Starting phenix.real_space_refine on Fri May 17 19:06:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rhn_19177/05_2024/8rhn_19177.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rhn_19177/05_2024/8rhn_19177.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rhn_19177/05_2024/8rhn_19177.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rhn_19177/05_2024/8rhn_19177.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rhn_19177/05_2024/8rhn_19177.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rhn_19177/05_2024/8rhn_19177.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.029 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 173 5.16 5 C 24353 2.51 5 N 6724 2.21 5 O 7118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 367": "OE1" <-> "OE2" Residue "K PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 430": "OE1" <-> "OE2" Residue "K GLU 441": "OE1" <-> "OE2" Residue "K PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 454": "OE1" <-> "OE2" Residue "K GLU 463": "OE1" <-> "OE2" Residue "K GLU 470": "OE1" <-> "OE2" Residue "K TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 633": "OE1" <-> "OE2" Residue "K PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 684": "OE1" <-> "OE2" Residue "K PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 747": "OD1" <-> "OD2" Residue "K GLU 756": "OE1" <-> "OE2" Residue "K ASP 765": "OD1" <-> "OD2" Residue "K TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 829": "OD1" <-> "OD2" Residue "K TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 422": "OE1" <-> "OE2" Residue "L PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 482": "OD1" <-> "OD2" Residue "L GLU 487": "OE1" <-> "OE2" Residue "L ARG 610": "NH1" <-> "NH2" Residue "L PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 696": "OE1" <-> "OE2" Residue "L GLU 704": "OE1" <-> "OE2" Residue "L PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 756": "OE1" <-> "OE2" Residue "L TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 883": "OD1" <-> "OD2" Residue "L TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 430": "OE1" <-> "OE2" Residue "M PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 453": "OD1" <-> "OD2" Residue "M GLU 454": "OE1" <-> "OE2" Residue "M ASP 506": "OD1" <-> "OD2" Residue "M GLU 520": "OE1" <-> "OE2" Residue "M TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 570": "OE1" <-> "OE2" Residue "M GLU 616": "OE1" <-> "OE2" Residue "M GLU 633": "OE1" <-> "OE2" Residue "M GLU 684": "OE1" <-> "OE2" Residue "M GLU 696": "OE1" <-> "OE2" Residue "M GLU 711": "OE1" <-> "OE2" Residue "M PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 829": "OD1" <-> "OD2" Residue "M TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 842": "OE1" <-> "OE2" Residue "M PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 432": "OE1" <-> "OE2" Residue "N PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 482": "OD1" <-> "OD2" Residue "N GLU 487": "OE1" <-> "OE2" Residue "N GLU 570": "OE1" <-> "OE2" Residue "N ARG 655": "NH1" <-> "NH2" Residue "N PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 761": "OE1" <-> "OE2" Residue "N ASP 820": "OD1" <-> "OD2" Residue "N ASP 822": "OD1" <-> "OD2" Residue "N PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 875": "OE1" <-> "OE2" Residue "N PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 883": "OD1" <-> "OD2" Residue "N GLU 886": "OE1" <-> "OE2" Residue "O TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 279": "OE1" <-> "OE2" Residue "O GLU 304": "OE1" <-> "OE2" Residue "O GLU 363": "OE1" <-> "OE2" Residue "O GLU 398": "OE1" <-> "OE2" Residue "O PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 457": "OD1" <-> "OD2" Residue "O PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 564": "OD1" <-> "OD2" Residue "O PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 280": "OE1" <-> "OE2" Residue "P PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 304": "OE1" <-> "OE2" Residue "P GLU 376": "OE1" <-> "OE2" Residue "P PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 471": "OD1" <-> "OD2" Residue "P PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 541": "OD1" <-> "OD2" Residue "P PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 565": "OE1" <-> "OE2" Residue "P GLU 584": "OE1" <-> "OE2" Residue "P GLU 593": "OE1" <-> "OE2" Residue "P PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 177": "OD1" <-> "OD2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 57": "OD1" <-> "OD2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 137": "OE1" <-> "OE2" Residue "J ASP 173": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 38368 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4056 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 32, 'TRANS': 493} Chain: "L" Number of atoms: 4226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4226 Classifications: {'peptide': 545} Link IDs: {'PTRANS': 32, 'TRANS': 512} Chain: "M" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4056 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 32, 'TRANS': 493} Chain: "N" Number of atoms: 4228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4228 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 513} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4016 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 33, 'TRANS': 493} Chain breaks: 2 Chain: "P" Number of atoms: 4027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4027 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 33, 'TRANS': 495} Chain breaks: 2 Chain: "A" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "B" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1585 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "C" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1211 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 3, 'TRANS': 146} Chain breaks: 2 Chain: "D" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1258 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 2 Chain: "E" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1392 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Chain: "F" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1346 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Chain: "G" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1379 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain breaks: 1 Chain: "H" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1358 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 1 Chain: "I" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1320 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 21, 'TRANS': 161} Chain: "J" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1306 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 21, 'TRANS': 159} Time building chain proxies: 18.36, per 1000 atoms: 0.48 Number of scatterers: 38368 At special positions: 0 Unit cell: (148, 143.56, 160.58, 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 173 16.00 O 7118 8.00 N 6724 7.00 C 24353 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: 16.13 Conformation dependent library (CDL) restraints added in 6.7 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9250 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 35 sheets defined 53.2% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'K' and resid 358 through 375 Proline residue: K 372 - end of helix Processing helix chain 'K' and resid 375 through 382 removed outlier: 3.733A pdb=" N PHE K 379 " --> pdb=" O GLN K 375 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 410 Processing helix chain 'K' and resid 421 through 424 Processing helix chain 'K' and resid 429 through 445 Processing helix chain 'K' and resid 454 through 459 removed outlier: 3.509A pdb=" N LEU K 458 " --> pdb=" O GLU K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 488 removed outlier: 3.793A pdb=" N LYS K 471 " --> pdb=" O ASN K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 506 through 510 Processing helix chain 'K' and resid 525 through 537 Processing helix chain 'K' and resid 538 through 540 No H-bonds generated for 'chain 'K' and resid 538 through 540' Processing helix chain 'K' and resid 545 through 555 Processing helix chain 'K' and resid 560 through 581 Processing helix chain 'K' and resid 598 through 609 removed outlier: 3.753A pdb=" N PHE K 602 " --> pdb=" O THR K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 632 through 649 Proline residue: K 646 - end of helix Processing helix chain 'K' and resid 649 through 656 Processing helix chain 'K' and resid 673 through 686 removed outlier: 3.522A pdb=" N GLY K 686 " --> pdb=" O ALA K 682 " (cutoff:3.500A) Processing helix chain 'K' and resid 694 through 698 Processing helix chain 'K' and resid 703 through 719 Processing helix chain 'K' and resid 728 through 732 Processing helix chain 'K' and resid 743 through 758 Processing helix chain 'K' and resid 779 through 784 Processing helix chain 'K' and resid 798 through 813 Processing helix chain 'K' and resid 820 through 829 removed outlier: 4.129A pdb=" N LEU K 824 " --> pdb=" O ASP K 820 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP K 829 " --> pdb=" O ILE K 825 " (cutoff:3.500A) Processing helix chain 'K' and resid 832 through 851 Processing helix chain 'K' and resid 858 through 869 removed outlier: 3.887A pdb=" N PHE K 862 " --> pdb=" O MET K 858 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 375 removed outlier: 3.909A pdb=" N LEU L 371 " --> pdb=" O GLU L 367 " (cutoff:3.500A) Proline residue: L 372 - end of helix Processing helix chain 'L' and resid 375 through 383 removed outlier: 3.631A pdb=" N PHE L 379 " --> pdb=" O GLN L 375 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 409 Processing helix chain 'L' and resid 419 through 424 Processing helix chain 'L' and resid 429 through 445 Processing helix chain 'L' and resid 454 through 459 Processing helix chain 'L' and resid 467 through 483 removed outlier: 3.554A pdb=" N LYS L 471 " --> pdb=" O ASN L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 506 through 511 Processing helix chain 'L' and resid 525 through 538 Processing helix chain 'L' and resid 545 through 556 Processing helix chain 'L' and resid 560 through 581 Processing helix chain 'L' and resid 587 through 595 Processing helix chain 'L' and resid 598 through 609 Processing helix chain 'L' and resid 625 through 629 Processing helix chain 'L' and resid 632 through 645 Processing helix chain 'L' and resid 648 through 656 Processing helix chain 'L' and resid 673 through 686 Processing helix chain 'L' and resid 694 through 698 Processing helix chain 'L' and resid 703 through 719 Processing helix chain 'L' and resid 742 through 758 removed outlier: 3.811A pdb=" N ALA L 746 " --> pdb=" O ALA L 742 " (cutoff:3.500A) Processing helix chain 'L' and resid 774 through 778 Processing helix chain 'L' and resid 779 through 784 removed outlier: 3.720A pdb=" N MET L 783 " --> pdb=" O ASP L 779 " (cutoff:3.500A) Processing helix chain 'L' and resid 798 through 811 Processing helix chain 'L' and resid 820 through 827 removed outlier: 3.502A pdb=" N LEU L 824 " --> pdb=" O ASP L 820 " (cutoff:3.500A) Processing helix chain 'L' and resid 832 through 851 Processing helix chain 'L' and resid 858 through 869 Processing helix chain 'L' and resid 874 through 887 removed outlier: 3.934A pdb=" N ARG L 878 " --> pdb=" O PRO L 874 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 375 Proline residue: M 372 - end of helix Processing helix chain 'M' and resid 375 through 382 removed outlier: 4.105A pdb=" N PHE M 379 " --> pdb=" O GLN M 375 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR M 382 " --> pdb=" O LEU M 378 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 411 Processing helix chain 'M' and resid 420 through 424 Processing helix chain 'M' and resid 429 through 445 Processing helix chain 'M' and resid 454 through 459 removed outlier: 4.131A pdb=" N LEU M 458 " --> pdb=" O GLU M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 467 through 484 removed outlier: 4.120A pdb=" N LYS M 471 " --> pdb=" O ASN M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 525 through 538 Processing helix chain 'M' and resid 545 through 555 Processing helix chain 'M' and resid 560 through 583 removed outlier: 3.504A pdb=" N GLN M 583 " --> pdb=" O ILE M 579 " (cutoff:3.500A) Processing helix chain 'M' and resid 587 through 591 Processing helix chain 'M' and resid 598 through 608 removed outlier: 3.724A pdb=" N PHE M 602 " --> pdb=" O THR M 598 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP M 608 " --> pdb=" O GLN M 604 " (cutoff:3.500A) Processing helix chain 'M' and resid 625 through 629 Processing helix chain 'M' and resid 632 through 653 Proline residue: M 646 - end of helix Proline residue: M 650 - end of helix Processing helix chain 'M' and resid 654 through 657 Processing helix chain 'M' and resid 673 through 686 removed outlier: 3.589A pdb=" N GLY M 686 " --> pdb=" O ALA M 682 " (cutoff:3.500A) Processing helix chain 'M' and resid 694 through 698 Processing helix chain 'M' and resid 703 through 719 Processing helix chain 'M' and resid 728 through 732 Processing helix chain 'M' and resid 742 through 758 removed outlier: 3.692A pdb=" N ALA M 746 " --> pdb=" O ALA M 742 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG M 748 " --> pdb=" O ASN M 744 " (cutoff:3.500A) Processing helix chain 'M' and resid 774 through 778 Processing helix chain 'M' and resid 779 through 784 Processing helix chain 'M' and resid 798 through 813 Processing helix chain 'M' and resid 820 through 828 removed outlier: 4.033A pdb=" N LEU M 824 " --> pdb=" O ASP M 820 " (cutoff:3.500A) Processing helix chain 'M' and resid 832 through 851 Processing helix chain 'M' and resid 858 through 869 Processing helix chain 'N' and resid 351 through 355 Processing helix chain 'N' and resid 358 through 375 removed outlier: 4.133A pdb=" N LEU N 371 " --> pdb=" O GLU N 367 " (cutoff:3.500A) Proline residue: N 372 - end of helix Processing helix chain 'N' and resid 375 through 381 Processing helix chain 'N' and resid 400 through 412 Processing helix chain 'N' and resid 419 through 424 removed outlier: 4.041A pdb=" N ILE N 424 " --> pdb=" O GLY N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 429 through 445 removed outlier: 3.630A pdb=" N ARG N 445 " --> pdb=" O GLU N 441 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 459 removed outlier: 3.801A pdb=" N LEU N 458 " --> pdb=" O GLU N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 467 through 483 removed outlier: 3.683A pdb=" N LYS N 471 " --> pdb=" O ASN N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 506 through 511 Processing helix chain 'N' and resid 525 through 538 Processing helix chain 'N' and resid 545 through 555 Processing helix chain 'N' and resid 560 through 583 Processing helix chain 'N' and resid 587 through 593 Processing helix chain 'N' and resid 598 through 607 removed outlier: 3.974A pdb=" N ASN N 607 " --> pdb=" O LEU N 603 " (cutoff:3.500A) Processing helix chain 'N' and resid 625 through 629 removed outlier: 3.516A pdb=" N ILE N 629 " --> pdb=" O TRP N 626 " (cutoff:3.500A) Processing helix chain 'N' and resid 632 through 649 Proline residue: N 646 - end of helix Processing helix chain 'N' and resid 649 through 657 removed outlier: 3.752A pdb=" N ARG N 655 " --> pdb=" O GLU N 651 " (cutoff:3.500A) Processing helix chain 'N' and resid 673 through 686 Processing helix chain 'N' and resid 695 through 698 Processing helix chain 'N' and resid 703 through 719 Processing helix chain 'N' and resid 741 through 759 removed outlier: 4.181A pdb=" N VAL N 745 " --> pdb=" O GLY N 741 " (cutoff:3.500A) Processing helix chain 'N' and resid 774 through 778 removed outlier: 3.549A pdb=" N ILE N 778 " --> pdb=" O PRO N 775 " (cutoff:3.500A) Processing helix chain 'N' and resid 798 through 811 Processing helix chain 'N' and resid 820 through 827 removed outlier: 3.625A pdb=" N LEU N 824 " --> pdb=" O ASP N 820 " (cutoff:3.500A) Processing helix chain 'N' and resid 832 through 851 Processing helix chain 'N' and resid 858 through 869 Processing helix chain 'N' and resid 874 through 888 removed outlier: 3.950A pdb=" N ARG N 878 " --> pdb=" O PRO N 874 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 221 Proline residue: O 219 - end of helix Processing helix chain 'O' and resid 246 through 259 Processing helix chain 'O' and resid 268 through 271 removed outlier: 4.207A pdb=" N GLN O 271 " --> pdb=" O PRO O 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 268 through 271' Processing helix chain 'O' and resid 276 through 294 Processing helix chain 'O' and resid 316 through 333 removed outlier: 3.592A pdb=" N ARG O 320 " --> pdb=" O ALA O 316 " (cutoff:3.500A) Processing helix chain 'O' and resid 346 through 350 Processing helix chain 'O' and resid 351 through 355 Processing helix chain 'O' and resid 370 through 383 Processing helix chain 'O' and resid 392 through 400 removed outlier: 3.605A pdb=" N LEU O 396 " --> pdb=" O ASP O 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 404 through 423 Processing helix chain 'O' and resid 433 through 443 removed outlier: 3.550A pdb=" N PHE O 437 " --> pdb=" O ASP O 433 " (cutoff:3.500A) Processing helix chain 'O' and resid 462 through 466 Processing helix chain 'O' and resid 469 through 480 Processing helix chain 'O' and resid 480 through 486 removed outlier: 3.987A pdb=" N LEU O 484 " --> pdb=" O ILE O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 486 through 494 Processing helix chain 'O' and resid 510 through 521 removed outlier: 3.858A pdb=" N LEU O 514 " --> pdb=" O ALA O 510 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 535 Processing helix chain 'O' and resid 540 through 556 removed outlier: 4.001A pdb=" N LYS O 544 " --> pdb=" O GLY O 540 " (cutoff:3.500A) Processing helix chain 'O' and resid 565 through 570 Processing helix chain 'O' and resid 580 through 595 removed outlier: 3.510A pdb=" N GLU O 584 " --> pdb=" O CYS O 580 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP O 595 " --> pdb=" O LEU O 591 " (cutoff:3.500A) Processing helix chain 'O' and resid 596 through 598 No H-bonds generated for 'chain 'O' and resid 596 through 598' Processing helix chain 'O' and resid 635 through 640 removed outlier: 3.748A pdb=" N LEU O 639 " --> pdb=" O ASP O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 654 through 667 Processing helix chain 'O' and resid 676 through 684 removed outlier: 4.368A pdb=" N LEU O 680 " --> pdb=" O SER O 676 " (cutoff:3.500A) Processing helix chain 'O' and resid 688 through 708 removed outlier: 3.503A pdb=" N ASN O 707 " --> pdb=" O ALA O 703 " (cutoff:3.500A) Processing helix chain 'O' and resid 717 through 726 Processing helix chain 'O' and resid 733 through 745 Processing helix chain 'P' and resid 205 through 221 Proline residue: P 219 - end of helix Processing helix chain 'P' and resid 246 through 259 Processing helix chain 'P' and resid 266 through 271 removed outlier: 3.990A pdb=" N GLN P 271 " --> pdb=" O PRO P 268 " (cutoff:3.500A) Processing helix chain 'P' and resid 276 through 296 Processing helix chain 'P' and resid 316 through 333 removed outlier: 3.793A pdb=" N ARG P 320 " --> pdb=" O ALA P 316 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 350 Processing helix chain 'P' and resid 351 through 355 Processing helix chain 'P' and resid 370 through 383 Processing helix chain 'P' and resid 392 through 400 removed outlier: 3.511A pdb=" N LEU P 396 " --> pdb=" O ASP P 392 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 422 Processing helix chain 'P' and resid 433 through 444 Processing helix chain 'P' and resid 469 through 480 Processing helix chain 'P' and resid 481 through 490 removed outlier: 4.110A pdb=" N LYS P 485 " --> pdb=" O GLU P 481 " (cutoff:3.500A) Proline residue: P 487 - end of helix removed outlier: 3.515A pdb=" N PHE P 490 " --> pdb=" O PHE P 486 " (cutoff:3.500A) Processing helix chain 'P' and resid 510 through 521 removed outlier: 3.921A pdb=" N LEU P 514 " --> pdb=" O ALA P 510 " (cutoff:3.500A) Processing helix chain 'P' and resid 530 through 535 Processing helix chain 'P' and resid 541 through 556 Processing helix chain 'P' and resid 565 through 570 Processing helix chain 'P' and resid 581 through 594 Processing helix chain 'P' and resid 630 through 634 Processing helix chain 'P' and resid 635 through 640 Processing helix chain 'P' and resid 654 through 666 Processing helix chain 'P' and resid 676 through 684 removed outlier: 3.867A pdb=" N LEU P 680 " --> pdb=" O SER P 676 " (cutoff:3.500A) Processing helix chain 'P' and resid 688 through 707 Processing helix chain 'P' and resid 715 through 726 removed outlier: 4.202A pdb=" N PHE P 719 " --> pdb=" O LYS P 715 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LYS P 724 " --> pdb=" O LEU P 720 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR P 725 " --> pdb=" O LYS P 721 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 745 Processing helix chain 'A' and resid 5 through 51 Proline residue: A 19 - end of helix removed outlier: 3.819A pdb=" N CYS A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Proline residue: A 37 - end of helix Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 69 through 117 removed outlier: 4.346A pdb=" N LYS A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 134 through 161 Processing helix chain 'A' and resid 169 through 172 Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.764A pdb=" N ASP A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'B' and resid 7 through 52 Proline residue: B 19 - end of helix Proline residue: B 37 - end of helix Processing helix chain 'B' and resid 60 through 65 removed outlier: 4.036A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 117 Processing helix chain 'B' and resid 123 through 127 removed outlier: 4.103A pdb=" N GLN B 127 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.782A pdb=" N TYR B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.699A pdb=" N ILE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 3.641A pdb=" N SER B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 4.390A pdb=" N PHE B 199 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 58 Processing helix chain 'C' and resid 88 through 124 Processing helix chain 'C' and resid 142 through 171 Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.818A pdb=" N THR C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 removed outlier: 3.760A pdb=" N LEU C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 57 Processing helix chain 'D' and resid 86 through 123 Processing helix chain 'D' and resid 142 through 171 removed outlier: 4.095A pdb=" N TYR D 146 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.853A pdb=" N THR D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 4.030A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 156 through 169 removed outlier: 3.708A pdb=" N THR E 161 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N CYS E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG E 166 " --> pdb=" O GLY E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 186 removed outlier: 3.925A pdb=" N GLY E 185 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG E 186 " --> pdb=" O PHE E 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 182 through 186' Processing helix chain 'F' and resid 60 through 66 removed outlier: 3.761A pdb=" N SER F 66 " --> pdb=" O THR F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'G' and resid 71 through 78 Processing helix chain 'G' and resid 114 through 121 Processing helix chain 'G' and resid 156 through 168 Processing helix chain 'G' and resid 182 through 186 removed outlier: 3.759A pdb=" N GLY G 185 " --> pdb=" O THR G 182 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 186 " --> pdb=" O PHE G 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 182 through 186' Processing helix chain 'H' and resid 60 through 66 removed outlier: 3.930A pdb=" N SER H 66 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'I' and resid 20 through 26 removed outlier: 4.000A pdb=" N THR I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 40 Processing helix chain 'I' and resid 84 through 88 Processing helix chain 'I' and resid 95 through 97 No H-bonds generated for 'chain 'I' and resid 95 through 97' Processing helix chain 'I' and resid 127 through 139 removed outlier: 3.889A pdb=" N VAL I 131 " --> pdb=" O ASN I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 removed outlier: 4.393A pdb=" N GLY J 25 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 40 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 124 through 128 removed outlier: 4.371A pdb=" N ASN J 127 " --> pdb=" O GLY J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 139 Processing sheet with id=AA1, first strand: chain 'K' and resid 498 through 499 removed outlier: 8.169A pdb=" N THR K 499 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU K 392 " --> pdb=" O THR K 499 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 414 through 419 removed outlier: 6.465A pdb=" N TYR K 414 " --> pdb=" O ILE K 449 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE K 451 " --> pdb=" O TYR K 414 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER K 416 " --> pdb=" O PHE K 451 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ASP K 453 " --> pdb=" O SER K 416 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE K 418 " --> pdb=" O ASP K 453 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 689 through 690 removed outlier: 3.528A pdb=" N LEU K 690 " --> pdb=" O ILE K 723 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR K 767 " --> pdb=" O SER K 722 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE K 724 " --> pdb=" O THR K 767 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU K 769 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL K 664 " --> pdb=" O ILE K 768 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 770 " --> pdb=" O VAL K 664 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLY K 663 " --> pdb=" O ARG K 790 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE K 792 " --> pdb=" O GLY K 663 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU K 665 " --> pdb=" O ILE K 792 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 414 through 418 removed outlier: 6.154A pdb=" N TYR L 414 " --> pdb=" O ILE L 449 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE L 451 " --> pdb=" O TYR L 414 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER L 416 " --> pdb=" O PHE L 451 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ASP L 453 " --> pdb=" O SER L 416 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE L 418 " --> pdb=" O ASP L 453 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU L 494 " --> pdb=" O SER L 448 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY L 497 " --> pdb=" O VAL L 390 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR L 499 " --> pdb=" O LEU L 392 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLY L 389 " --> pdb=" O LYS L 517 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ILE L 519 " --> pdb=" O GLY L 389 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU L 391 " --> pdb=" O ILE L 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 689 through 690 removed outlier: 6.422A pdb=" N LEU L 690 " --> pdb=" O PHE L 725 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ASP L 727 " --> pdb=" O LEU L 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE L 724 " --> pdb=" O LEU L 769 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ALA L 771 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE L 726 " --> pdb=" O ALA L 771 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL L 664 " --> pdb=" O ILE L 768 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY L 663 " --> pdb=" O ARG L 790 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE L 792 " --> pdb=" O GLY L 663 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU L 665 " --> pdb=" O ILE L 792 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 390 through 393 Processing sheet with id=AA7, first strand: chain 'M' and resid 414 through 418 removed outlier: 3.611A pdb=" N SER M 416 " --> pdb=" O ILE M 449 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE M 451 " --> pdb=" O SER M 416 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE M 418 " --> pdb=" O PHE M 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 688 through 689 removed outlier: 6.374A pdb=" N ASN M 688 " --> pdb=" O ILE M 723 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER M 722 " --> pdb=" O THR M 767 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N LEU M 769 " --> pdb=" O SER M 722 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL M 664 " --> pdb=" O ILE M 768 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY M 663 " --> pdb=" O ILE M 788 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 692 through 693 removed outlier: 6.911A pdb=" N ILE M 692 " --> pdb=" O ASP M 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'N' and resid 414 through 418 removed outlier: 3.564A pdb=" N PHE N 451 " --> pdb=" O SER N 416 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP N 453 " --> pdb=" O ILE N 418 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 494 " --> pdb=" O SER N 448 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL N 390 " --> pdb=" O VAL N 495 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY N 497 " --> pdb=" O VAL N 390 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE N 519 " --> pdb=" O GLY N 389 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU N 391 " --> pdb=" O ILE N 519 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 689 through 693 removed outlier: 6.259A pdb=" N LEU N 690 " --> pdb=" O PHE N 725 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASP N 727 " --> pdb=" O LEU N 690 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE N 692 " --> pdb=" O ASP N 727 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE N 724 " --> pdb=" O LEU N 769 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ALA N 771 " --> pdb=" O ILE N 724 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N PHE N 726 " --> pdb=" O ALA N 771 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL N 664 " --> pdb=" O ALA N 770 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N THR N 772 " --> pdb=" O VAL N 664 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU N 666 " --> pdb=" O THR N 772 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 341 through 344 removed outlier: 6.373A pdb=" N VAL O 237 " --> pdb=" O GLY O 342 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR O 344 " --> pdb=" O VAL O 237 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU O 239 " --> pdb=" O THR O 344 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU O 238 " --> pdb=" O VAL O 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'O' and resid 265 through 266 removed outlier: 7.261A pdb=" N VAL O 265 " --> pdb=" O ASP O 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'O' and resid 525 through 529 removed outlier: 6.313A pdb=" N VAL O 501 " --> pdb=" O ALA O 626 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N THR O 628 " --> pdb=" O VAL O 501 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU O 503 " --> pdb=" O THR O 628 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE O 648 " --> pdb=" O GLY O 500 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU O 502 " --> pdb=" O ILE O 648 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 263 through 265 removed outlier: 4.118A pdb=" N LEU P 263 " --> pdb=" O LEU P 299 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE P 301 " --> pdb=" O LEU P 263 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL P 265 " --> pdb=" O PHE P 301 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASP P 303 " --> pdb=" O VAL P 265 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER P 298 " --> pdb=" O VAL P 339 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL P 341 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU P 300 " --> pdb=" O VAL P 341 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ALA P 343 " --> pdb=" O LEU P 300 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU P 302 " --> pdb=" O ALA P 343 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU P 238 " --> pdb=" O VAL P 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 525 through 529 removed outlier: 6.622A pdb=" N SER P 525 " --> pdb=" O ILE P 560 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE P 562 " --> pdb=" O SER P 525 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL P 527 " --> pdb=" O PHE P 562 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA P 559 " --> pdb=" O MET P 623 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE P 625 " --> pdb=" O ALA P 559 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU P 561 " --> pdb=" O ILE P 625 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA P 627 " --> pdb=" O LEU P 561 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU P 563 " --> pdb=" O ALA P 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL P 501 " --> pdb=" O ILE P 624 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR P 628 " --> pdb=" O LEU P 503 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY P 500 " --> pdb=" O LYS P 646 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ILE P 648 " --> pdb=" O GLY P 500 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU P 502 " --> pdb=" O ILE P 648 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 67 through 69 removed outlier: 5.901A pdb=" N ILE E 68 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL E 111 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR E 47 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU E 113 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR E 49 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 201 through 203 removed outlier: 5.820A pdb=" N VAL E 192 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA E 147 " --> pdb=" O VAL E 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 325 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 201 through 203 removed outlier: 5.820A pdb=" N VAL E 192 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA E 147 " --> pdb=" O VAL E 192 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 46 through 50 removed outlier: 3.528A pdb=" N LEU F 113 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 137 through 140 Processing sheet with id=AC4, first strand: chain 'F' and resid 178 through 183 removed outlier: 3.609A pdb=" N ARG F 186 " --> pdb=" O PHE F 183 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP F 145 " --> pdb=" O LEU F 193 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL F 195 " --> pdb=" O GLU F 143 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLU F 143 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 45 through 47 removed outlier: 5.945A pdb=" N ILE G 68 " --> pdb=" O TRP G 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 178 through 179 removed outlier: 3.701A pdb=" N LEU G 190 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 178 through 179 removed outlier: 3.701A pdb=" N LEU G 190 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL G 192 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA G 147 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG G 194 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU G 142 " --> pdb=" O ARG G 331 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN G 333 " --> pdb=" O GLU G 142 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET G 144 " --> pdb=" O ASN G 333 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 47 through 50 removed outlier: 6.802A pdb=" N THR H 47 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU H 113 " --> pdb=" O THR H 47 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR H 49 " --> pdb=" O LEU H 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AD1, first strand: chain 'H' and resid 137 through 140 removed outlier: 6.475A pdb=" N ALA H 137 " --> pdb=" O PHE H 323 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N PHE H 325 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU H 139 " --> pdb=" O PHE H 325 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR H 324 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 195 through 196 removed outlier: 6.341A pdb=" N MET H 144 " --> pdb=" O ASN H 333 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 182 through 183 removed outlier: 3.630A pdb=" N ARG H 186 " --> pdb=" O PHE H 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 29 through 31 Processing sheet with id=AD5, first strand: chain 'I' and resid 164 through 168 removed outlier: 5.851A pdb=" N ILE I 165 " --> pdb=" O TRP I 113 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TRP I 113 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL I 110 " --> pdb=" O SER I 185 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 143 through 144 Processing sheet with id=AD7, first strand: chain 'J' and resid 15 through 16 removed outlier: 5.904A pdb=" N LYS J 15 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU J 74 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN J 73 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 15 through 16 removed outlier: 5.904A pdb=" N LYS J 15 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU J 74 " --> pdb=" O LYS J 15 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN J 73 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS J 78 " --> pdb=" O LEU J 58 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS J 148 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU J 163 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL J 115 " --> pdb=" O LEU J 163 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE J 165 " --> pdb=" O TRP J 113 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP J 113 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL J 110 " --> pdb=" O ARG J 183 " (cutoff:3.500A) 1891 hydrogen bonds defined for protein. 5439 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: 15.81 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6568 1.31 - 1.44: 8958 1.44 - 1.57: 23219 1.57 - 1.70: 0 1.70 - 1.82: 272 Bond restraints: 39017 Sorted by residual: bond pdb=" N PRO P 483 " pdb=" CD PRO P 483 " ideal model delta sigma weight residual 1.473 1.329 0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" N PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 1.473 1.418 0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" CA LEU A 168 " pdb=" C LEU A 168 " ideal model delta sigma weight residual 1.522 1.458 0.064 1.72e-02 3.38e+03 1.39e+01 bond pdb=" C PRO G 60 " pdb=" O PRO G 60 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" N LYS G 58 " pdb=" CA LYS G 58 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.18e-02 7.18e+03 8.28e+00 ... (remaining 39012 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.56: 1047 105.56 - 112.72: 21568 112.72 - 119.87: 12566 119.87 - 127.02: 17236 127.02 - 134.17: 426 Bond angle restraints: 52843 Sorted by residual: angle pdb=" C HIS A 186 " pdb=" CA HIS A 186 " pdb=" CB HIS A 186 " ideal model delta sigma weight residual 109.54 125.39 -15.85 1.84e+00 2.95e-01 7.42e+01 angle pdb=" C ILE G 59 " pdb=" N PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 125.00 103.32 21.68 4.10e+00 5.95e-02 2.80e+01 angle pdb=" CA ASP G 56 " pdb=" C ASP G 56 " pdb=" N ASP G 57 " ideal model delta sigma weight residual 117.23 110.91 6.32 1.31e+00 5.83e-01 2.32e+01 angle pdb=" C ILE G 59 " pdb=" CA ILE G 59 " pdb=" CB ILE G 59 " ideal model delta sigma weight residual 111.36 119.46 -8.10 1.82e+00 3.02e-01 1.98e+01 angle pdb=" CA HIS A 186 " pdb=" CB HIS A 186 " pdb=" CG HIS A 186 " ideal model delta sigma weight residual 113.80 118.00 -4.20 1.00e+00 1.00e+00 1.77e+01 ... (remaining 52838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.47: 21861 18.47 - 36.93: 1931 36.93 - 55.40: 242 55.40 - 73.87: 43 73.87 - 92.33: 33 Dihedral angle restraints: 24110 sinusoidal: 9820 harmonic: 14290 Sorted by residual: dihedral pdb=" C ILE G 59 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " pdb=" CB ILE G 59 " ideal model delta harmonic sigma weight residual -122.00 -138.79 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C HIS A 186 " pdb=" N HIS A 186 " pdb=" CA HIS A 186 " pdb=" CB HIS A 186 " ideal model delta harmonic sigma weight residual -122.60 -138.07 15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" CA GLU G 53 " pdb=" C GLU G 53 " pdb=" N LYS G 54 " pdb=" CA LYS G 54 " ideal model delta harmonic sigma weight residual 180.00 151.82 28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 24107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 5763 0.089 - 0.178: 396 0.178 - 0.267: 8 0.267 - 0.357: 0 0.357 - 0.446: 2 Chirality restraints: 6169 Sorted by residual: chirality pdb=" CA ILE G 59 " pdb=" N ILE G 59 " pdb=" C ILE G 59 " pdb=" CB ILE G 59 " both_signs ideal model delta sigma weight residual False 2.43 1.99 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA HIS A 186 " pdb=" N HIS A 186 " pdb=" C HIS A 186 " pdb=" CB HIS A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA THR I 169 " pdb=" N THR I 169 " pdb=" C THR I 169 " pdb=" CB THR I 169 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 6166 not shown) Planarity restraints: 6842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 59 " 0.084 5.00e-02 4.00e+02 1.41e-01 3.16e+01 pdb=" N PRO G 60 " -0.243 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.087 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 56 " 0.023 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ASP G 56 " -0.083 2.00e-02 2.50e+03 pdb=" O ASP G 56 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP G 57 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 185 " 0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C GLU A 185 " -0.077 2.00e-02 2.50e+03 pdb=" O GLU A 185 " 0.029 2.00e-02 2.50e+03 pdb=" N HIS A 186 " 0.026 2.00e-02 2.50e+03 ... (remaining 6839 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 26 2.01 - 2.73: 4296 2.73 - 3.46: 61290 3.46 - 4.18: 87686 4.18 - 4.90: 147311 Nonbonded interactions: 300609 Sorted by model distance: nonbonded pdb=" O LEU P 701 " pdb=" OE1 GLN P 705 " model vdw 1.290 3.040 nonbonded pdb=" CD1 LEU B 195 " pdb=" CD1 ILE G 59 " model vdw 1.310 3.880 nonbonded pdb=" CE1 HIS D 172 " pdb=" NH2 ARG E 186 " model vdw 1.469 3.340 nonbonded pdb=" O GLN M 752 " pdb=" OE1 GLU M 756 " model vdw 1.568 3.040 nonbonded pdb=" CB LEU B 195 " pdb=" CG2 ILE G 59 " model vdw 1.578 3.860 ... (remaining 300604 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' and resid 6 through 201) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 19 through 58 or resid 86 through 208)) selection = (chain 'D' and (resid 19 through 58 or resid 86 through 125 or resid 138 or resi \ d 141 through 208)) } ncs_group { reference = (chain 'E' and (resid 45 through 202 or resid 318 through 334)) selection = chain 'F' selection = (chain 'G' and (resid 45 through 202 or resid 318 through 334)) selection = (chain 'H' and (resid 45 through 202 or resid 318 through 334)) } ncs_group { reference = (chain 'I' and resid 12 through 192) selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 350 through 874) selection = (chain 'L' and resid 350 through 874) selection = (chain 'M' and resid 350 through 874) selection = (chain 'N' and resid 350 through 874) } ncs_group { reference = (chain 'O' and (resid 201 through 603 or resid 617 through 746)) selection = (chain 'P' and (resid 201 through 449 or resid 457 through 746)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.62 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.530 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: 0.030 Extract box with map and model: 13.740 Check model and map are aligned: 0.170 Set scattering table: 0.290 Process input model: 97.470 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 39017 Z= 0.409 Angle : 0.799 21.684 52843 Z= 0.435 Chirality : 0.046 0.446 6169 Planarity : 0.005 0.141 6842 Dihedral : 13.997 92.333 14860 Min Nonbonded Distance : 1.290 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.89 % Favored : 86.97 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.04 % 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: -4.53 (0.10), residues: 4920 helix: -2.29 (0.09), residues: 2322 sheet: -2.80 (0.19), residues: 505 loop : -3.88 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 28 HIS 0.009 0.001 HIS M 557 PHE 0.022 0.002 PHE G 325 TYR 0.027 0.002 TYR M 667 ARG 0.009 0.001 ARG L 501 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8348 (ttm170) REVERT: A 138 MET cc_start: 0.9054 (mmm) cc_final: 0.8661 (tpp) REVERT: B 172 GLN cc_start: 0.8888 (tt0) cc_final: 0.8408 (tp40) REVERT: B 189 LEU cc_start: 0.8397 (mt) cc_final: 0.8166 (mt) REVERT: B 192 ASP cc_start: 0.8755 (m-30) cc_final: 0.8486 (m-30) REVERT: C 155 MET cc_start: 0.9259 (mtm) cc_final: 0.8960 (mtp) REVERT: D 29 ASP cc_start: 0.9186 (m-30) cc_final: 0.8976 (m-30) REVERT: G 58 LYS cc_start: 0.8615 (tttt) cc_final: 0.7948 (ptpt) REVERT: G 67 LEU cc_start: 0.8579 (mt) cc_final: 0.8300 (tp) REVERT: G 118 GLN cc_start: 0.7806 (mt0) cc_final: 0.7500 (mt0) REVERT: I 133 GLU cc_start: 0.8558 (tt0) cc_final: 0.8187 (tt0) REVERT: J 132 LEU cc_start: 0.8727 (tp) cc_final: 0.8403 (tt) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.5818 time to fit residues: 470.5189 Evaluate side-chains 355 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 7.9990 chunk 384 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 444 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 77 GLN A 148 HIS A 186 HIS A 187 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 GLN B 148 HIS C 26 ASN C 31 HIS ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 HIS D 144 HIS ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39017 Z= 0.290 Angle : 0.717 9.511 52843 Z= 0.364 Chirality : 0.045 0.232 6169 Planarity : 0.005 0.101 6842 Dihedral : 5.528 27.599 5355 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.04 % Rotamer: Outliers : 0.14 % Allowed : 7.22 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.11), residues: 4920 helix: -0.84 (0.10), residues: 2349 sheet: -2.33 (0.19), residues: 536 loop : -3.26 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP G 101 HIS 0.010 0.001 HIS H 69 PHE 0.039 0.002 PHE P 486 TYR 0.025 0.002 TYR O 649 ARG 0.013 0.001 ARG M 445 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 453 time to evaluate : 4.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8632 (mtt180) cc_final: 0.8203 (ttm170) REVERT: A 138 MET cc_start: 0.9117 (mmm) cc_final: 0.8300 (mmm) REVERT: A 184 ASP cc_start: 0.8714 (t0) cc_final: 0.8188 (t0) REVERT: B 172 GLN cc_start: 0.8790 (tt0) cc_final: 0.8298 (tp40) REVERT: B 189 LEU cc_start: 0.8440 (mt) cc_final: 0.8210 (mt) REVERT: B 192 ASP cc_start: 0.8511 (m-30) cc_final: 0.8178 (m-30) REVERT: C 25 ASP cc_start: 0.9424 (m-30) cc_final: 0.9219 (m-30) REVERT: C 100 ASP cc_start: 0.8985 (m-30) cc_final: 0.8685 (m-30) REVERT: C 155 MET cc_start: 0.9186 (mtm) cc_final: 0.8939 (mtp) REVERT: D 25 ASP cc_start: 0.9440 (m-30) cc_final: 0.9176 (m-30) REVERT: D 29 ASP cc_start: 0.9279 (m-30) cc_final: 0.8922 (m-30) REVERT: D 100 ASP cc_start: 0.8964 (m-30) cc_final: 0.8620 (m-30) REVERT: G 58 LYS cc_start: 0.8815 (tttt) cc_final: 0.8220 (ptpt) REVERT: G 67 LEU cc_start: 0.8579 (mt) cc_final: 0.8133 (tp) REVERT: G 118 GLN cc_start: 0.7720 (mt0) cc_final: 0.7489 (mt0) REVERT: J 132 LEU cc_start: 0.8756 (tp) cc_final: 0.8449 (tt) outliers start: 6 outliers final: 2 residues processed: 457 average time/residue: 0.5519 time to fit residues: 406.3620 Evaluate side-chains 355 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 353 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 303 optimal weight: 30.0000 chunk 122 optimal weight: 0.0270 chunk 445 optimal weight: 7.9990 chunk 481 optimal weight: 20.0000 chunk 397 optimal weight: 0.8980 chunk 442 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 48 GLN D 31 HIS ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39017 Z= 0.194 Angle : 0.661 11.208 52843 Z= 0.331 Chirality : 0.044 0.378 6169 Planarity : 0.005 0.089 6842 Dihedral : 5.179 30.482 5355 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.58 % Favored : 91.38 % Rotamer: Outliers : 0.02 % Allowed : 4.68 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.98 (0.12), residues: 4920 helix: -0.00 (0.10), residues: 2391 sheet: -1.82 (0.20), residues: 525 loop : -2.84 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 101 HIS 0.018 0.001 HIS K 861 PHE 0.024 0.001 PHE P 486 TYR 0.022 0.002 TYR M 667 ARG 0.011 0.000 ARG O 643 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 485 time to evaluate : 4.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8192 (ttm170) REVERT: A 138 MET cc_start: 0.9005 (mmm) cc_final: 0.8296 (mmm) REVERT: A 184 ASP cc_start: 0.8509 (t0) cc_final: 0.8023 (t0) REVERT: B 172 GLN cc_start: 0.8691 (tt0) cc_final: 0.8173 (tp40) REVERT: C 25 ASP cc_start: 0.9398 (m-30) cc_final: 0.9099 (m-30) REVERT: C 29 ASP cc_start: 0.9279 (m-30) cc_final: 0.8987 (m-30) REVERT: C 100 ASP cc_start: 0.8924 (m-30) cc_final: 0.8598 (m-30) REVERT: C 155 MET cc_start: 0.9090 (mtm) cc_final: 0.8857 (mtp) REVERT: D 25 ASP cc_start: 0.9419 (m-30) cc_final: 0.9155 (m-30) REVERT: D 29 ASP cc_start: 0.9240 (m-30) cc_final: 0.8895 (m-30) REVERT: D 100 ASP cc_start: 0.8907 (m-30) cc_final: 0.8566 (m-30) REVERT: G 111 VAL cc_start: 0.8413 (p) cc_final: 0.8115 (p) REVERT: G 118 GLN cc_start: 0.7703 (mt0) cc_final: 0.7254 (mt0) REVERT: J 132 LEU cc_start: 0.8731 (tp) cc_final: 0.8432 (tt) outliers start: 1 outliers final: 0 residues processed: 485 average time/residue: 0.5497 time to fit residues: 431.4952 Evaluate side-chains 353 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 0.7980 chunk 335 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 212 optimal weight: 30.0000 chunk 299 optimal weight: 20.0000 chunk 447 optimal weight: 9.9990 chunk 473 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 424 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN D 53 ASN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39017 Z= 0.286 Angle : 0.685 10.996 52843 Z= 0.344 Chirality : 0.044 0.228 6169 Planarity : 0.005 0.091 6842 Dihedral : 5.177 34.187 5355 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.53 % Favored : 90.43 % Rotamer: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.71 (0.12), residues: 4920 helix: 0.20 (0.10), residues: 2390 sheet: -1.69 (0.21), residues: 544 loop : -2.67 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 140 HIS 0.011 0.001 HIS K 861 PHE 0.038 0.002 PHE P 486 TYR 0.022 0.002 TYR M 414 ARG 0.011 0.001 ARG M 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 432 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8598 (mtt180) cc_final: 0.8261 (ttm170) REVERT: A 138 MET cc_start: 0.9012 (mmm) cc_final: 0.8242 (mmm) REVERT: A 184 ASP cc_start: 0.8625 (t0) cc_final: 0.8096 (t0) REVERT: B 189 LEU cc_start: 0.8330 (mt) cc_final: 0.8120 (mt) REVERT: C 25 ASP cc_start: 0.9373 (m-30) cc_final: 0.9086 (m-30) REVERT: C 29 ASP cc_start: 0.9284 (m-30) cc_final: 0.8993 (m-30) REVERT: C 100 ASP cc_start: 0.8961 (m-30) cc_final: 0.8655 (m-30) REVERT: C 155 MET cc_start: 0.9133 (mtm) cc_final: 0.8865 (mtp) REVERT: D 25 ASP cc_start: 0.9414 (m-30) cc_final: 0.9150 (m-30) REVERT: D 29 ASP cc_start: 0.9261 (m-30) cc_final: 0.8925 (m-30) REVERT: D 100 ASP cc_start: 0.8945 (m-30) cc_final: 0.8587 (m-30) REVERT: J 132 LEU cc_start: 0.8742 (tp) cc_final: 0.8415 (tt) outliers start: 1 outliers final: 0 residues processed: 433 average time/residue: 0.5285 time to fit residues: 372.1434 Evaluate side-chains 341 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 404 optimal weight: 8.9990 chunk 327 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 425 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39017 Z= 0.258 Angle : 0.667 10.236 52843 Z= 0.335 Chirality : 0.044 0.234 6169 Planarity : 0.005 0.092 6842 Dihedral : 5.082 33.810 5355 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.68 % Favored : 91.26 % Rotamer: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.48 (0.12), residues: 4920 helix: 0.36 (0.10), residues: 2400 sheet: -1.51 (0.21), residues: 554 loop : -2.55 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 28 HIS 0.011 0.001 HIS H 69 PHE 0.024 0.001 PHE A 110 TYR 0.019 0.002 TYR M 667 ARG 0.023 0.000 ARG M 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 442 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8135 (mtm-85) REVERT: A 184 ASP cc_start: 0.8512 (t0) cc_final: 0.8003 (t0) REVERT: B 189 LEU cc_start: 0.8331 (mt) cc_final: 0.8054 (mt) REVERT: B 192 ASP cc_start: 0.8442 (m-30) cc_final: 0.8172 (m-30) REVERT: C 25 ASP cc_start: 0.9369 (m-30) cc_final: 0.8680 (t0) REVERT: C 29 ASP cc_start: 0.9281 (m-30) cc_final: 0.8823 (m-30) REVERT: C 100 ASP cc_start: 0.8927 (m-30) cc_final: 0.8625 (m-30) REVERT: C 155 MET cc_start: 0.9100 (mtm) cc_final: 0.8843 (mtp) REVERT: D 25 ASP cc_start: 0.9402 (m-30) cc_final: 0.9120 (m-30) REVERT: D 29 ASP cc_start: 0.9253 (m-30) cc_final: 0.8898 (m-30) REVERT: D 100 ASP cc_start: 0.8917 (m-30) cc_final: 0.8564 (m-30) REVERT: J 132 LEU cc_start: 0.8741 (tp) cc_final: 0.8437 (tt) outliers start: 2 outliers final: 0 residues processed: 443 average time/residue: 0.5220 time to fit residues: 377.5717 Evaluate side-chains 350 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 2.9990 chunk 426 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 278 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 474 optimal weight: 9.9990 chunk 393 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 156 optimal weight: 0.0270 chunk 248 optimal weight: 50.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39017 Z= 0.212 Angle : 0.646 9.636 52843 Z= 0.322 Chirality : 0.043 0.443 6169 Planarity : 0.005 0.091 6842 Dihedral : 4.915 33.423 5355 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.48 % Favored : 91.48 % Rotamer: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.14 (0.12), residues: 4920 helix: 0.64 (0.11), residues: 2395 sheet: -1.41 (0.21), residues: 550 loop : -2.37 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 28 HIS 0.011 0.001 HIS D 172 PHE 0.012 0.001 PHE A 110 TYR 0.027 0.002 TYR M 414 ARG 0.015 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 460 time to evaluate : 4.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8141 (mtm-85) REVERT: A 138 MET cc_start: 0.8915 (mmm) cc_final: 0.8623 (mmm) REVERT: A 184 ASP cc_start: 0.8460 (t0) cc_final: 0.7971 (t0) REVERT: B 189 LEU cc_start: 0.8076 (mt) cc_final: 0.7858 (mt) REVERT: B 192 ASP cc_start: 0.8391 (m-30) cc_final: 0.8094 (m-30) REVERT: C 25 ASP cc_start: 0.9358 (m-30) cc_final: 0.8682 (t0) REVERT: C 29 ASP cc_start: 0.9222 (m-30) cc_final: 0.8752 (m-30) REVERT: C 100 ASP cc_start: 0.8912 (m-30) cc_final: 0.8595 (m-30) REVERT: D 25 ASP cc_start: 0.9375 (m-30) cc_final: 0.9103 (m-30) REVERT: D 29 ASP cc_start: 0.9214 (m-30) cc_final: 0.8866 (m-30) REVERT: D 100 ASP cc_start: 0.8887 (m-30) cc_final: 0.8571 (m-30) REVERT: J 132 LEU cc_start: 0.8710 (tp) cc_final: 0.8422 (tt) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.5201 time to fit residues: 390.5398 Evaluate side-chains 345 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 270 optimal weight: 0.9980 chunk 346 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 399 optimal weight: 0.6980 chunk 264 optimal weight: 5.9990 chunk 472 optimal weight: 0.1980 chunk 295 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 218 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39017 Z= 0.167 Angle : 0.633 10.741 52843 Z= 0.312 Chirality : 0.043 0.334 6169 Planarity : 0.005 0.089 6842 Dihedral : 4.721 31.567 5355 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.26 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.79 (0.12), residues: 4920 helix: 0.92 (0.11), residues: 2387 sheet: -1.27 (0.21), residues: 558 loop : -2.14 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 28 HIS 0.009 0.001 HIS M 446 PHE 0.036 0.001 PHE P 441 TYR 0.025 0.002 TYR M 414 ARG 0.010 0.000 ARG M 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8149 (mtm-85) REVERT: A 64 ARG cc_start: 0.9083 (ttm110) cc_final: 0.8829 (ttp-110) REVERT: A 138 MET cc_start: 0.8909 (mmm) cc_final: 0.8595 (mmm) REVERT: A 184 ASP cc_start: 0.8165 (t0) cc_final: 0.7898 (t0) REVERT: B 86 ASP cc_start: 0.8440 (m-30) cc_final: 0.8154 (t70) REVERT: B 138 MET cc_start: 0.8930 (mmm) cc_final: 0.8293 (mmm) REVERT: B 192 ASP cc_start: 0.8413 (m-30) cc_final: 0.8173 (m-30) REVERT: C 25 ASP cc_start: 0.9349 (m-30) cc_final: 0.8683 (t0) REVERT: C 29 ASP cc_start: 0.9170 (m-30) cc_final: 0.8721 (m-30) REVERT: C 34 ILE cc_start: 0.9452 (mm) cc_final: 0.9198 (mm) REVERT: C 100 ASP cc_start: 0.8842 (m-30) cc_final: 0.8542 (m-30) REVERT: C 175 ASP cc_start: 0.8560 (p0) cc_final: 0.8332 (p0) REVERT: D 25 ASP cc_start: 0.9371 (m-30) cc_final: 0.9087 (m-30) REVERT: D 29 ASP cc_start: 0.9195 (m-30) cc_final: 0.8851 (m-30) REVERT: D 100 ASP cc_start: 0.8827 (m-30) cc_final: 0.8514 (m-30) REVERT: J 132 LEU cc_start: 0.8676 (tp) cc_final: 0.8413 (tt) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.5220 time to fit residues: 406.9871 Evaluate side-chains 363 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 4.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 233 optimal weight: 20.0000 chunk 44 optimal weight: 4.9990 chunk 371 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN C 96 GLN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39017 Z= 0.191 Angle : 0.635 9.420 52843 Z= 0.316 Chirality : 0.043 0.405 6169 Planarity : 0.005 0.090 6842 Dihedral : 4.679 31.447 5355 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.50 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.69 (0.12), residues: 4920 helix: 0.97 (0.11), residues: 2383 sheet: -1.14 (0.21), residues: 545 loop : -2.06 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 28 HIS 0.008 0.001 HIS H 69 PHE 0.018 0.001 PHE P 441 TYR 0.025 0.002 TYR M 414 ARG 0.009 0.000 ARG M 445 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 4.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8129 (mtm-85) REVERT: A 64 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8689 (ttm110) REVERT: A 184 ASP cc_start: 0.8295 (t0) cc_final: 0.7892 (t0) REVERT: B 86 ASP cc_start: 0.8433 (m-30) cc_final: 0.8136 (t70) REVERT: B 138 MET cc_start: 0.8944 (mmm) cc_final: 0.8529 (mmm) REVERT: B 192 ASP cc_start: 0.8436 (m-30) cc_final: 0.8196 (m-30) REVERT: B 197 VAL cc_start: 0.9002 (t) cc_final: 0.8697 (p) REVERT: C 25 ASP cc_start: 0.9339 (m-30) cc_final: 0.8661 (t0) REVERT: C 29 ASP cc_start: 0.9176 (m-30) cc_final: 0.8735 (m-30) REVERT: C 34 ILE cc_start: 0.9462 (mm) cc_final: 0.9203 (mm) REVERT: C 100 ASP cc_start: 0.8883 (m-30) cc_final: 0.8596 (m-30) REVERT: D 25 ASP cc_start: 0.9377 (m-30) cc_final: 0.9090 (m-30) REVERT: D 29 ASP cc_start: 0.9201 (m-30) cc_final: 0.8856 (m-30) REVERT: D 100 ASP cc_start: 0.8856 (m-30) cc_final: 0.8545 (m-30) REVERT: J 132 LEU cc_start: 0.8699 (tp) cc_final: 0.8395 (tt) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.5159 time to fit residues: 380.2533 Evaluate side-chains 340 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 4.9990 chunk 452 optimal weight: 4.9990 chunk 412 optimal weight: 20.0000 chunk 440 optimal weight: 0.0970 chunk 264 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 345 optimal weight: 4.9990 chunk 135 optimal weight: 0.1980 chunk 397 optimal weight: 1.9990 chunk 416 optimal weight: 0.8980 chunk 438 optimal weight: 6.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39017 Z= 0.179 Angle : 0.632 9.452 52843 Z= 0.313 Chirality : 0.043 0.470 6169 Planarity : 0.005 0.089 6842 Dihedral : 4.606 30.776 5355 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % 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: -0.53 (0.12), residues: 4920 helix: 1.09 (0.11), residues: 2380 sheet: -1.00 (0.21), residues: 545 loop : -1.98 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 28 HIS 0.007 0.001 HIS N 649 PHE 0.027 0.001 PHE P 486 TYR 0.024 0.002 TYR M 414 ARG 0.010 0.000 ARG M 860 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8592 (mtt180) cc_final: 0.8162 (mtm-85) REVERT: A 64 ARG cc_start: 0.9090 (ttm110) cc_final: 0.8825 (ttp-110) REVERT: A 86 ASP cc_start: 0.8479 (m-30) cc_final: 0.8051 (t70) REVERT: A 184 ASP cc_start: 0.8198 (t0) cc_final: 0.7827 (t0) REVERT: B 86 ASP cc_start: 0.8420 (m-30) cc_final: 0.8123 (t70) REVERT: B 138 MET cc_start: 0.9015 (mmm) cc_final: 0.8526 (mmm) REVERT: B 167 ASP cc_start: 0.8297 (p0) cc_final: 0.7890 (p0) REVERT: B 192 ASP cc_start: 0.8432 (m-30) cc_final: 0.8200 (m-30) REVERT: C 25 ASP cc_start: 0.9330 (m-30) cc_final: 0.8629 (t0) REVERT: C 29 ASP cc_start: 0.9176 (m-30) cc_final: 0.8736 (m-30) REVERT: C 34 ILE cc_start: 0.9447 (mm) cc_final: 0.9184 (mm) REVERT: C 100 ASP cc_start: 0.8851 (m-30) cc_final: 0.8568 (m-30) REVERT: C 175 ASP cc_start: 0.8608 (p0) cc_final: 0.8370 (p0) REVERT: D 25 ASP cc_start: 0.9368 (m-30) cc_final: 0.9080 (m-30) REVERT: D 29 ASP cc_start: 0.9173 (m-30) cc_final: 0.8826 (m-30) REVERT: D 100 ASP cc_start: 0.8847 (m-30) cc_final: 0.8548 (m-30) REVERT: J 132 LEU cc_start: 0.8688 (tp) cc_final: 0.8411 (tt) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.5107 time to fit residues: 382.8759 Evaluate side-chains 349 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 2.9990 chunk 465 optimal weight: 10.0000 chunk 284 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 488 optimal weight: 3.9990 chunk 449 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 300 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN C 96 GLN ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39017 Z= 0.195 Angle : 0.641 11.650 52843 Z= 0.317 Chirality : 0.043 0.367 6169 Planarity : 0.005 0.088 6842 Dihedral : 4.585 30.905 5355 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.46 (0.12), residues: 4920 helix: 1.09 (0.11), residues: 2401 sheet: -1.00 (0.21), residues: 551 loop : -1.88 (0.15), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 28 HIS 0.008 0.001 HIS C 126 PHE 0.022 0.001 PHE P 486 TYR 0.025 0.002 TYR M 414 ARG 0.010 0.000 ARG O 284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8560 (mtt180) cc_final: 0.8152 (mtm-85) REVERT: A 64 ARG cc_start: 0.9107 (ttm110) cc_final: 0.8666 (ttm110) REVERT: A 184 ASP cc_start: 0.8258 (t0) cc_final: 0.7867 (t0) REVERT: B 86 ASP cc_start: 0.8433 (m-30) cc_final: 0.8140 (t70) REVERT: B 138 MET cc_start: 0.9044 (mmm) cc_final: 0.8535 (mmm) REVERT: B 167 ASP cc_start: 0.8332 (p0) cc_final: 0.7912 (p0) REVERT: B 192 ASP cc_start: 0.8488 (m-30) cc_final: 0.8268 (m-30) REVERT: B 197 VAL cc_start: 0.8807 (t) cc_final: 0.8606 (t) REVERT: C 25 ASP cc_start: 0.9332 (m-30) cc_final: 0.8653 (t0) REVERT: C 29 ASP cc_start: 0.9164 (m-30) cc_final: 0.8724 (m-30) REVERT: C 34 ILE cc_start: 0.9453 (mm) cc_final: 0.9199 (mm) REVERT: C 100 ASP cc_start: 0.8876 (m-30) cc_final: 0.8583 (m-30) REVERT: C 175 ASP cc_start: 0.8614 (p0) cc_final: 0.8362 (p0) REVERT: D 25 ASP cc_start: 0.9375 (m-30) cc_final: 0.9087 (m-30) REVERT: D 29 ASP cc_start: 0.9181 (m-30) cc_final: 0.8828 (m-30) REVERT: D 100 ASP cc_start: 0.8857 (m-30) cc_final: 0.8548 (m-30) REVERT: J 132 LEU cc_start: 0.8707 (tp) cc_final: 0.8421 (tt) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.4895 time to fit residues: 360.1496 Evaluate side-chains 337 residues out of total 4170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 9.9990 chunk 414 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 358 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 108 optimal weight: 0.0470 chunk 389 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.117592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.097166 restraints weight = 129564.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097768 restraints weight = 86351.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.098014 restraints weight = 67173.796| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 39017 Z= 0.198 Angle : 0.635 10.072 52843 Z= 0.316 Chirality : 0.043 0.393 6169 Planarity : 0.005 0.088 6842 Dihedral : 4.561 31.030 5355 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.36 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.39 (0.12), residues: 4920 helix: 1.15 (0.11), residues: 2397 sheet: -0.97 (0.21), residues: 558 loop : -1.86 (0.15), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 28 HIS 0.007 0.001 HIS H 69 PHE 0.022 0.001 PHE P 486 TYR 0.024 0.002 TYR M 414 ARG 0.011 0.000 ARG O 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7727.82 seconds wall clock time: 139 minutes 50.03 seconds (8390.03 seconds total)