chain 'A' and resid 640 through 641 Processing sheet with id=AA3, first strand: chain 'A' and resid 334 through 336 removed outlier: 6.428A pdb=" N LEU A 334 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 364 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 392 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET A 366 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LYS A 389 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR A 418 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE A 391 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY A 442 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN A 441 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN A 501 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY A 499 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 528 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR A 530 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 503 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 532 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLN A 505 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA A 577 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 601 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AA5, first strand: chain 'A' and resid 795 through 801 removed outlier: 3.744A pdb=" N TYR A 751 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR A 757 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE A 838 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 671 " --> pdb=" O ILE A 841 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 843 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N LEU A 669 " --> pdb=" O ALA A 843 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR A 845 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 667 " --> pdb=" O TYR A 845 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 732 removed outlier: 3.972A pdb=" N LEU A 727 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.445A pdb=" N ILE B 841 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN B 672 " --> pdb=" O LEU B 839 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 839 " --> pdb=" O ASN B 672 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 838 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR B 757 " --> pdb=" O PHE B 838 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 220 through 225 removed outlier: 5.659A pdb=" N SER B 225 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 239 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.392A pdb=" N PHE B 274 " --> pdb=" O ASN B 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB3, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AB4, first strand: chain 'B' and resid 727 through 732 removed outlier: 3.974A pdb=" N LEU B 727 " --> pdb=" O PHE B 813 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 858 through 859 removed outlier: 6.393A pdb=" N ILE C 841 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 672 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU C 839 " --> pdb=" O ASN C 672 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N PHE C 838 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR C 757 " --> pdb=" O PHE C 838 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 751 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 220 through 225 removed outlier: 5.570A pdb=" N SER C 225 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY C 239 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 263 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.519A pdb=" N PHE C 274 " --> pdb=" O ASN C 320 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 318 through 320 current: chain 'C' and resid 375 through 382 removed outlier: 7.069A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 405 " --> pdb=" O HIS C 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 428 through 431 current: chain 'C' and resid 640 through 641 Processing sheet with id=AB8, first strand: chain 'C' and resid 334 through 336 removed outlier: 6.493A pdb=" N LEU C 334 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA C 364 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN C 392 " --> pdb=" O ALA C 364 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET C 366 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N PHE C 417 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN C 392 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL C 419 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP C 415 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE C 444 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE C 417 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU C 446 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL C 419 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN C 441 " --> pdb=" O GLY C 499 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLN C 501 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS C 500 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 528 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N ALA C 577 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER C 527 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 579 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA C 529 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N SER C 581 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 531 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR C 601 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N TRP C 627 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE C 602 " --> pdb=" O TRP C 627 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 480 through 482 Processing sheet with id=AC1, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AC2, first strand: chain 'C' and resid 727 through 732 removed outlier: 3.916A pdb=" N LEU C 727 " --> pdb=" O PHE C 813 " (cutoff:3.500A) 370 hydrogen bonds defined for protein. 966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.23 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4700 1.33 - 1.47: 5221 1.47 - 1.60: 7086 1.60 - 1.74: 1 1.74 - 1.87: 104 Bond restraints: 17112 Sorted by residual: bond pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " ideal model delta sigma weight residual 1.520 1.419 0.101 3.00e-02 1.11e+03 1.14e+01 bond pdb=" C LEU A 212 " pdb=" N LYS A 213 " ideal model delta sigma weight residual 1.328 1.273 0.055 1.67e-02 3.59e+03 1.08e+01 bond pdb=" CG GLN A 755 " pdb=" CD GLN A 755 " ideal model delta sigma weight residual 1.516 1.595 -0.079 2.50e-02 1.60e+03 1.00e+01 bond pdb=" CG LEU B 311 " pdb=" CD1 LEU B 311 " ideal model delta sigma weight residual 1.521 1.424 0.097 3.30e-02 9.18e+02 8.57e+00 bond pdb=" CG LEU C 311 " pdb=" CD1 LEU C 311 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.08e+00 ... (remaining 17107 not shown) Histogram of bond angle deviations from ideal: 98.51 - 105.64: 357 105.64 - 112.76: 8562 112.76 - 119.89: 6109 119.89 - 127.01: 8045 127.01 - 134.14: 165 Bond angle restraints: 23238 Sorted by residual: angle pdb=" N LYS A 750 " pdb=" CA LYS A 750 " pdb=" C LYS A 750 " ideal model delta sigma weight residual 112.12 120.32 -8.20 1.34e+00 5.57e-01 3.74e+01 angle pdb=" N ILE B 693 " pdb=" CA ILE B 693 " pdb=" C ILE B 693 " ideal model delta sigma weight residual 110.62 116.49 -5.87 1.02e+00 9.61e-01 3.31e+01 angle pdb=" N ILE A 693 " pdb=" CA ILE A 693 " pdb=" C ILE A 693 " ideal model delta sigma weight residual 110.62 116.47 -5.85 1.02e+00 9.61e-01 3.29e+01 angle pdb=" N GLU A 748 " pdb=" CA GLU A 748 " pdb=" C GLU A 748 " ideal model delta sigma weight residual 111.36 117.34 -5.98 1.09e+00 8.42e-01 3.01e+01 angle pdb=" N GLU C 748 " pdb=" CA GLU C 748 " pdb=" C GLU C 748 " ideal model delta sigma weight residual 111.36 117.33 -5.97 1.09e+00 8.42e-01 3.00e+01 ... (remaining 23233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9243 17.95 - 35.90: 609 35.90 - 53.84: 85 53.84 - 71.79: 16 71.79 - 89.74: 22 Dihedral angle restraints: 9975 sinusoidal: 3783 harmonic: 6192 Sorted by residual: dihedral pdb=" CA ASP C 847 " pdb=" C ASP C 847 " pdb=" N LEU C 848 " pdb=" CA LEU C 848 " ideal model delta harmonic sigma weight residual -180.00 -150.28 -29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ASP B 847 " pdb=" C ASP B 847 " pdb=" N LEU B 848 " pdb=" CA LEU B 848 " ideal model delta harmonic sigma weight residual -180.00 -150.57 -29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ASN C 400 " pdb=" C ASN C 400 " pdb=" N ARG C 401 " pdb=" CA ARG C 401 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 9972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2013 0.081 - 0.163: 455 0.163 - 0.244: 43 0.244 - 0.325: 6 0.325 - 0.407: 3 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA VAL A 885 " pdb=" N VAL A 885 " pdb=" C VAL A 885 " pdb=" CB VAL A 885 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CA VAL B 885 " pdb=" N VAL B 885 " pdb=" C VAL B 885 " pdb=" CB VAL B 885 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA VAL C 885 " pdb=" N VAL C 885 " pdb=" C VAL C 885 " pdb=" CB VAL C 885 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 2517 not shown) Planarity restraints: 3051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 782 " 0.095 2.00e-02 2.50e+03 6.74e-02 1.13e+02 pdb=" CG TRP B 782 " -0.167 2.00e-02 2.50e+03 pdb=" CD1 TRP B 782 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP B 782 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP B 782 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP B 782 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 782 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 782 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 782 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP B 782 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 782 " -0.078 2.00e-02 2.50e+03 5.92e-02 8.77e+01 pdb=" CG TRP C 782 " 0.153 2.00e-02 2.50e+03 pdb=" CD1 TRP C 782 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 TRP C 782 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP C 782 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 782 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 782 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 782 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 782 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 782 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 782 " 0.080 2.00e-02 2.50e+03 5.92e-02 8.76e+01 pdb=" CG TRP A 782 " -0.152 2.00e-02 2.50e+03 pdb=" CD1 TRP A 782 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 782 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 782 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 782 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 782 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 782 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 782 " 0.015 2.00e-02 2.50e+03 ... (remaining 3048 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2883 2.77 - 3.30: 15318 3.30 - 3.83: 28079 3.83 - 4.37: 36520 4.37 - 4.90: 61142 Nonbonded interactions: 143942 Sorted by model distance: nonbonded pdb=" NH1 ARG B 395 " pdb=" O GLU B 423 " model vdw 2.235 2.520 nonbonded pdb=" NH1 ARG A 395 " pdb=" O GLU A 423 " model vdw 2.274 2.520 nonbonded pdb=" O PHE B 291 " pdb=" O ASN B 384 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP C 572 " pdb=" OG SER C 574 " model vdw 2.295 2.440 nonbonded pdb=" O PHE A 291 " pdb=" O ASN A 384 " model vdw 2.324 3.040 ... (remaining 143937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.930 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: 4.680 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 44.940 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 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 0.101 17112 Z= 0.609 Angle : 1.098 9.735 23238 Z= 0.638 Chirality : 0.068 0.407 2520 Planarity : 0.007 0.067 3051 Dihedral : 13.116 89.740 6045 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 10.00 % 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: -1.40 (0.17), residues: 2154 helix: -0.99 (0.28), residues: 303 sheet: -0.22 (0.21), residues: 639 loop : -1.30 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.167 0.010 TRP B 782 HIS 0.012 0.003 HIS C 461 PHE 0.042 0.005 PHE B 382 TYR 0.027 0.004 TYR A 842 ARG 0.009 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.977 Fit side-chains REVERT: A 305 MET cc_start: 0.9226 (tpp) cc_final: 0.8839 (tpp) REVERT: A 453 GLU cc_start: 0.7802 (pm20) cc_final: 0.7383 (pm20) REVERT: B 563 ASP cc_start: 0.8068 (m-30) cc_final: 0.7805 (m-30) REVERT: B 700 MET cc_start: 0.9342 (mmm) cc_final: 0.9077 (mmm) REVERT: C 236 MET cc_start: 0.9186 (mmm) cc_final: 0.8844 (mmm) REVERT: C 660 MET cc_start: 0.9143 (ttt) cc_final: 0.8698 (ttt) REVERT: C 902 ASN cc_start: 0.8611 (m-40) cc_final: 0.8307 (m110) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 1.5930 time to fit residues: 305.5637 Evaluate side-chains 129 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 356 ASN A 400 ASN A 509 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 HIS A 889 ASN A 902 ASN B 193 GLN B 292 ASN B 384 ASN B 400 ASN B 427 GLN B 431 HIS B 456 HIS B 464 ASN B 509 ASN B 744 ASN B 755 GLN B 826 HIS B 873 GLN B 889 ASN C 211 ASN C 219 GLN C 292 ASN C 431 HIS C 501 GLN C 607 ASN C 625 ASN C 744 ASN C 873 GLN C 902 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17112 Z= 0.164 Angle : 0.555 6.988 23238 Z= 0.309 Chirality : 0.046 0.147 2520 Planarity : 0.005 0.044 3051 Dihedral : 5.418 22.547 2337 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.53 % Favored : 96.33 % Rotamer: Outliers : 0.93 % Allowed : 5.92 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.03 (0.17), residues: 2154 helix: -0.13 (0.30), residues: 303 sheet: -0.12 (0.21), residues: 660 loop : -1.15 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP C 782 HIS 0.003 0.001 HIS C 461 PHE 0.014 0.001 PHE C 382 TYR 0.017 0.001 TYR A 256 ARG 0.007 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 2.099 Fit side-chains REVERT: A 453 GLU cc_start: 0.7779 (pm20) cc_final: 0.7411 (pm20) REVERT: A 548 ASN cc_start: 0.8782 (t0) cc_final: 0.8487 (t0) REVERT: A 902 ASN cc_start: 0.8088 (m110) cc_final: 0.7342 (m110) REVERT: B 198 ASP cc_start: 0.8515 (t0) cc_final: 0.8145 (t0) REVERT: B 700 MET cc_start: 0.9303 (mmm) cc_final: 0.8999 (mmm) REVERT: B 855 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7859 (pt0) REVERT: C 236 MET cc_start: 0.9191 (mmm) cc_final: 0.8911 (mmm) REVERT: C 660 MET cc_start: 0.9022 (ttt) cc_final: 0.8667 (ttt) outliers start: 17 outliers final: 3 residues processed: 154 average time/residue: 1.5224 time to fit residues: 258.5782 Evaluate side-chains 137 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 212 optimal weight: 0.0980 chunk 175 optimal weight: 7.9990 chunk 194 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 486 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 GLN B 292 ASN B 367 ASN B 392 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17112 Z= 0.286 Angle : 0.635 7.833 23238 Z= 0.354 Chirality : 0.050 0.173 2520 Planarity : 0.005 0.045 3051 Dihedral : 5.572 24.357 2337 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.69 % Favored : 95.17 % Rotamer: Outliers : 1.32 % Allowed : 7.35 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.98 (0.17), residues: 2154 helix: -0.07 (0.30), residues: 303 sheet: -0.11 (0.21), residues: 660 loop : -1.10 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 782 HIS 0.005 0.001 HIS C 431 PHE 0.024 0.002 PHE B 382 TYR 0.020 0.002 TYR C 609 ARG 0.006 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 1.999 Fit side-chains REVERT: A 548 ASN cc_start: 0.8814 (t0) cc_final: 0.8503 (t0) REVERT: A 902 ASN cc_start: 0.8225 (m110) cc_final: 0.7575 (m110) REVERT: B 198 ASP cc_start: 0.8514 (t0) cc_final: 0.8084 (t0) REVERT: B 700 MET cc_start: 0.9217 (mmm) cc_final: 0.8976 (mmm) REVERT: B 855 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7895 (pt0) REVERT: C 198 ASP cc_start: 0.8477 (t0) cc_final: 0.8026 (t0) REVERT: C 660 MET cc_start: 0.8994 (ttt) cc_final: 0.8595 (ttt) outliers start: 24 outliers final: 7 residues processed: 147 average time/residue: 1.5056 time to fit residues: 245.0030 Evaluate side-chains 138 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.6980 chunk 147 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 367 ASN A 392 ASN A 760 ASN B 292 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17112 Z= 0.351 Angle : 0.686 8.598 23238 Z= 0.382 Chirality : 0.052 0.189 2520 Planarity : 0.005 0.047 3051 Dihedral : 5.767 25.563 2337 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.27 % Favored : 95.59 % Rotamer: Outliers : 1.37 % Allowed : 8.28 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.10 (0.17), residues: 2154 helix: -0.24 (0.29), residues: 303 sheet: -0.19 (0.21), residues: 636 loop : -1.15 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 782 HIS 0.007 0.002 HIS C 826 PHE 0.029 0.002 PHE B 382 TYR 0.020 0.002 TYR C 609 ARG 0.008 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 2.014 Fit side-chains REVERT: A 548 ASN cc_start: 0.8826 (t0) cc_final: 0.8419 (t0) REVERT: A 597 LYS cc_start: 0.9127 (tptp) cc_final: 0.8817 (tmtt) REVERT: A 864 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8506 (ttm170) REVERT: A 902 ASN cc_start: 0.8323 (m110) cc_final: 0.7705 (m110) REVERT: B 198 ASP cc_start: 0.8518 (t0) cc_final: 0.8087 (t0) REVERT: B 700 MET cc_start: 0.9135 (mmm) cc_final: 0.8835 (mmm) REVERT: B 855 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7909 (pt0) REVERT: C 660 MET cc_start: 0.8985 (ttt) cc_final: 0.8576 (ttt) outliers start: 25 outliers final: 9 residues processed: 148 average time/residue: 1.4579 time to fit residues: 239.0950 Evaluate side-chains 143 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 760 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17112 Z= 0.232 Angle : 0.592 8.082 23238 Z= 0.329 Chirality : 0.048 0.157 2520 Planarity : 0.005 0.043 3051 Dihedral : 5.493 24.873 2337 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.18 % Favored : 95.68 % Rotamer: Outliers : 1.26 % Allowed : 8.88 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.05 (0.17), residues: 2154 helix: -0.08 (0.30), residues: 303 sheet: -0.17 (0.20), residues: 696 loop : -1.19 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 782 HIS 0.004 0.001 HIS C 826 PHE 0.024 0.002 PHE B 382 TYR 0.015 0.002 TYR C 609 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.065 Fit side-chains REVERT: A 548 ASN cc_start: 0.8729 (t0) cc_final: 0.8408 (t0) REVERT: A 864 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8415 (ttm170) REVERT: A 902 ASN cc_start: 0.8258 (m110) cc_final: 0.7612 (m110) REVERT: B 198 ASP cc_start: 0.8514 (t0) cc_final: 0.8089 (t0) REVERT: B 855 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7869 (pt0) outliers start: 23 outliers final: 9 residues processed: 146 average time/residue: 1.4893 time to fit residues: 241.8158 Evaluate side-chains 142 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 17 optimal weight: 0.0980 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 760 ASN B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17112 Z= 0.254 Angle : 0.609 8.171 23238 Z= 0.338 Chirality : 0.049 0.158 2520 Planarity : 0.005 0.044 3051 Dihedral : 5.510 25.137 2337 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.36 % Favored : 95.50 % Rotamer: Outliers : 1.54 % Allowed : 9.32 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.02 (0.17), residues: 2154 helix: -0.08 (0.30), residues: 303 sheet: -0.15 (0.20), residues: 675 loop : -1.14 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 782 HIS 0.005 0.001 HIS C 826 PHE 0.025 0.002 PHE B 382 TYR 0.016 0.002 TYR C 488 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.751 Fit side-chains REVERT: A 548 ASN cc_start: 0.8738 (t0) cc_final: 0.8410 (t0) REVERT: A 853 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: A 864 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8429 (ttm170) REVERT: A 902 ASN cc_start: 0.8253 (m110) cc_final: 0.7563 (m110) REVERT: B 198 ASP cc_start: 0.8516 (t0) cc_final: 0.8085 (t0) REVERT: B 855 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7846 (pt0) outliers start: 28 outliers final: 11 residues processed: 147 average time/residue: 1.4103 time to fit residues: 229.7809 Evaluate side-chains 146 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 760 ASN B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS C 873 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17112 Z= 0.284 Angle : 0.631 8.375 23238 Z= 0.350 Chirality : 0.050 0.164 2520 Planarity : 0.005 0.044 3051 Dihedral : 5.573 25.056 2337 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.46 % Favored : 95.40 % Rotamer: Outliers : 1.64 % Allowed : 9.32 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.17), residues: 2154 helix: -0.13 (0.30), residues: 303 sheet: -0.19 (0.20), residues: 696 loop : -1.20 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 695 HIS 0.005 0.001 HIS C 826 PHE 0.026 0.002 PHE B 382 TYR 0.017 0.002 TYR C 488 ARG 0.005 0.001 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 2.074 Fit side-chains REVERT: A 548 ASN cc_start: 0.8756 (t0) cc_final: 0.8426 (t0) REVERT: A 902 ASN cc_start: 0.8260 (m110) cc_final: 0.7588 (m110) REVERT: B 198 ASP cc_start: 0.8520 (t0) cc_final: 0.8075 (t0) REVERT: B 855 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7839 (pt0) outliers start: 30 outliers final: 14 residues processed: 153 average time/residue: 1.3630 time to fit residues: 232.3256 Evaluate side-chains 149 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 456 HIS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17112 Z= 0.160 Angle : 0.533 7.726 23238 Z= 0.294 Chirality : 0.046 0.144 2520 Planarity : 0.004 0.042 3051 Dihedral : 5.222 23.900 2337 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.32 % Favored : 95.54 % Rotamer: Outliers : 1.10 % Allowed : 10.20 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.94 (0.17), residues: 2154 helix: 0.06 (0.31), residues: 303 sheet: -0.10 (0.20), residues: 696 loop : -1.12 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 695 HIS 0.004 0.001 HIS B 456 PHE 0.018 0.001 PHE B 382 TYR 0.013 0.001 TYR A 256 ARG 0.004 0.000 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.794 Fit side-chains REVERT: A 548 ASN cc_start: 0.8626 (t0) cc_final: 0.8293 (t0) REVERT: A 864 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8477 (ttm170) REVERT: A 902 ASN cc_start: 0.8230 (m110) cc_final: 0.7547 (m110) REVERT: B 198 ASP cc_start: 0.8511 (t0) cc_final: 0.8093 (t0) REVERT: B 599 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8824 (tt) REVERT: B 855 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7750 (pt0) outliers start: 20 outliers final: 7 residues processed: 148 average time/residue: 1.4332 time to fit residues: 235.3447 Evaluate side-chains 141 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 864 ARG Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 152 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 760 ASN B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17112 Z= 0.249 Angle : 0.600 7.949 23238 Z= 0.333 Chirality : 0.048 0.154 2520 Planarity : 0.005 0.043 3051 Dihedral : 5.412 24.585 2337 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 1.04 % Allowed : 10.42 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.99 (0.17), residues: 2154 helix: -0.01 (0.30), residues: 303 sheet: -0.13 (0.20), residues: 696 loop : -1.15 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 695 HIS 0.005 0.001 HIS B 456 PHE 0.024 0.002 PHE B 382 TYR 0.016 0.002 TYR C 609 ARG 0.005 0.001 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 135 time to evaluate : 1.901 Fit side-chains REVERT: A 548 ASN cc_start: 0.8706 (t0) cc_final: 0.8374 (t0) REVERT: A 902 ASN cc_start: 0.8258 (m110) cc_final: 0.7572 (m110) REVERT: B 198 ASP cc_start: 0.8510 (t0) cc_final: 0.8089 (t0) REVERT: B 375 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7901 (ttm-80) REVERT: B 599 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8825 (tt) REVERT: B 855 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7802 (pt0) outliers start: 19 outliers final: 9 residues processed: 147 average time/residue: 1.3974 time to fit residues: 228.1670 Evaluate side-chains 143 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 553 ASP Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 456 HIS Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 198 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.0020 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 136 optimal weight: 0.4980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN B 359 ASN B 456 HIS C 219 GLN C 292 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17112 Z= 0.121 Angle : 0.494 7.451 23238 Z= 0.272 Chirality : 0.044 0.139 2520 Planarity : 0.004 0.042 3051 Dihedral : 5.024 23.066 2337 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 0.66 % Allowed : 10.91 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.71 (0.17), residues: 2154 helix: 0.48 (0.32), residues: 285 sheet: -0.05 (0.20), residues: 696 loop : -0.95 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 265 HIS 0.039 0.001 HIS C 456 PHE 0.016 0.001 PHE A 797 TYR 0.012 0.001 TYR A 256 ARG 0.002 0.000 ARG A 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.958 Fit side-chains REVERT: A 290 ASN cc_start: 0.8758 (m-40) cc_final: 0.8335 (m110) REVERT: A 548 ASN cc_start: 0.8522 (t0) cc_final: 0.8175 (t0) REVERT: A 902 ASN cc_start: 0.8167 (m110) cc_final: 0.7479 (m110) REVERT: B 198 ASP cc_start: 0.8497 (t0) cc_final: 0.8150 (t0) REVERT: B 855 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7736 (pt0) outliers start: 12 outliers final: 6 residues processed: 146 average time/residue: 1.4485 time to fit residues: 237.7078 Evaluate side-chains 142 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain B residue 855 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 855 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 760 ASN B 219 GLN B 359 ASN B 456 HIS C 219 GLN C 292 ASN C 456 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.072415 restraints weight = 19891.595| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.27 r_work: 0.2644 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17112 Z= 0.252 Angle : 0.592 7.939 23238 Z= 0.328 Chirality : 0.048 0.152 2520 Planarity : 0.005 0.042 3051 Dihedral : 5.332 24.429 2337 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 0.99 % Allowed : 10.75 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.90 (0.17), residues: 2154 helix: 0.07 (0.30), residues: 303 sheet: -0.09 (0.20), residues: 696 loop : -1.08 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 695 HIS 0.005 0.001 HIS B 456 PHE 0.024 0.002 PHE B 382 TYR 0.015 0.002 TYR C 609 ARG 0.005 0.001 ARG B 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5153.14 seconds wall clock time: 93 minutes 0.82 seconds (5580.82 seconds total)