Starting phenix.real_space_refine on Sun Dec 10 20:43:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wj9_8841/12_2023/5wj9_8841_neut_updated.pdb" } resolution = 3.49 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= 0.015 sd= 0.186 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 100 5.16 5 C 10172 2.51 5 N 2584 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D ARG 347": "NH1" <-> "NH2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15540 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "B" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "C" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "D" Number of atoms: 3858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3858 Classifications: {'peptide': 479} Link IDs: {'PTRANS': 18, 'TRANS': 460} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'AQV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.47, per 1000 atoms: 0.55 Number of scatterers: 15540 At special positions: 0 Unit cell: (109, 109, 120, 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 100 16.00 O 2684 8.00 N 2584 7.00 C 10172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 253 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 166 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 166 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 253 " - pdb=" SG CYS D 284 " distance=2.03 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: 5.93 Conformation dependent library (CDL) restraints added in 2.8 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 57.2% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 4.046A pdb=" N PHE A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 64 through 105 removed outlier: 3.520A pdb=" N GLN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 137 Processing helix chain 'A' and resid 139 through 142 No H-bonds generated for 'chain 'A' and resid 139 through 142' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 292 through 336 removed outlier: 3.891A pdb=" N SER A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 353 through 377 Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.942A pdb=" N VAL A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 417 through 447 Proline residue: A 423 - end of helix removed outlier: 4.081A pdb=" N CYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 removed outlier: 3.921A pdb=" N PHE A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A 480 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 524 Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.047A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 105 removed outlier: 3.521A pdb=" N GLN B 69 " --> pdb=" O LYS B 65 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 292 through 336 removed outlier: 3.891A pdb=" N SER B 296 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 353 through 377 Processing helix chain 'B' and resid 383 through 404 removed outlier: 3.945A pdb=" N VAL B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 402 " --> pdb=" O TRP B 398 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 417 through 447 Proline residue: B 423 - end of helix removed outlier: 4.082A pdb=" N CYS B 431 " --> pdb=" O ARG B 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 removed outlier: 3.922A pdb=" N PHE B 477 " --> pdb=" O MET B 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET B 480 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 481 " --> pdb=" O PHE B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 524 Processing helix chain 'C' and resid 42 through 49 removed outlier: 4.045A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 64 through 105 removed outlier: 3.517A pdb=" N GLN C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 139 through 142 No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 292 through 336 removed outlier: 3.889A pdb=" N SER C 296 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 299 " --> pdb=" O ASN C 295 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY C 332 " --> pdb=" O ASN C 328 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 353 through 376 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.944A pdb=" N VAL C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 417 through 447 Proline residue: C 423 - end of helix removed outlier: 4.083A pdb=" N CYS C 431 " --> pdb=" O ARG C 427 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 removed outlier: 3.921A pdb=" N PHE C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET C 480 " --> pdb=" O THR C 476 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN C 481 " --> pdb=" O PHE C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 485 No H-bonds generated for 'chain 'C' and resid 483 through 485' Processing helix chain 'C' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU C 496 " --> pdb=" O LEU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 524 Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.048A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 64 through 105 removed outlier: 3.518A pdb=" N GLN D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 292 through 336 removed outlier: 3.890A pdb=" N SER D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 299 " --> pdb=" O ASN D 295 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY D 332 " --> pdb=" O ASN D 328 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 353 through 377 Processing helix chain 'D' and resid 383 through 404 removed outlier: 3.943A pdb=" N VAL D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 417 through 447 Proline residue: D 423 - end of helix removed outlier: 4.081A pdb=" N CYS D 431 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 469 removed outlier: 3.528A pdb=" N PHE D 465 " --> pdb=" O SER D 461 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 469 " --> pdb=" O PHE D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 481 removed outlier: 3.921A pdb=" N PHE D 477 " --> pdb=" O MET D 473 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET D 480 " --> pdb=" O THR D 476 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 481 " --> pdb=" O PHE D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 485 No H-bonds generated for 'chain 'D' and resid 483 through 485' Processing helix chain 'D' and resid 488 through 506 removed outlier: 3.554A pdb=" N LEU D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 524 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 195 removed outlier: 3.566A pdb=" N HIS A 234 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR A 170 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 228 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 278 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 188 through 195 removed outlier: 3.566A pdb=" N HIS B 234 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B 170 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU B 228 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 278 " --> pdb=" O SER B 257 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 188 through 195 removed outlier: 3.566A pdb=" N HIS C 234 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TYR C 170 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 228 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 278 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 188 through 195 removed outlier: 3.565A pdb=" N HIS D 234 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR D 170 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU D 228 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 278 " --> pdb=" O SER D 257 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2469 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: 4.68 Time building geometry restraints manager: 6.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.12: 1 1.12 - 1.34: 4699 1.34 - 1.56: 11081 1.56 - 1.78: 26 1.78 - 2.01: 141 Bond restraints: 15948 Sorted by residual: bond pdb=" C PRO B 205 " pdb=" O PRO B 205 " ideal model delta sigma weight residual 1.231 2.007 -0.776 2.00e-02 2.50e+03 1.51e+03 bond pdb=" C HIS D 526 " pdb=" O HIS D 526 " ideal model delta sigma weight residual 1.231 1.761 -0.530 2.00e-02 2.50e+03 7.02e+02 bond pdb=" C HIS A 526 " pdb=" O HIS A 526 " ideal model delta sigma weight residual 1.231 1.678 -0.447 2.00e-02 2.50e+03 5.00e+02 bond pdb=" C HIS C 526 " pdb=" O HIS C 526 " ideal model delta sigma weight residual 1.231 1.668 -0.437 2.00e-02 2.50e+03 4.78e+02 bond pdb=" C PRO D 205 " pdb=" O PRO D 205 " ideal model delta sigma weight residual 1.231 0.893 0.338 2.00e-02 2.50e+03 2.85e+02 ... (remaining 15943 not shown) Histogram of bond angle deviations from ideal: 99.42 - 107.23: 534 107.23 - 115.05: 9100 115.05 - 122.87: 9492 122.87 - 130.69: 2460 130.69 - 138.51: 94 Bond angle restraints: 21680 Sorted by residual: angle pdb=" CA HIS A 526 " pdb=" C HIS A 526 " pdb=" O HIS A 526 " ideal model delta sigma weight residual 120.80 138.51 -17.71 1.70e+00 3.46e-01 1.09e+02 angle pdb=" CA HIS D 526 " pdb=" C HIS D 526 " pdb=" O HIS D 526 " ideal model delta sigma weight residual 120.80 136.18 -15.38 1.70e+00 3.46e-01 8.18e+01 angle pdb=" CA HIS B 526 " pdb=" C HIS B 526 " pdb=" O HIS B 526 " ideal model delta sigma weight residual 120.80 135.60 -14.80 1.70e+00 3.46e-01 7.58e+01 angle pdb=" C VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta sigma weight residual 112.22 121.95 -9.73 1.38e+00 5.25e-01 4.97e+01 angle pdb=" O GLY D 448 " pdb=" C GLY D 448 " pdb=" N PRO D 449 " ideal model delta sigma weight residual 121.07 123.02 -1.95 3.60e-01 7.72e+00 2.94e+01 ... (remaining 21675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.07: 8946 28.07 - 56.15: 334 56.15 - 84.22: 40 84.22 - 112.29: 0 112.29 - 140.37: 4 Dihedral angle restraints: 9324 sinusoidal: 3712 harmonic: 5612 Sorted by residual: dihedral pdb=" C VAL A 359 " pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta harmonic sigma weight residual -122.00 -148.43 26.43 0 2.50e+00 1.60e-01 1.12e+02 dihedral pdb=" N VAL A 359 " pdb=" C VAL A 359 " pdb=" CA VAL A 359 " pdb=" CB VAL A 359 " ideal model delta harmonic sigma weight residual 123.40 146.17 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" N PHE B 324 " pdb=" C PHE B 324 " pdb=" CA PHE B 324 " pdb=" CB PHE B 324 " ideal model delta harmonic sigma weight residual 122.80 141.88 -19.08 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2392 0.187 - 0.374: 53 0.374 - 0.561: 4 0.561 - 0.748: 1 0.748 - 0.935: 2 Chirality restraints: 2452 Sorted by residual: chirality pdb=" CA VAL A 359 " pdb=" N VAL A 359 " pdb=" C VAL A 359 " pdb=" CB VAL A 359 " both_signs ideal model delta sigma weight residual False 2.44 1.51 0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" CA PHE B 324 " pdb=" N PHE B 324 " pdb=" C PHE B 324 " pdb=" CB PHE B 324 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA PHE A 350 " pdb=" N PHE A 350 " pdb=" C PHE A 350 " pdb=" CB PHE A 350 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.37e+00 ... (remaining 2449 not shown) Planarity restraints: 2692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 378 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LYS C 378 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS C 378 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN C 379 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 422 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 423 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 422 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 423 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " 0.028 5.00e-02 4.00e+02 ... (remaining 2689 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 493 2.76 - 3.29: 17478 3.29 - 3.83: 24871 3.83 - 4.36: 31204 4.36 - 4.90: 51451 Nonbonded interactions: 125497 Sorted by model distance: nonbonded pdb=" OG1 THR B 77 " pdb=" CZ2 TRP B 398 " model vdw 2.225 3.340 nonbonded pdb=" O THR B 394 " pdb=" CD1 TRP B 398 " model vdw 2.323 3.260 nonbonded pdb=" O TYR A 439 " pdb=" OH TYR A 497 " model vdw 2.495 2.440 nonbonded pdb=" O TYR B 439 " pdb=" OH TYR B 497 " model vdw 2.496 2.440 nonbonded pdb=" O TYR C 439 " pdb=" OH TYR C 497 " model vdw 2.496 2.440 ... (remaining 125492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.340 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.980 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.014 0.776 15948 Z= 1.026 Angle : 1.228 17.712 21680 Z= 0.819 Chirality : 0.074 0.935 2452 Planarity : 0.005 0.051 2692 Dihedral : 15.074 140.365 5684 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.05 % Favored : 90.68 % Rotamer: Outliers : 1.93 % Allowed : 7.55 % Favored : 90.52 % Cbeta Deviations : 0.22 % 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: -3.89 (0.15), residues: 1900 helix: -1.76 (0.12), residues: 1028 sheet: -3.07 (0.32), residues: 196 loop : -3.57 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 345 HIS 0.009 0.002 HIS B 103 PHE 0.027 0.003 PHE C 182 TYR 0.023 0.002 TYR A 355 ARG 0.010 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 643 time to evaluate : 1.992 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 outliers start: 33 outliers final: 10 residues processed: 658 average time/residue: 0.2681 time to fit residues: 260.6348 Evaluate side-chains 399 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 389 time to evaluate : 1.898 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1387 time to fit residues: 4.9655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN A 483 GLN B 69 GLN B 79 GLN B 97 ASN B 243 GLN B 483 GLN C 69 GLN C 79 GLN C 97 ASN C 483 GLN D 69 GLN D 79 GLN D 97 ASN D 483 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15948 Z= 0.260 Angle : 0.824 12.072 21680 Z= 0.413 Chirality : 0.049 0.203 2452 Planarity : 0.006 0.049 2692 Dihedral : 9.224 136.109 2132 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 4.22 % Allowed : 18.09 % Favored : 77.69 % 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: -2.06 (0.17), residues: 1900 helix: -0.51 (0.13), residues: 1092 sheet: -1.77 (0.35), residues: 176 loop : -2.66 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 491 HIS 0.013 0.002 HIS D 451 PHE 0.024 0.003 PHE A 330 TYR 0.021 0.002 TYR D 436 ARG 0.004 0.000 ARG D 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 395 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 43 residues processed: 432 average time/residue: 0.2485 time to fit residues: 164.5730 Evaluate side-chains 392 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 349 time to evaluate : 1.922 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.1428 time to fit residues: 14.0333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 483 GLN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 15948 Z= 0.510 Angle : 0.850 9.323 21680 Z= 0.434 Chirality : 0.049 0.179 2452 Planarity : 0.005 0.045 2692 Dihedral : 8.775 135.119 2132 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.16 % Favored : 92.79 % Rotamer: Outliers : 5.04 % Allowed : 18.68 % Favored : 76.29 % 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: -1.70 (0.18), residues: 1900 helix: -0.10 (0.14), residues: 1060 sheet: -1.46 (0.37), residues: 196 loop : -2.70 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 354 HIS 0.010 0.002 HIS C 451 PHE 0.023 0.003 PHE A 493 TYR 0.016 0.002 TYR B 218 ARG 0.006 0.001 ARG C 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 361 time to evaluate : 1.930 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 outliers start: 86 outliers final: 33 residues processed: 395 average time/residue: 0.2539 time to fit residues: 152.0778 Evaluate side-chains 339 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 306 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1486 time to fit residues: 11.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 171 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 162 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15948 Z= 0.218 Angle : 0.728 9.250 21680 Z= 0.365 Chirality : 0.045 0.296 2452 Planarity : 0.004 0.038 2692 Dihedral : 8.511 133.339 2132 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 3.86 % Allowed : 20.67 % Favored : 75.47 % 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: -1.56 (0.19), residues: 1900 helix: -0.04 (0.14), residues: 1076 sheet: -1.20 (0.38), residues: 204 loop : -2.68 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 444 HIS 0.009 0.001 HIS C 451 PHE 0.032 0.002 PHE A 49 TYR 0.012 0.001 TYR D 497 ARG 0.008 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 360 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 26 residues processed: 398 average time/residue: 0.2474 time to fit residues: 153.0523 Evaluate side-chains 353 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 327 time to evaluate : 2.048 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1597 time to fit residues: 10.1807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15948 Z= 0.221 Angle : 0.747 13.818 21680 Z= 0.362 Chirality : 0.046 0.320 2452 Planarity : 0.004 0.044 2692 Dihedral : 8.350 132.276 2132 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 1.70 % Allowed : 24.36 % Favored : 73.95 % 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 (0.19), residues: 1900 helix: 0.09 (0.15), residues: 1072 sheet: -0.98 (0.38), residues: 204 loop : -2.64 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 444 HIS 0.011 0.001 HIS C 451 PHE 0.027 0.002 PHE C 49 TYR 0.016 0.001 TYR A 411 ARG 0.004 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 354 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 360 average time/residue: 0.2389 time to fit residues: 133.2051 Evaluate side-chains 345 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 336 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1450 time to fit residues: 5.0620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 0.1980 chunk 150 optimal weight: 1.9990 chunk 84 optimal weight: 0.0000 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15948 Z= 0.201 Angle : 0.740 13.421 21680 Z= 0.356 Chirality : 0.046 0.398 2452 Planarity : 0.004 0.044 2692 Dihedral : 8.273 131.455 2132 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 1.87 % Allowed : 25.70 % Favored : 72.42 % 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: -1.35 (0.19), residues: 1900 helix: 0.12 (0.15), residues: 1088 sheet: -0.89 (0.37), residues: 204 loop : -2.70 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 444 HIS 0.014 0.001 HIS C 451 PHE 0.016 0.002 PHE C 493 TYR 0.022 0.001 TYR A 436 ARG 0.007 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 378 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 397 average time/residue: 0.2412 time to fit residues: 149.3704 Evaluate side-chains 346 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 329 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1392 time to fit residues: 6.9132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15948 Z= 0.230 Angle : 0.752 11.578 21680 Z= 0.364 Chirality : 0.046 0.306 2452 Planarity : 0.004 0.045 2692 Dihedral : 8.209 130.013 2132 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 2.22 % Allowed : 25.41 % Favored : 72.37 % 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: -1.26 (0.19), residues: 1900 helix: 0.16 (0.15), residues: 1088 sheet: -0.80 (0.38), residues: 204 loop : -2.63 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 444 HIS 0.015 0.001 HIS A 451 PHE 0.035 0.002 PHE D 493 TYR 0.017 0.001 TYR C 436 ARG 0.005 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 344 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 23 residues processed: 359 average time/residue: 0.2238 time to fit residues: 128.6477 Evaluate side-chains 362 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 339 time to evaluate : 1.887 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1439 time to fit residues: 8.6901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15948 Z= 0.227 Angle : 0.754 11.517 21680 Z= 0.366 Chirality : 0.046 0.360 2452 Planarity : 0.004 0.044 2692 Dihedral : 8.225 128.364 2132 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 1.29 % Allowed : 27.46 % Favored : 71.25 % 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: -1.31 (0.19), residues: 1900 helix: 0.10 (0.15), residues: 1080 sheet: -0.74 (0.38), residues: 204 loop : -2.59 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP D 444 HIS 0.009 0.001 HIS A 451 PHE 0.031 0.002 PHE D 493 TYR 0.018 0.001 TYR C 411 ARG 0.004 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 358 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 369 average time/residue: 0.2254 time to fit residues: 131.6388 Evaluate side-chains 334 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 325 time to evaluate : 1.974 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1320 time to fit residues: 4.8551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15948 Z= 0.224 Angle : 0.775 12.474 21680 Z= 0.376 Chirality : 0.046 0.299 2452 Planarity : 0.004 0.044 2692 Dihedral : 8.191 127.740 2132 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 0.76 % Allowed : 27.93 % Favored : 71.31 % 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 (0.19), residues: 1900 helix: 0.18 (0.15), residues: 1084 sheet: -0.68 (0.39), residues: 204 loop : -2.50 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP D 444 HIS 0.008 0.001 HIS C 451 PHE 0.032 0.002 PHE D 493 TYR 0.017 0.001 TYR C 436 ARG 0.007 0.000 ARG D 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 345 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 352 average time/residue: 0.2274 time to fit residues: 126.9769 Evaluate side-chains 340 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 1.638 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1452 time to fit residues: 5.0966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 0.0980 chunk 91 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15948 Z= 0.243 Angle : 0.796 12.129 21680 Z= 0.387 Chirality : 0.047 0.312 2452 Planarity : 0.004 0.044 2692 Dihedral : 8.210 127.346 2132 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 0.12 % Allowed : 28.92 % Favored : 70.96 % 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: -1.09 (0.19), residues: 1900 helix: 0.23 (0.15), residues: 1080 sheet: -0.37 (0.40), residues: 196 loop : -2.51 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP C 444 HIS 0.006 0.001 HIS C 451 PHE 0.030 0.002 PHE A 493 TYR 0.032 0.001 TYR D 436 ARG 0.006 0.000 ARG C 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 345 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 346 average time/residue: 0.2215 time to fit residues: 122.6178 Evaluate side-chains 317 residues out of total 1708 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1308 time to fit residues: 2.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 131 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.116446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.092898 restraints weight = 41586.713| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.76 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15948 Z= 0.247 Angle : 0.801 11.623 21680 Z= 0.388 Chirality : 0.047 0.289 2452 Planarity : 0.004 0.046 2692 Dihedral : 8.163 126.732 2132 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 0.88 % Allowed : 28.92 % Favored : 70.20 % 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: -1.12 (0.19), residues: 1900 helix: 0.19 (0.15), residues: 1080 sheet: -0.27 (0.40), residues: 196 loop : -2.54 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 444 HIS 0.006 0.001 HIS C 451 PHE 0.030 0.002 PHE B 493 TYR 0.025 0.001 TYR D 436 ARG 0.005 0.000 ARG C 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.75 seconds wall clock time: 66 minutes 47.37 seconds (4007.37 seconds total)