Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 06:47:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2023/7d0i_30535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2023/7d0i_30535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2023/7d0i_30535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2023/7d0i_30535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2023/7d0i_30535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d0i_30535/04_2023/7d0i_30535_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 14742 2.51 5 N 3516 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B ARG 406": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B ASP 585": "OD1" <-> "OD2" Residue "B PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 637": "NH1" <-> "NH2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 368": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 399": "NH1" <-> "NH2" Residue "D ARG 404": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 500": "NH1" <-> "NH2" Residue "D GLU 559": "OE1" <-> "OE2" Residue "D ASP 585": "OD1" <-> "OD2" Residue "D PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 610": "OE1" <-> "OE2" Residue "D PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 368": "NH1" <-> "NH2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "F ARG 399": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F ARG 406": "NH1" <-> "NH2" Residue "F ARG 414": "NH1" <-> "NH2" Residue "F TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 500": "NH1" <-> "NH2" Residue "F GLU 559": "OE1" <-> "OE2" Residue "F ASP 585": "OD1" <-> "OD2" Residue "F PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 610": "OE1" <-> "OE2" Residue "F PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 637": "NH1" <-> "NH2" Residue "F PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 278": "NH1" <-> "NH2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 345": "NH1" <-> "NH2" Residue "H PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 368": "NH1" <-> "NH2" Residue "H ARG 369": "NH1" <-> "NH2" Residue "H ARG 399": "NH1" <-> "NH2" Residue "H ARG 404": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "H ARG 414": "NH1" <-> "NH2" Residue "H TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 470": "OE1" <-> "OE2" Residue "H PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 500": "NH1" <-> "NH2" Residue "H GLU 559": "OE1" <-> "OE2" Residue "H ASP 585": "OD1" <-> "OD2" Residue "H PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 610": "OE1" <-> "OE2" Residue "H PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 637": "NH1" <-> "NH2" Residue "H PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 278": "NH1" <-> "NH2" Residue "J PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 345": "NH1" <-> "NH2" Residue "J PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 368": "NH1" <-> "NH2" Residue "J ARG 369": "NH1" <-> "NH2" Residue "J ARG 399": "NH1" <-> "NH2" Residue "J ARG 404": "NH1" <-> "NH2" Residue "J ARG 406": "NH1" <-> "NH2" Residue "J ARG 414": "NH1" <-> "NH2" Residue "J TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 470": "OE1" <-> "OE2" Residue "J PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 500": "NH1" <-> "NH2" Residue "J GLU 559": "OE1" <-> "OE2" Residue "J ASP 585": "OD1" <-> "OD2" Residue "J PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 610": "OE1" <-> "OE2" Residue "J PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 637": "NH1" <-> "NH2" Residue "J PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 278": "NH1" <-> "NH2" Residue "L PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 345": "NH1" <-> "NH2" Residue "L PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 368": "NH1" <-> "NH2" Residue "L ARG 369": "NH1" <-> "NH2" Residue "L ARG 399": "NH1" <-> "NH2" Residue "L ARG 404": "NH1" <-> "NH2" Residue "L ARG 406": "NH1" <-> "NH2" Residue "L ARG 414": "NH1" <-> "NH2" Residue "L TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 470": "OE1" <-> "OE2" Residue "L PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 500": "NH1" <-> "NH2" Residue "L GLU 559": "OE1" <-> "OE2" Residue "L ASP 585": "OD1" <-> "OD2" Residue "L PHE 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 610": "OE1" <-> "OE2" Residue "L PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 637": "NH1" <-> "NH2" Residue "L PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22164 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.04, per 1000 atoms: 0.54 Number of scatterers: 22164 At special positions: 0 Unit cell: (122.01, 125.745, 153.135, 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 72 16.00 O 3834 8.00 N 3516 7.00 C 14742 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: 9.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 12 sheets defined 69.1% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 253 through 287 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 302 through 312 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 345 through 355 removed outlier: 3.908A pdb=" N TYR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 382 Processing helix chain 'B' and resid 384 through 387 No H-bonds generated for 'chain 'B' and resid 384 through 387' Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 401 through 404 removed outlier: 3.737A pdb=" N ARG B 404 " --> pdb=" O PRO B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 404' Processing helix chain 'B' and resid 407 through 410 No H-bonds generated for 'chain 'B' and resid 407 through 410' Processing helix chain 'B' and resid 412 through 425 removed outlier: 4.134A pdb=" N VAL B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 447 removed outlier: 4.100A pdb=" N TYR B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 472 through 491 removed outlier: 3.928A pdb=" N SER B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA B 484 " --> pdb=" O ASN B 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA B 485 " --> pdb=" O ASP B 481 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 520 removed outlier: 3.740A pdb=" N LEU B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 576 removed outlier: 4.085A pdb=" N PHE B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 591 through 599 Processing helix chain 'B' and resid 603 through 623 removed outlier: 3.959A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 626 through 638 removed outlier: 4.980A pdb=" N GLN B 630 " --> pdb=" O SER B 627 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP B 631 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 638 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 198 through 223 Processing helix chain 'D' and resid 253 through 287 Proline residue: D 277 - end of helix Processing helix chain 'D' and resid 302 through 312 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 345 through 355 removed outlier: 3.908A pdb=" N TYR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 382 Processing helix chain 'D' and resid 384 through 387 No H-bonds generated for 'chain 'D' and resid 384 through 387' Processing helix chain 'D' and resid 396 through 398 No H-bonds generated for 'chain 'D' and resid 396 through 398' Processing helix chain 'D' and resid 401 through 404 removed outlier: 3.738A pdb=" N ARG D 404 " --> pdb=" O PRO D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 407 through 410 No H-bonds generated for 'chain 'D' and resid 407 through 410' Processing helix chain 'D' and resid 412 through 425 removed outlier: 4.134A pdb=" N VAL D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 447 removed outlier: 4.099A pdb=" N TYR D 432 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASN D 443 " --> pdb=" O PHE D 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 452 Processing helix chain 'D' and resid 461 through 464 No H-bonds generated for 'chain 'D' and resid 461 through 464' Processing helix chain 'D' and resid 472 through 491 removed outlier: 3.929A pdb=" N SER D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA D 484 " --> pdb=" O ASN D 480 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA D 485 " --> pdb=" O ASP D 481 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER D 491 " --> pdb=" O SER D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 520 removed outlier: 3.739A pdb=" N LEU D 501 " --> pdb=" O ASN D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 576 removed outlier: 4.085A pdb=" N PHE D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 591 through 599 Processing helix chain 'D' and resid 603 through 623 removed outlier: 3.960A pdb=" N ILE D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Proline residue: D 618 - end of helix Processing helix chain 'D' and resid 626 through 638 removed outlier: 4.979A pdb=" N GLN D 630 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP D 631 " --> pdb=" O CYS D 628 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 638 " --> pdb=" O PHE D 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 198 through 223 Processing helix chain 'F' and resid 253 through 287 Proline residue: F 277 - end of helix Processing helix chain 'F' and resid 302 through 312 Processing helix chain 'F' and resid 336 through 343 Processing helix chain 'F' and resid 345 through 355 removed outlier: 3.909A pdb=" N TYR F 349 " --> pdb=" O ARG F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 382 Processing helix chain 'F' and resid 384 through 387 No H-bonds generated for 'chain 'F' and resid 384 through 387' Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 401 through 404 removed outlier: 3.738A pdb=" N ARG F 404 " --> pdb=" O PRO F 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 401 through 404' Processing helix chain 'F' and resid 407 through 410 No H-bonds generated for 'chain 'F' and resid 407 through 410' Processing helix chain 'F' and resid 412 through 425 removed outlier: 4.134A pdb=" N VAL F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 424 " --> pdb=" O PHE F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 447 removed outlier: 4.101A pdb=" N TYR F 432 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN F 443 " --> pdb=" O PHE F 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU F 444 " --> pdb=" O ARG F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 461 through 464 No H-bonds generated for 'chain 'F' and resid 461 through 464' Processing helix chain 'F' and resid 472 through 491 removed outlier: 3.928A pdb=" N SER F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA F 484 " --> pdb=" O ASN F 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA F 485 " --> pdb=" O ASP F 481 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER F 491 " --> pdb=" O SER F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 520 removed outlier: 3.739A pdb=" N LEU F 501 " --> pdb=" O ASN F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE F 555 " --> pdb=" O VAL F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 576 removed outlier: 4.084A pdb=" N PHE F 575 " --> pdb=" O ARG F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 583 No H-bonds generated for 'chain 'F' and resid 581 through 583' Processing helix chain 'F' and resid 591 through 599 Processing helix chain 'F' and resid 603 through 623 removed outlier: 3.958A pdb=" N ILE F 614 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 615 " --> pdb=" O ILE F 611 " (cutoff:3.500A) Proline residue: F 618 - end of helix Processing helix chain 'F' and resid 626 through 638 removed outlier: 4.980A pdb=" N GLN F 630 " --> pdb=" O SER F 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP F 631 " --> pdb=" O CYS F 628 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 638 " --> pdb=" O PHE F 635 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 195 Processing helix chain 'H' and resid 198 through 223 Processing helix chain 'H' and resid 253 through 287 Proline residue: H 277 - end of helix Processing helix chain 'H' and resid 302 through 312 Processing helix chain 'H' and resid 336 through 343 Processing helix chain 'H' and resid 345 through 355 removed outlier: 3.909A pdb=" N TYR H 349 " --> pdb=" O ARG H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 382 Processing helix chain 'H' and resid 384 through 387 No H-bonds generated for 'chain 'H' and resid 384 through 387' Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 401 through 404 removed outlier: 3.737A pdb=" N ARG H 404 " --> pdb=" O PRO H 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 401 through 404' Processing helix chain 'H' and resid 407 through 410 No H-bonds generated for 'chain 'H' and resid 407 through 410' Processing helix chain 'H' and resid 412 through 425 removed outlier: 4.133A pdb=" N VAL H 417 " --> pdb=" O ARG H 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 424 " --> pdb=" O PHE H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 447 removed outlier: 4.102A pdb=" N TYR H 432 " --> pdb=" O ILE H 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN H 443 " --> pdb=" O PHE H 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 452 Processing helix chain 'H' and resid 461 through 464 No H-bonds generated for 'chain 'H' and resid 461 through 464' Processing helix chain 'H' and resid 472 through 491 removed outlier: 3.927A pdb=" N SER H 482 " --> pdb=" O ARG H 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR H 483 " --> pdb=" O ILE H 479 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA H 484 " --> pdb=" O ASN H 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA H 485 " --> pdb=" O ASP H 481 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER H 491 " --> pdb=" O SER H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 520 removed outlier: 3.741A pdb=" N LEU H 501 " --> pdb=" O ASN H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 555 removed outlier: 3.702A pdb=" N SER H 554 " --> pdb=" O ALA H 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 555 " --> pdb=" O VAL H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 576 removed outlier: 4.084A pdb=" N PHE H 575 " --> pdb=" O ARG H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 583 No H-bonds generated for 'chain 'H' and resid 581 through 583' Processing helix chain 'H' and resid 591 through 599 Processing helix chain 'H' and resid 603 through 623 removed outlier: 3.961A pdb=" N ILE H 614 " --> pdb=" O GLU H 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU H 615 " --> pdb=" O ILE H 611 " (cutoff:3.500A) Proline residue: H 618 - end of helix Processing helix chain 'H' and resid 626 through 638 removed outlier: 4.981A pdb=" N GLN H 630 " --> pdb=" O SER H 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP H 631 " --> pdb=" O CYS H 628 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU H 638 " --> pdb=" O PHE H 635 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 195 Processing helix chain 'J' and resid 198 through 223 Processing helix chain 'J' and resid 253 through 287 Proline residue: J 277 - end of helix Processing helix chain 'J' and resid 302 through 312 Processing helix chain 'J' and resid 336 through 343 Processing helix chain 'J' and resid 345 through 355 removed outlier: 3.909A pdb=" N TYR J 349 " --> pdb=" O ARG J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 373 through 382 Processing helix chain 'J' and resid 384 through 387 No H-bonds generated for 'chain 'J' and resid 384 through 387' Processing helix chain 'J' and resid 396 through 398 No H-bonds generated for 'chain 'J' and resid 396 through 398' Processing helix chain 'J' and resid 401 through 404 removed outlier: 3.736A pdb=" N ARG J 404 " --> pdb=" O PRO J 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 401 through 404' Processing helix chain 'J' and resid 407 through 410 No H-bonds generated for 'chain 'J' and resid 407 through 410' Processing helix chain 'J' and resid 412 through 425 removed outlier: 4.135A pdb=" N VAL J 417 " --> pdb=" O ARG J 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU J 424 " --> pdb=" O PHE J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 447 removed outlier: 4.101A pdb=" N TYR J 432 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN J 443 " --> pdb=" O PHE J 439 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU J 444 " --> pdb=" O ARG J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 452 Processing helix chain 'J' and resid 461 through 464 No H-bonds generated for 'chain 'J' and resid 461 through 464' Processing helix chain 'J' and resid 472 through 491 removed outlier: 3.927A pdb=" N SER J 482 " --> pdb=" O ARG J 478 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR J 483 " --> pdb=" O ILE J 479 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA J 484 " --> pdb=" O ASN J 480 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA J 485 " --> pdb=" O ASP J 481 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER J 491 " --> pdb=" O SER J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 496 through 520 removed outlier: 3.741A pdb=" N LEU J 501 " --> pdb=" O ASN J 497 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 555 removed outlier: 3.701A pdb=" N SER J 554 " --> pdb=" O ALA J 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE J 555 " --> pdb=" O VAL J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 565 through 576 removed outlier: 4.083A pdb=" N PHE J 575 " --> pdb=" O ARG J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 583 No H-bonds generated for 'chain 'J' and resid 581 through 583' Processing helix chain 'J' and resid 591 through 599 Processing helix chain 'J' and resid 603 through 623 removed outlier: 3.958A pdb=" N ILE J 614 " --> pdb=" O GLU J 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 615 " --> pdb=" O ILE J 611 " (cutoff:3.500A) Proline residue: J 618 - end of helix Processing helix chain 'J' and resid 626 through 638 removed outlier: 4.982A pdb=" N GLN J 630 " --> pdb=" O SER J 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP J 631 " --> pdb=" O CYS J 628 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU J 638 " --> pdb=" O PHE J 635 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 195 Processing helix chain 'L' and resid 198 through 223 Processing helix chain 'L' and resid 253 through 287 Proline residue: L 277 - end of helix Processing helix chain 'L' and resid 302 through 312 Processing helix chain 'L' and resid 336 through 343 Processing helix chain 'L' and resid 345 through 355 removed outlier: 3.907A pdb=" N TYR L 349 " --> pdb=" O ARG L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 382 Processing helix chain 'L' and resid 384 through 387 No H-bonds generated for 'chain 'L' and resid 384 through 387' Processing helix chain 'L' and resid 396 through 398 No H-bonds generated for 'chain 'L' and resid 396 through 398' Processing helix chain 'L' and resid 401 through 404 removed outlier: 3.738A pdb=" N ARG L 404 " --> pdb=" O PRO L 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 401 through 404' Processing helix chain 'L' and resid 407 through 410 No H-bonds generated for 'chain 'L' and resid 407 through 410' Processing helix chain 'L' and resid 412 through 425 removed outlier: 4.133A pdb=" N VAL L 417 " --> pdb=" O ARG L 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L 424 " --> pdb=" O PHE L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 427 through 447 removed outlier: 4.101A pdb=" N TYR L 432 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN L 443 " --> pdb=" O PHE L 439 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU L 444 " --> pdb=" O ARG L 440 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 452 Processing helix chain 'L' and resid 461 through 464 No H-bonds generated for 'chain 'L' and resid 461 through 464' Processing helix chain 'L' and resid 472 through 491 removed outlier: 3.928A pdb=" N SER L 482 " --> pdb=" O ARG L 478 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR L 483 " --> pdb=" O ILE L 479 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ALA L 484 " --> pdb=" O ASN L 480 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA L 485 " --> pdb=" O ASP L 481 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER L 491 " --> pdb=" O SER L 487 " (cutoff:3.500A) Processing helix chain 'L' and resid 496 through 520 removed outlier: 3.740A pdb=" N LEU L 501 " --> pdb=" O ASN L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 538 through 555 removed outlier: 3.701A pdb=" N SER L 554 " --> pdb=" O ALA L 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE L 555 " --> pdb=" O VAL L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 565 through 576 removed outlier: 4.086A pdb=" N PHE L 575 " --> pdb=" O ARG L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 583 No H-bonds generated for 'chain 'L' and resid 581 through 583' Processing helix chain 'L' and resid 591 through 599 Processing helix chain 'L' and resid 603 through 623 removed outlier: 3.960A pdb=" N ILE L 614 " --> pdb=" O GLU L 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU L 615 " --> pdb=" O ILE L 611 " (cutoff:3.500A) Proline residue: L 618 - end of helix Processing helix chain 'L' and resid 626 through 638 removed outlier: 4.979A pdb=" N GLN L 630 " --> pdb=" O SER L 627 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP L 631 " --> pdb=" O CYS L 628 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU L 638 " --> pdb=" O PHE L 635 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 455 through 457 Processing sheet with id= B, first strand: chain 'B' and resid 640 through 643 Processing sheet with id= C, first strand: chain 'D' and resid 455 through 457 Processing sheet with id= D, first strand: chain 'D' and resid 640 through 643 Processing sheet with id= E, first strand: chain 'F' and resid 455 through 457 Processing sheet with id= F, first strand: chain 'F' and resid 640 through 643 Processing sheet with id= G, first strand: chain 'H' and resid 455 through 457 Processing sheet with id= H, first strand: chain 'H' and resid 640 through 643 Processing sheet with id= I, first strand: chain 'J' and resid 455 through 457 Processing sheet with id= J, first strand: chain 'J' and resid 640 through 643 Processing sheet with id= K, first strand: chain 'L' and resid 455 through 457 Processing sheet with id= L, first strand: chain 'L' and resid 640 through 643 1110 hydrogen bonds defined for protein. 3168 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: 6.72 Time building geometry restraints manager: 10.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6129 1.33 - 1.45: 4312 1.45 - 1.57: 12209 1.57 - 1.69: 84 1.69 - 1.80: 108 Bond restraints: 22842 Sorted by residual: bond pdb=" C1 LMN B 801 " pdb=" O5 LMN B 801 " ideal model delta sigma weight residual 1.403 1.548 -0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C1 LMN L 801 " pdb=" O5 LMN L 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C1 LMN J 801 " pdb=" O5 LMN J 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C1 LMN H 801 " pdb=" O5 LMN H 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C1 LMN F 801 " pdb=" O5 LMN F 801 " ideal model delta sigma weight residual 1.403 1.546 -0.143 2.00e-02 2.50e+03 5.13e+01 ... (remaining 22837 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.92: 540 106.92 - 113.72: 13155 113.72 - 120.51: 9696 120.51 - 127.31: 7388 127.31 - 134.10: 289 Bond angle restraints: 31068 Sorted by residual: angle pdb=" CBJ LMN B 802 " pdb=" CBL LMN B 802 " pdb=" CBR LMN B 802 " ideal model delta sigma weight residual 112.20 133.40 -21.20 3.00e+00 1.11e-01 4.99e+01 angle pdb=" CBJ LMN F 802 " pdb=" CBL LMN F 802 " pdb=" CBR LMN F 802 " ideal model delta sigma weight residual 112.20 133.34 -21.14 3.00e+00 1.11e-01 4.97e+01 angle pdb=" CBJ LMN J 802 " pdb=" CBL LMN J 802 " pdb=" CBR LMN J 802 " ideal model delta sigma weight residual 112.20 133.30 -21.10 3.00e+00 1.11e-01 4.95e+01 angle pdb=" CBJ LMN D 802 " pdb=" CBL LMN D 802 " pdb=" CBR LMN D 802 " ideal model delta sigma weight residual 112.20 133.26 -21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" CBJ LMN H 802 " pdb=" CBL LMN H 802 " pdb=" CBR LMN H 802 " ideal model delta sigma weight residual 112.20 133.24 -21.04 3.00e+00 1.11e-01 4.92e+01 ... (remaining 31063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.53: 12552 29.53 - 59.05: 258 59.05 - 88.58: 54 88.58 - 118.10: 6 118.10 - 147.63: 6 Dihedral angle restraints: 12876 sinusoidal: 5292 harmonic: 7584 Sorted by residual: dihedral pdb=" CBH LMN H 801 " pdb=" CBJ LMN H 801 " pdb=" CBL LMN H 801 " pdb=" CBR LMN H 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.39 147.63 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CBH LMN B 801 " pdb=" CBJ LMN B 801 " pdb=" CBL LMN B 801 " pdb=" CBR LMN B 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.45 147.57 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CBH LMN D 801 " pdb=" CBJ LMN D 801 " pdb=" CBL LMN D 801 " pdb=" CBR LMN D 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.47 147.55 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2384 0.045 - 0.090: 926 0.090 - 0.136: 211 0.136 - 0.181: 24 0.181 - 0.226: 13 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CCQ LMN D 801 " pdb=" CCF LMN D 801 " pdb=" CCH LMN D 801 " pdb=" OCB LMN D 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CCQ LMN F 801 " pdb=" CCF LMN F 801 " pdb=" CCH LMN F 801 " pdb=" OCB LMN F 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CCQ LMN L 801 " pdb=" CCF LMN L 801 " pdb=" CCH LMN L 801 " pdb=" OCB LMN L 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3555 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 617 " 0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO L 618 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 618 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 618 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 617 " -0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO J 618 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 618 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 618 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 617 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO F 618 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 618 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 618 " -0.026 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4932 2.77 - 3.30: 21422 3.30 - 3.83: 37072 3.83 - 4.37: 45249 4.37 - 4.90: 76701 Nonbonded interactions: 185376 Sorted by model distance: nonbonded pdb=" OAN LMN B 802 " pdb=" OBZ LMN B 802 " model vdw 2.237 2.440 nonbonded pdb=" OAN LMN D 802 " pdb=" OBZ LMN D 802 " model vdw 2.237 2.440 nonbonded pdb=" OAN LMN F 802 " pdb=" OBZ LMN F 802 " model vdw 2.238 2.440 nonbonded pdb=" OAN LMN J 802 " pdb=" OBZ LMN J 802 " model vdw 2.238 2.440 nonbonded pdb=" OAN LMN L 802 " pdb=" OBZ LMN L 802 " model vdw 2.238 2.440 ... (remaining 185371 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 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.020 Extract box with map and model: 4.330 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 58.010 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.011 0.145 22842 Z= 0.736 Angle : 0.950 21.201 31068 Z= 0.413 Chirality : 0.049 0.226 3558 Planarity : 0.004 0.046 3678 Dihedral : 14.321 147.628 7956 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.60 % 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: -2.14 (0.15), residues: 2496 helix: -1.08 (0.11), residues: 1818 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 470 time to evaluate : 2.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 7 residues processed: 524 average time/residue: 1.3213 time to fit residues: 788.4238 Evaluate side-chains 292 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 285 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 3.5756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 0.0470 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 228 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 443 ASN D 179 ASN D 367 HIS D 391 GLN D 443 ASN H 179 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 ASN J 179 ASN J 367 HIS J 443 ASN L 281 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 22842 Z= 0.151 Angle : 0.544 8.680 31068 Z= 0.258 Chirality : 0.040 0.172 3558 Planarity : 0.004 0.039 3678 Dihedral : 10.918 114.584 3072 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2496 helix: 0.23 (0.12), residues: 1866 sheet: None (None), residues: 0 loop : -1.06 (0.23), residues: 630 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 342 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 19 residues processed: 403 average time/residue: 1.2751 time to fit residues: 588.2566 Evaluate side-chains 286 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 2.709 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 12 residues processed: 7 average time/residue: 0.2595 time to fit residues: 6.7878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN D 209 GLN D 443 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN J 209 GLN J 443 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.032 22842 Z= 0.296 Angle : 0.601 9.032 31068 Z= 0.286 Chirality : 0.044 0.275 3558 Planarity : 0.004 0.063 3678 Dihedral : 10.800 107.397 3072 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 5.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2496 helix: 0.57 (0.12), residues: 1830 sheet: None (None), residues: 0 loop : -0.70 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 337 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 53 residues processed: 437 average time/residue: 1.2791 time to fit residues: 644.8605 Evaluate side-chains 355 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 302 time to evaluate : 2.471 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 43 residues processed: 10 average time/residue: 0.2554 time to fit residues: 7.7724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 153 optimal weight: 0.3980 chunk 230 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 380 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 179 ASN D 209 GLN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 ASN H 209 GLN H 437 ASN J 179 ASN J 209 GLN J 443 ASN L 209 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 22842 Z= 0.161 Angle : 0.554 10.745 31068 Z= 0.254 Chirality : 0.041 0.325 3558 Planarity : 0.004 0.042 3678 Dihedral : 10.217 100.458 3072 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 2496 helix: 0.94 (0.12), residues: 1836 sheet: None (None), residues: 0 loop : -0.28 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 329 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 47 residues processed: 410 average time/residue: 1.2401 time to fit residues: 585.9140 Evaluate side-chains 348 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 301 time to evaluate : 2.710 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 38 residues processed: 10 average time/residue: 0.2663 time to fit residues: 8.3942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 0.3980 chunk 138 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 168 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 380 ASN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 179 ASN D 209 GLN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 209 GLN H 437 ASN J 209 GLN J 281 GLN L 373 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 22842 Z= 0.157 Angle : 0.547 10.648 31068 Z= 0.249 Chirality : 0.042 0.351 3558 Planarity : 0.004 0.048 3678 Dihedral : 9.887 94.323 3072 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.16), residues: 2496 helix: 1.18 (0.12), residues: 1836 sheet: None (None), residues: 0 loop : -0.12 (0.22), residues: 660 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 336 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 50 residues processed: 413 average time/residue: 1.2187 time to fit residues: 581.6394 Evaluate side-chains 355 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 305 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 41 residues processed: 9 average time/residue: 0.4084 time to fit residues: 8.5890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 143 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 0.0770 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 209 GLN H 437 ASN J 281 GLN L 443 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 22842 Z= 0.153 Angle : 0.542 11.017 31068 Z= 0.246 Chirality : 0.041 0.348 3558 Planarity : 0.004 0.045 3678 Dihedral : 9.734 89.221 3072 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 4.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2496 helix: 1.34 (0.12), residues: 1830 sheet: None (None), residues: 0 loop : -0.06 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 332 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 53 residues processed: 412 average time/residue: 1.2276 time to fit residues: 583.0738 Evaluate side-chains 361 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 308 time to evaluate : 2.633 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 44 residues processed: 9 average time/residue: 0.2408 time to fit residues: 7.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 152 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 209 GLN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 437 ASN J 209 GLN J 281 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 22842 Z= 0.151 Angle : 0.542 13.106 31068 Z= 0.246 Chirality : 0.041 0.364 3558 Planarity : 0.004 0.043 3678 Dihedral : 9.678 85.584 3072 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2496 helix: 1.44 (0.12), residues: 1824 sheet: None (None), residues: 0 loop : -0.10 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 317 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 48 residues processed: 380 average time/residue: 1.3047 time to fit residues: 571.0030 Evaluate side-chains 351 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 43 residues processed: 5 average time/residue: 0.4923 time to fit residues: 6.6895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN H 437 ASN J 281 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 22842 Z= 0.172 Angle : 0.555 12.399 31068 Z= 0.254 Chirality : 0.042 0.362 3558 Planarity : 0.004 0.042 3678 Dihedral : 9.708 82.662 3072 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2496 helix: 1.40 (0.12), residues: 1830 sheet: None (None), residues: 0 loop : 0.00 (0.22), residues: 666 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 315 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 51 residues processed: 372 average time/residue: 1.2625 time to fit residues: 540.3687 Evaluate side-chains 349 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 298 time to evaluate : 2.701 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 45 residues processed: 6 average time/residue: 0.2304 time to fit residues: 5.7762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 1.9990 chunk 212 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 136 optimal weight: 0.4980 chunk 98 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN D 373 HIS ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN J 281 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 22842 Z= 0.151 Angle : 0.550 15.185 31068 Z= 0.250 Chirality : 0.041 0.349 3558 Planarity : 0.004 0.043 3678 Dihedral : 9.619 79.837 3072 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.17), residues: 2496 helix: 1.53 (0.12), residues: 1818 sheet: None (None), residues: 0 loop : -0.09 (0.22), residues: 678 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 310 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 47 residues processed: 365 average time/residue: 1.3104 time to fit residues: 547.2015 Evaluate side-chains 338 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 291 time to evaluate : 2.494 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 5 average time/residue: 0.2163 time to fit residues: 5.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.0670 chunk 146 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 154 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN J 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 22842 Z= 0.139 Angle : 0.548 15.122 31068 Z= 0.249 Chirality : 0.041 0.370 3558 Planarity : 0.004 0.043 3678 Dihedral : 9.508 77.734 3072 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.17), residues: 2496 helix: 1.79 (0.12), residues: 1788 sheet: None (None), residues: 0 loop : -0.21 (0.22), residues: 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 305 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 44 residues processed: 353 average time/residue: 1.2931 time to fit residues: 524.3467 Evaluate side-chains 330 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 286 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 41 residues processed: 3 average time/residue: 0.2478 time to fit residues: 4.8478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN J 281 GLN ** J 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.162064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.126753 restraints weight = 25739.778| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.63 r_work: 0.3225 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 22842 Z= 0.215 Angle : 0.582 14.139 31068 Z= 0.269 Chirality : 0.043 0.362 3558 Planarity : 0.004 0.044 3678 Dihedral : 9.776 78.995 3072 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.16), residues: 2496 helix: 1.56 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -0.02 (0.22), residues: 696 =============================================================================== Job complete usr+sys time: 8548.49 seconds wall clock time: 152 minutes 43.23 seconds (9163.23 seconds total)