Starting phenix.real_space_refine on Sat Feb 17 05:28:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wek_21650/02_2024/6wek_21650_neut_updated.pdb" } resolution = 2.7 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= -0.001 sd= 0.142 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 96 5.16 5 C 11520 2.51 5 N 2880 2.21 5 O 3104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A ARG 106": "NH1" <-> "NH2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 537": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B ARG 421": "NH1" <-> "NH2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 537": "NH1" <-> "NH2" Residue "B ARG 580": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C ARG 421": "NH1" <-> "NH2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 537": "NH1" <-> "NH2" Residue "C ARG 580": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D ARG 421": "NH1" <-> "NH2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 537": "NH1" <-> "NH2" Residue "D ARG 580": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17616 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4243 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 bond proxies already assigned to first conformer: 4326 Chain: "B" Number of atoms: 4243 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 bond proxies already assigned to first conformer: 4326 Chain: "C" Number of atoms: 4243 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 bond proxies already assigned to first conformer: 4326 Chain: "D" Number of atoms: 4243 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 512, 4234 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 15, 'TRANS': 496} Chain breaks: 1 bond proxies already assigned to first conformer: 4326 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Unusual residues: {'CPL': 6, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Unusual residues: {'CPL': 6, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Unusual residues: {'CPL': 6, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 161 Unusual residues: {'CPL': 6, 'PCG': 1, 'PX2': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 249 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CPL:plan-4': 6, 'CPL:plan-3': 6, 'CPL:plan-2': 4, 'CPL:plan-1': 4} Unresolved non-hydrogen planarities: 75 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN A 230 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 230 " occ=0.50 residue: pdb=" N AGLN B 230 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 230 " occ=0.50 residue: pdb=" N AGLN C 230 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 230 " occ=0.50 residue: pdb=" N AGLN D 230 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 230 " occ=0.50 Time building chain proxies: 16.70, per 1000 atoms: 0.95 Number of scatterers: 17616 At special positions: 0 Unit cell: (123.05, 123.05, 132.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 16 15.00 O 3104 8.00 N 2880 7.00 C 11520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 172 " distance=2.02 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 172 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 172 " distance=2.02 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 172 " distance=2.02 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 5.7 seconds 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 56.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 120 through 144 removed outlier: 4.731A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 223 removed outlier: 6.236A pdb=" N HIS A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 249 through 257 removed outlier: 3.622A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 277 through 285 removed outlier: 4.151A pdb=" N ASN A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 Processing helix chain 'A' and resid 304 through 334 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 418 removed outlier: 3.840A pdb=" N MET A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 485 through 488 No H-bonds generated for 'chain 'A' and resid 485 through 488' Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 499 through 508 removed outlier: 4.074A pdb=" N LYS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 601 Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 120 through 144 removed outlier: 4.731A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 223 removed outlier: 6.235A pdb=" N HIS B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 249 through 257 removed outlier: 3.622A pdb=" N LEU B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 277 through 285 removed outlier: 4.151A pdb=" N ASN B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 304 through 334 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 418 removed outlier: 3.840A pdb=" N MET B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 437 Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 485 through 488 No H-bonds generated for 'chain 'B' and resid 485 through 488' Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 499 through 508 removed outlier: 4.074A pdb=" N LYS B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 592 through 601 Processing helix chain 'B' and resid 603 through 619 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 120 through 144 removed outlier: 4.732A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 223 removed outlier: 6.236A pdb=" N HIS C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.622A pdb=" N LEU C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 277 through 285 removed outlier: 4.150A pdb=" N ASN C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 304 through 334 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 418 removed outlier: 3.841A pdb=" N MET C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 437 Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 485 through 488 No H-bonds generated for 'chain 'C' and resid 485 through 488' Processing helix chain 'C' and resid 492 through 495 No H-bonds generated for 'chain 'C' and resid 492 through 495' Processing helix chain 'C' and resid 499 through 508 removed outlier: 4.073A pdb=" N LYS C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 563 No H-bonds generated for 'chain 'C' and resid 560 through 563' Processing helix chain 'C' and resid 592 through 601 Processing helix chain 'C' and resid 603 through 619 Processing helix chain 'D' and resid 104 through 110 Processing helix chain 'D' and resid 120 through 144 removed outlier: 4.731A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 223 removed outlier: 6.236A pdb=" N HIS D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 249 through 257 removed outlier: 3.622A pdb=" N LEU D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 277 through 285 removed outlier: 4.150A pdb=" N ASN D 282 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 304 through 334 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 418 removed outlier: 3.840A pdb=" N MET D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 437 Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 488 No H-bonds generated for 'chain 'D' and resid 485 through 488' Processing helix chain 'D' and resid 492 through 495 No H-bonds generated for 'chain 'D' and resid 492 through 495' Processing helix chain 'D' and resid 499 through 508 removed outlier: 4.073A pdb=" N LYS D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 563 No H-bonds generated for 'chain 'D' and resid 560 through 563' Processing helix chain 'D' and resid 592 through 601 Processing helix chain 'D' and resid 603 through 619 Processing sheet with id= A, first strand: chain 'A' and resid 157 through 159 Processing sheet with id= B, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.150A pdb=" N PHE A 588 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL A 533 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 590 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR A 531 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 550 through 552 removed outlier: 3.890A pdb=" N VAL A 550 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 157 through 159 Processing sheet with id= E, first strand: chain 'B' and resid 510 through 514 removed outlier: 6.150A pdb=" N PHE B 588 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 533 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 590 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR B 531 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 550 through 552 removed outlier: 3.890A pdb=" N VAL B 550 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 157 through 159 Processing sheet with id= H, first strand: chain 'C' and resid 510 through 514 removed outlier: 6.150A pdb=" N PHE C 588 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL C 533 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 590 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR C 531 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 550 through 552 removed outlier: 3.890A pdb=" N VAL C 550 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 157 through 159 Processing sheet with id= K, first strand: chain 'D' and resid 510 through 514 removed outlier: 6.151A pdb=" N PHE D 588 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL D 533 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 590 " --> pdb=" O TYR D 531 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR D 531 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 550 through 552 removed outlier: 3.890A pdb=" N VAL D 550 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.37 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 157 1.22 - 1.37: 5891 1.37 - 1.51: 7095 1.51 - 1.66: 4713 1.66 - 1.81: 156 Bond restraints: 18012 Sorted by residual: bond pdb=" C3' PCG D 801 " pdb=" C4' PCG D 801 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C3' PCG B 801 " pdb=" C4' PCG B 801 " ideal model delta sigma weight residual 1.808 1.494 0.314 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG C 801 " pdb=" C4' PCG C 801 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.46e+02 bond pdb=" C3' PCG A 801 " pdb=" C4' PCG A 801 " ideal model delta sigma weight residual 1.808 1.495 0.313 2.00e-02 2.50e+03 2.45e+02 bond pdb=" C2' PCG C 801 " pdb=" C3' PCG C 801 " ideal model delta sigma weight residual 1.200 1.492 -0.292 2.00e-02 2.50e+03 2.13e+02 ... (remaining 18007 not shown) Histogram of bond angle deviations from ideal: 86.49 - 96.39: 12 96.39 - 106.29: 499 106.29 - 116.20: 11159 116.20 - 126.10: 12270 126.10 - 136.00: 384 Bond angle restraints: 24324 Sorted by residual: angle pdb=" CA GLN D 425 " pdb=" C GLN D 425 " pdb=" O GLN D 425 " ideal model delta sigma weight residual 120.10 132.15 -12.05 1.13e+00 7.83e-01 1.14e+02 angle pdb=" CA GLN A 425 " pdb=" C GLN A 425 " pdb=" O GLN A 425 " ideal model delta sigma weight residual 120.10 132.13 -12.03 1.13e+00 7.83e-01 1.13e+02 angle pdb=" CA GLN B 425 " pdb=" C GLN B 425 " pdb=" O GLN B 425 " ideal model delta sigma weight residual 120.10 132.12 -12.02 1.13e+00 7.83e-01 1.13e+02 angle pdb=" CA GLN C 425 " pdb=" C GLN C 425 " pdb=" O GLN C 425 " ideal model delta sigma weight residual 120.10 132.11 -12.01 1.13e+00 7.83e-01 1.13e+02 angle pdb=" C ASN A 409 " pdb=" CA ASN A 409 " pdb=" CB ASN A 409 " ideal model delta sigma weight residual 110.79 95.16 15.63 1.66e+00 3.63e-01 8.87e+01 ... (remaining 24319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.56: 10225 30.56 - 61.11: 467 61.11 - 91.67: 32 91.67 - 122.23: 4 122.23 - 152.78: 16 Dihedral angle restraints: 10744 sinusoidal: 4684 harmonic: 6060 Sorted by residual: dihedral pdb=" C ASN A 409 " pdb=" N ASN A 409 " pdb=" CA ASN A 409 " pdb=" CB ASN A 409 " ideal model delta harmonic sigma weight residual -122.60 -106.33 -16.27 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" C ASN B 409 " pdb=" N ASN B 409 " pdb=" CA ASN B 409 " pdb=" CB ASN B 409 " ideal model delta harmonic sigma weight residual -122.60 -106.33 -16.27 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" C ASN D 409 " pdb=" N ASN D 409 " pdb=" CA ASN D 409 " pdb=" CB ASN D 409 " ideal model delta harmonic sigma weight residual -122.60 -106.34 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 10741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2515 0.133 - 0.267: 77 0.267 - 0.400: 32 0.400 - 0.534: 10 0.534 - 0.667: 10 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CA LYS B 523 " pdb=" N LYS B 523 " pdb=" C LYS B 523 " pdb=" CB LYS B 523 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA LYS A 523 " pdb=" N LYS A 523 " pdb=" C LYS A 523 " pdb=" CB LYS A 523 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA LYS C 523 " pdb=" N LYS C 523 " pdb=" C LYS C 523 " pdb=" CB LYS C 523 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 2641 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BGLN A 230 " -0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C BGLN A 230 " 0.073 2.00e-02 2.50e+03 pdb=" O BGLN A 230 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY A 231 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BGLN B 230 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C BGLN B 230 " -0.073 2.00e-02 2.50e+03 pdb=" O BGLN B 230 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY B 231 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BGLN C 230 " 0.021 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C BGLN C 230 " -0.073 2.00e-02 2.50e+03 pdb=" O BGLN C 230 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY C 231 " 0.025 2.00e-02 2.50e+03 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 171 2.57 - 3.15: 14183 3.15 - 3.74: 26632 3.74 - 4.32: 39904 4.32 - 4.90: 65847 Nonbonded interactions: 146737 Sorted by model distance: nonbonded pdb=" NH2 ARG C 537 " pdb=" OE1AGLN D 230 " model vdw 1.988 2.520 nonbonded pdb=" NH2 ARG A 537 " pdb=" OE1AGLN B 230 " model vdw 2.125 2.520 nonbonded pdb=" OE1AGLN A 230 " pdb=" NH2 ARG D 537 " model vdw 2.142 2.520 nonbonded pdb=" NH2 ARG B 537 " pdb=" OE1AGLN C 230 " model vdw 2.154 2.520 nonbonded pdb=" OG SER A 562 " pdb=" O1A PCG A 801 " model vdw 2.169 2.440 ... (remaining 146732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 103 through 229 or resid 231 through 620 or resid 801 thro \ ugh 808)) selection = (chain 'B' and (resid 103 through 229 or resid 231 through 620 or resid 801 thro \ ugh 808)) selection = (chain 'C' and (resid 103 through 229 or resid 231 through 620 or resid 801 thro \ ugh 808)) selection = (chain 'D' and (resid 103 through 229 or resid 231 through 620 or resid 801 thro \ ugh 808)) } 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=0.50 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: 0.910 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: 0.270 Set scattering table: 0.180 Process input model: 58.760 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.140 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 0.019 0.314 18012 Z= 1.251 Angle : 1.556 27.392 24324 Z= 0.771 Chirality : 0.081 0.667 2644 Planarity : 0.006 0.059 2948 Dihedral : 17.505 152.784 6844 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.95 % Allowed : 7.96 % Favored : 87.10 % Cbeta Deviations : 1.23 % 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: -1.65 (0.17), residues: 2044 helix: -0.65 (0.13), residues: 1176 sheet: -0.45 (0.43), residues: 116 loop : -1.75 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 596 HIS 0.004 0.002 HIS D 199 PHE 0.022 0.002 PHE C 403 TYR 0.016 0.002 TYR C 223 ARG 0.003 0.001 ARG C 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 290 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7582 (ttm110) REVERT: A 272 ASN cc_start: 0.8154 (t0) cc_final: 0.7790 (t0) REVERT: A 274 ARG cc_start: 0.7706 (mmt90) cc_final: 0.7132 (mmt180) REVERT: A 326 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 397 MET cc_start: 0.8452 (mmm) cc_final: 0.8218 (mmm) REVERT: A 428 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8598 (tpt) REVERT: A 433 GLN cc_start: 0.8135 (tt0) cc_final: 0.7746 (tt0) REVERT: A 537 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7652 (ttp-170) REVERT: A 571 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7341 (p0) REVERT: A 615 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: B 158 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7621 (ttm110) REVERT: B 272 ASN cc_start: 0.8230 (t0) cc_final: 0.7897 (t0) REVERT: B 274 ARG cc_start: 0.7823 (mmt90) cc_final: 0.7452 (mmt180) REVERT: B 397 MET cc_start: 0.8567 (mmm) cc_final: 0.8229 (mmm) REVERT: B 413 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7678 (mtt) REVERT: B 428 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8738 (tpt) REVERT: B 433 GLN cc_start: 0.8089 (tt0) cc_final: 0.7750 (tt0) REVERT: B 537 ARG cc_start: 0.8088 (ttm-80) cc_final: 0.7615 (ttp-170) REVERT: B 571 ASN cc_start: 0.7317 (OUTLIER) cc_final: 0.7018 (p0) REVERT: B 614 ARG cc_start: 0.7355 (ttm170) cc_final: 0.7012 (mtp85) REVERT: C 158 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7646 (ttm110) REVERT: C 188 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8784 (mt0) REVERT: C 272 ASN cc_start: 0.8178 (t0) cc_final: 0.7880 (t0) REVERT: C 274 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7142 (mmt180) REVERT: C 397 MET cc_start: 0.8559 (mmm) cc_final: 0.8306 (tpt) REVERT: C 413 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7502 (mtt) REVERT: C 417 MET cc_start: 0.7788 (mtt) cc_final: 0.7581 (mtt) REVERT: C 433 GLN cc_start: 0.8054 (tt0) cc_final: 0.7650 (tt0) REVERT: C 537 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7508 (ttp-170) REVERT: C 571 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7303 (p0) REVERT: C 591 SER cc_start: 0.8532 (t) cc_final: 0.8316 (p) REVERT: D 158 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7665 (ttm110) REVERT: D 272 ASN cc_start: 0.8316 (t0) cc_final: 0.8017 (t0) REVERT: D 274 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7319 (mmt180) REVERT: D 326 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7944 (tp) REVERT: D 397 MET cc_start: 0.8565 (mmm) cc_final: 0.8291 (tpt) REVERT: D 413 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7578 (mtt) REVERT: D 428 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8795 (tpt) REVERT: D 433 GLN cc_start: 0.7965 (tt0) cc_final: 0.7689 (tt0) REVERT: D 537 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7639 (ttp-170) REVERT: D 614 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6959 (mtp85) outliers start: 92 outliers final: 35 residues processed: 361 average time/residue: 1.5727 time to fit residues: 622.2515 Evaluate side-chains 268 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 220 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 571 ASN Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain B residue 576 THR Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 526 ILE Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain C residue 576 THR Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 470 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 571 ASN Chi-restraints excluded: chain D residue 576 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 179 ASN A 188 GLN A 199 HIS A 323 ASN A 386 ASN A 416 ASN A 425 GLN A 433 GLN A 458 ASN A 466 GLN A 597 ASN B 146 ASN B 179 ASN B 188 GLN B 199 HIS B 323 ASN B 386 ASN B 433 GLN B 443 GLN B 458 ASN B 495 GLN B 597 ASN C 146 ASN C 179 ASN C 199 HIS C 323 ASN C 386 ASN C 425 GLN C 433 GLN C 458 ASN C 597 ASN D 146 ASN D 179 ASN D 188 GLN D 199 HIS D 323 ASN D 386 ASN D 426 ASN D 433 GLN D 443 GLN D 458 ASN D 495 GLN D 597 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18012 Z= 0.170 Angle : 0.548 6.298 24324 Z= 0.285 Chirality : 0.040 0.172 2644 Planarity : 0.004 0.051 2948 Dihedral : 15.931 143.200 2833 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.58 % Allowed : 14.95 % Favored : 82.47 % 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: -0.09 (0.18), residues: 2044 helix: 0.70 (0.15), residues: 1196 sheet: 0.48 (0.45), residues: 116 loop : -1.39 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 596 HIS 0.004 0.001 HIS B 199 PHE 0.011 0.001 PHE D 138 TYR 0.022 0.001 TYR B 160 ARG 0.005 0.000 ARG C 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 257 time to evaluate : 1.844 Fit side-chains REVERT: A 272 ASN cc_start: 0.8126 (t0) cc_final: 0.7664 (t0) REVERT: A 326 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8206 (tp) REVERT: A 397 MET cc_start: 0.8388 (mmm) cc_final: 0.8001 (tpt) REVERT: A 407 VAL cc_start: 0.7454 (t) cc_final: 0.7037 (m) REVERT: A 433 GLN cc_start: 0.7914 (tt0) cc_final: 0.7615 (tt0) REVERT: A 537 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7764 (ttp80) REVERT: B 158 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7098 (mtm180) REVERT: B 272 ASN cc_start: 0.8170 (t0) cc_final: 0.7920 (t0) REVERT: B 291 ARG cc_start: 0.7617 (ttm110) cc_final: 0.7363 (ttp-110) REVERT: B 397 MET cc_start: 0.8349 (mmm) cc_final: 0.7930 (tpt) REVERT: B 407 VAL cc_start: 0.7479 (t) cc_final: 0.6931 (m) REVERT: B 433 GLN cc_start: 0.7915 (tt0) cc_final: 0.7591 (tt0) REVERT: B 537 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7732 (ttp80) REVERT: B 591 SER cc_start: 0.7968 (t) cc_final: 0.7723 (p) REVERT: B 614 ARG cc_start: 0.7237 (ttm170) cc_final: 0.6999 (mtp-110) REVERT: C 158 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7484 (ttm110) REVERT: C 188 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8663 (mt0) REVERT: C 272 ASN cc_start: 0.8144 (t0) cc_final: 0.7853 (t0) REVERT: C 274 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7050 (mmt180) REVERT: C 291 ARG cc_start: 0.7598 (ttm110) cc_final: 0.7381 (ttp-110) REVERT: C 397 MET cc_start: 0.8407 (mmm) cc_final: 0.8001 (tpt) REVERT: C 407 VAL cc_start: 0.7535 (t) cc_final: 0.7023 (m) REVERT: C 433 GLN cc_start: 0.7932 (tt0) cc_final: 0.7635 (tt0) REVERT: C 537 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7489 (ttp-170) REVERT: C 591 SER cc_start: 0.8344 (t) cc_final: 0.8028 (p) REVERT: D 158 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7495 (ttm110) REVERT: D 272 ASN cc_start: 0.8256 (t0) cc_final: 0.7969 (t0) REVERT: D 291 ARG cc_start: 0.7634 (ttm110) cc_final: 0.7425 (ttp-110) REVERT: D 326 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8141 (tp) REVERT: D 397 MET cc_start: 0.8363 (mmm) cc_final: 0.8012 (tpt) REVERT: D 433 GLN cc_start: 0.7856 (tt0) cc_final: 0.7549 (tt0) REVERT: D 537 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7708 (ttp80) REVERT: D 614 ARG cc_start: 0.7269 (ttm170) cc_final: 0.6999 (mtp-110) outliers start: 48 outliers final: 18 residues processed: 292 average time/residue: 1.4014 time to fit residues: 451.5805 Evaluate side-chains 251 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 470 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 571 ASN Chi-restraints excluded: chain C residue 188 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 571 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 565 ASN B 188 GLN D 188 GLN D 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18012 Z= 0.350 Angle : 0.603 6.186 24324 Z= 0.313 Chirality : 0.044 0.202 2644 Planarity : 0.005 0.057 2948 Dihedral : 15.153 140.954 2777 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.53 % Allowed : 16.08 % Favored : 81.40 % 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: 0.17 (0.18), residues: 2044 helix: 0.93 (0.15), residues: 1176 sheet: 0.56 (0.45), residues: 116 loop : -1.25 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 596 HIS 0.005 0.002 HIS B 199 PHE 0.019 0.002 PHE C 138 TYR 0.014 0.002 TYR C 365 ARG 0.012 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 239 time to evaluate : 2.070 Fit side-chains REVERT: A 158 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7215 (mtm180) REVERT: A 274 ARG cc_start: 0.7722 (mmm160) cc_final: 0.7494 (mmt90) REVERT: A 326 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8052 (tp) REVERT: A 397 MET cc_start: 0.8368 (mmm) cc_final: 0.8002 (tpt) REVERT: A 407 VAL cc_start: 0.7438 (t) cc_final: 0.7074 (m) REVERT: A 433 GLN cc_start: 0.7953 (tt0) cc_final: 0.7610 (tt0) REVERT: A 537 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7737 (ttp80) REVERT: B 158 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7502 (ttm110) REVERT: B 291 ARG cc_start: 0.7633 (ttm110) cc_final: 0.7374 (ttp-110) REVERT: B 397 MET cc_start: 0.8398 (mmm) cc_final: 0.8021 (tpt) REVERT: B 407 VAL cc_start: 0.7538 (t) cc_final: 0.7238 (m) REVERT: B 433 GLN cc_start: 0.7951 (tt0) cc_final: 0.7597 (tt0) REVERT: B 537 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7756 (ttp80) REVERT: B 591 SER cc_start: 0.8004 (t) cc_final: 0.7774 (p) REVERT: B 614 ARG cc_start: 0.7317 (ttm170) cc_final: 0.7109 (mtp-110) REVERT: C 158 ARG cc_start: 0.7809 (ttm-80) cc_final: 0.7604 (ttm110) REVERT: C 272 ASN cc_start: 0.8208 (t0) cc_final: 0.7816 (t0) REVERT: C 291 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7289 (ttp-110) REVERT: C 326 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8205 (tp) REVERT: C 397 MET cc_start: 0.8367 (mmm) cc_final: 0.7998 (tpt) REVERT: C 407 VAL cc_start: 0.7487 (t) cc_final: 0.7114 (m) REVERT: C 433 GLN cc_start: 0.7931 (tt0) cc_final: 0.7564 (tt0) REVERT: C 537 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7702 (ttp80) REVERT: C 591 SER cc_start: 0.8274 (t) cc_final: 0.7870 (p) REVERT: D 158 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7623 (ttm110) REVERT: D 272 ASN cc_start: 0.8221 (t0) cc_final: 0.7898 (t0) REVERT: D 274 ARG cc_start: 0.7688 (mmt90) cc_final: 0.7391 (mmt90) REVERT: D 326 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8214 (tp) REVERT: D 397 MET cc_start: 0.8412 (mmm) cc_final: 0.8036 (tpt) REVERT: D 407 VAL cc_start: 0.7568 (t) cc_final: 0.7259 (m) REVERT: D 433 GLN cc_start: 0.7920 (tt0) cc_final: 0.7576 (tt0) REVERT: D 537 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7664 (ttp80) REVERT: D 614 ARG cc_start: 0.7393 (ttm170) cc_final: 0.7063 (mtp-110) outliers start: 47 outliers final: 23 residues processed: 273 average time/residue: 1.4872 time to fit residues: 446.5221 Evaluate side-chains 251 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 225 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 571 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18012 Z= 0.168 Angle : 0.511 6.141 24324 Z= 0.262 Chirality : 0.039 0.181 2644 Planarity : 0.004 0.053 2948 Dihedral : 14.252 133.358 2768 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 16.94 % Favored : 81.51 % 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: 0.61 (0.18), residues: 2044 helix: 1.32 (0.15), residues: 1192 sheet: 0.62 (0.47), residues: 116 loop : -1.13 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 124 HIS 0.002 0.001 HIS D 321 PHE 0.010 0.001 PHE B 138 TYR 0.017 0.001 TYR B 160 ARG 0.009 0.000 ARG C 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 2.083 Fit side-chains REVERT: A 158 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7167 (mtm180) REVERT: A 274 ARG cc_start: 0.7711 (mmm160) cc_final: 0.7491 (mmt90) REVERT: A 326 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8048 (tp) REVERT: A 397 MET cc_start: 0.8329 (mmm) cc_final: 0.7927 (tpt) REVERT: A 433 GLN cc_start: 0.7937 (tt0) cc_final: 0.7675 (tt0) REVERT: B 158 ARG cc_start: 0.7818 (ttm-80) cc_final: 0.7485 (ttm110) REVERT: B 291 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7378 (ttp-110) REVERT: B 397 MET cc_start: 0.8361 (mmm) cc_final: 0.7968 (tpt) REVERT: B 433 GLN cc_start: 0.7859 (tt0) cc_final: 0.7586 (tt0) REVERT: B 591 SER cc_start: 0.7842 (t) cc_final: 0.7612 (p) REVERT: B 614 ARG cc_start: 0.7228 (ttm170) cc_final: 0.7006 (mtp-110) REVERT: C 158 ARG cc_start: 0.7778 (ttm-80) cc_final: 0.7079 (mtm180) REVERT: C 272 ASN cc_start: 0.8160 (t0) cc_final: 0.7794 (t0) REVERT: C 291 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7388 (ttp-110) REVERT: C 397 MET cc_start: 0.8338 (mmm) cc_final: 0.7939 (tpt) REVERT: C 433 GLN cc_start: 0.7879 (tt0) cc_final: 0.7591 (tt0) REVERT: C 591 SER cc_start: 0.8047 (t) cc_final: 0.7663 (p) REVERT: D 158 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7456 (ttm110) REVERT: D 274 ARG cc_start: 0.7683 (mmt90) cc_final: 0.7429 (mmt90) REVERT: D 291 ARG cc_start: 0.7575 (ttm110) cc_final: 0.7342 (ttp-110) REVERT: D 326 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8026 (tp) REVERT: D 397 MET cc_start: 0.8363 (mmm) cc_final: 0.7977 (tpt) REVERT: D 413 MET cc_start: 0.7382 (mtt) cc_final: 0.7129 (mtm) REVERT: D 433 GLN cc_start: 0.7898 (tt0) cc_final: 0.7591 (tt0) REVERT: D 537 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7726 (ttp80) outliers start: 29 outliers final: 10 residues processed: 265 average time/residue: 1.5619 time to fit residues: 454.4626 Evaluate side-chains 244 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 232 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 571 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 565 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 18012 Z= 0.461 Angle : 0.657 8.293 24324 Z= 0.335 Chirality : 0.046 0.221 2644 Planarity : 0.005 0.057 2948 Dihedral : 14.646 129.745 2766 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.33 % Allowed : 16.56 % Favored : 80.11 % 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: 0.28 (0.18), residues: 2044 helix: 1.00 (0.15), residues: 1200 sheet: 0.78 (0.48), residues: 116 loop : -1.26 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 596 HIS 0.006 0.003 HIS D 199 PHE 0.020 0.002 PHE A 138 TYR 0.015 0.002 TYR C 365 ARG 0.010 0.001 ARG C 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 231 time to evaluate : 2.010 Fit side-chains REVERT: A 274 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7048 (mmt180) REVERT: A 326 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8061 (tp) REVERT: A 397 MET cc_start: 0.8337 (mmm) cc_final: 0.8014 (tpt) REVERT: A 407 VAL cc_start: 0.7363 (t) cc_final: 0.6979 (m) REVERT: A 433 GLN cc_start: 0.7922 (tt0) cc_final: 0.7564 (tt0) REVERT: B 158 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7620 (ttm110) REVERT: B 291 ARG cc_start: 0.7594 (ttm110) cc_final: 0.7378 (ttp-110) REVERT: B 397 MET cc_start: 0.8342 (mmm) cc_final: 0.8016 (tpt) REVERT: B 407 VAL cc_start: 0.7409 (t) cc_final: 0.7018 (m) REVERT: B 433 GLN cc_start: 0.7964 (tt0) cc_final: 0.7624 (tt0) REVERT: B 591 SER cc_start: 0.8033 (t) cc_final: 0.7817 (p) REVERT: B 614 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7142 (mtp-110) REVERT: C 272 ASN cc_start: 0.8130 (t0) cc_final: 0.7769 (t0) REVERT: C 326 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8195 (tp) REVERT: C 397 MET cc_start: 0.8338 (mmm) cc_final: 0.8020 (tpt) REVERT: C 407 VAL cc_start: 0.7469 (t) cc_final: 0.7073 (m) REVERT: C 433 GLN cc_start: 0.7959 (tt0) cc_final: 0.7649 (tt0) REVERT: C 591 SER cc_start: 0.8244 (t) cc_final: 0.7834 (p) REVERT: D 158 ARG cc_start: 0.7816 (ttm-80) cc_final: 0.7608 (ttm110) REVERT: D 274 ARG cc_start: 0.7658 (mmt90) cc_final: 0.7266 (mmt180) REVERT: D 326 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8065 (tp) REVERT: D 397 MET cc_start: 0.8335 (mmm) cc_final: 0.8019 (tpt) REVERT: D 407 VAL cc_start: 0.7362 (t) cc_final: 0.6992 (m) REVERT: D 433 GLN cc_start: 0.7979 (tt0) cc_final: 0.7645 (tt0) REVERT: D 537 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7738 (ttp80) outliers start: 62 outliers final: 33 residues processed: 268 average time/residue: 1.4880 time to fit residues: 439.3381 Evaluate side-chains 255 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 415 SER Chi-restraints excluded: chain B residue 428 MET Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 616 ILE Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 571 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18012 Z= 0.190 Angle : 0.536 7.484 24324 Z= 0.274 Chirality : 0.040 0.192 2644 Planarity : 0.004 0.055 2948 Dihedral : 13.939 116.742 2766 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.94 % Allowed : 17.74 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2044 helix: 1.29 (0.15), residues: 1200 sheet: 0.68 (0.48), residues: 116 loop : -1.11 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.003 0.001 HIS A 321 PHE 0.011 0.001 PHE A 138 TYR 0.014 0.001 TYR B 160 ARG 0.015 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 3.276 Fit side-chains REVERT: A 158 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7281 (mtm180) REVERT: A 274 ARG cc_start: 0.7687 (mmm160) cc_final: 0.7448 (mmt90) REVERT: A 326 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 397 MET cc_start: 0.8286 (mmm) cc_final: 0.7938 (tpt) REVERT: A 433 GLN cc_start: 0.7902 (tt0) cc_final: 0.7609 (tt0) REVERT: B 158 ARG cc_start: 0.7787 (ttm-80) cc_final: 0.7451 (ttm110) REVERT: B 291 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7349 (ttp-110) REVERT: B 397 MET cc_start: 0.8322 (mmm) cc_final: 0.7967 (tpt) REVERT: B 433 GLN cc_start: 0.7897 (tt0) cc_final: 0.7596 (tt0) REVERT: B 591 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7668 (p) REVERT: C 158 ARG cc_start: 0.8124 (ttm110) cc_final: 0.7297 (mtm180) REVERT: C 397 MET cc_start: 0.8317 (mmm) cc_final: 0.7971 (tpt) REVERT: C 433 GLN cc_start: 0.7875 (tt0) cc_final: 0.7582 (tt0) REVERT: C 591 SER cc_start: 0.8021 (t) cc_final: 0.7639 (p) REVERT: D 274 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7033 (mmt180) REVERT: D 326 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8021 (tp) REVERT: D 397 MET cc_start: 0.8283 (mmm) cc_final: 0.7938 (tpt) REVERT: D 433 GLN cc_start: 0.7885 (tt0) cc_final: 0.7587 (tt0) outliers start: 36 outliers final: 11 residues processed: 240 average time/residue: 1.5876 time to fit residues: 419.8496 Evaluate side-chains 235 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18012 Z= 0.263 Angle : 0.567 7.486 24324 Z= 0.290 Chirality : 0.042 0.196 2644 Planarity : 0.004 0.055 2948 Dihedral : 13.911 116.813 2764 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.31 % Allowed : 17.69 % Favored : 80.00 % 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: 0.63 (0.18), residues: 2044 helix: 1.29 (0.15), residues: 1200 sheet: 0.64 (0.48), residues: 116 loop : -1.07 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 596 HIS 0.004 0.002 HIS D 321 PHE 0.015 0.001 PHE C 138 TYR 0.012 0.001 TYR A 160 ARG 0.015 0.001 ARG D 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 2.159 Fit side-chains REVERT: A 158 ARG cc_start: 0.8011 (ttm110) cc_final: 0.7306 (mtm180) REVERT: A 274 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7443 (mmt90) REVERT: A 326 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8007 (tp) REVERT: A 397 MET cc_start: 0.8313 (mmm) cc_final: 0.7989 (tpt) REVERT: A 433 GLN cc_start: 0.7904 (tt0) cc_final: 0.7619 (tt0) REVERT: A 455 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7985 (mm) REVERT: B 291 ARG cc_start: 0.7582 (ttm110) cc_final: 0.7370 (ttp-110) REVERT: B 397 MET cc_start: 0.8316 (mmm) cc_final: 0.7990 (tpt) REVERT: B 433 GLN cc_start: 0.7915 (tt0) cc_final: 0.7627 (tt0) REVERT: B 591 SER cc_start: 0.7912 (OUTLIER) cc_final: 0.7698 (p) REVERT: C 158 ARG cc_start: 0.8141 (ttm110) cc_final: 0.7335 (mtm180) REVERT: C 397 MET cc_start: 0.8298 (mmm) cc_final: 0.7975 (tpt) REVERT: C 433 GLN cc_start: 0.7910 (tt0) cc_final: 0.7605 (tt0) REVERT: C 455 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (mm) REVERT: C 591 SER cc_start: 0.8066 (t) cc_final: 0.7680 (p) REVERT: D 158 ARG cc_start: 0.8113 (ttm110) cc_final: 0.7345 (mtm180) REVERT: D 326 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8010 (tp) REVERT: D 397 MET cc_start: 0.8315 (mmm) cc_final: 0.7996 (tpt) REVERT: D 433 GLN cc_start: 0.7923 (tt0) cc_final: 0.7610 (tt0) outliers start: 43 outliers final: 25 residues processed: 248 average time/residue: 1.4492 time to fit residues: 397.3574 Evaluate side-chains 252 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0570 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18012 Z= 0.160 Angle : 0.517 7.231 24324 Z= 0.263 Chirality : 0.039 0.175 2644 Planarity : 0.004 0.058 2948 Dihedral : 13.450 115.461 2764 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.45 % Allowed : 18.44 % Favored : 80.11 % 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: 0.88 (0.18), residues: 2044 helix: 1.51 (0.15), residues: 1196 sheet: 0.57 (0.47), residues: 116 loop : -0.96 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.003 0.001 HIS D 321 PHE 0.010 0.001 PHE C 328 TYR 0.013 0.001 TYR D 160 ARG 0.013 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 1.964 Fit side-chains REVERT: A 158 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7269 (mtm180) REVERT: A 274 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7441 (mmt90) REVERT: A 326 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8082 (tp) REVERT: A 397 MET cc_start: 0.8304 (mmm) cc_final: 0.7963 (tpt) REVERT: A 433 GLN cc_start: 0.7841 (tt0) cc_final: 0.7589 (tt0) REVERT: A 455 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7942 (mm) REVERT: A 608 LEU cc_start: 0.7562 (mm) cc_final: 0.7205 (mp) REVERT: B 158 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7313 (mtm180) REVERT: B 291 ARG cc_start: 0.7614 (ttm110) cc_final: 0.7366 (ttp-110) REVERT: B 397 MET cc_start: 0.8307 (mmm) cc_final: 0.7961 (tpt) REVERT: B 433 GLN cc_start: 0.7852 (tt0) cc_final: 0.7599 (tt0) REVERT: C 158 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7328 (mtm180) REVERT: C 397 MET cc_start: 0.8302 (mmm) cc_final: 0.7967 (tpt) REVERT: C 433 GLN cc_start: 0.7913 (tt0) cc_final: 0.7673 (tt0) REVERT: C 455 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7911 (mm) REVERT: C 542 ASP cc_start: 0.8185 (t0) cc_final: 0.7984 (t0) REVERT: D 158 ARG cc_start: 0.8103 (ttm110) cc_final: 0.7336 (mtm180) REVERT: D 326 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8082 (tp) REVERT: D 397 MET cc_start: 0.8301 (mmm) cc_final: 0.7965 (tpt) REVERT: D 413 MET cc_start: 0.7452 (mtt) cc_final: 0.7157 (mtm) REVERT: D 433 GLN cc_start: 0.7855 (tt0) cc_final: 0.7589 (tt0) outliers start: 27 outliers final: 17 residues processed: 253 average time/residue: 1.4331 time to fit residues: 401.5672 Evaluate side-chains 248 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 571 ASN Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 507 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 165 optimal weight: 0.0970 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18012 Z= 0.260 Angle : 0.565 7.645 24324 Z= 0.288 Chirality : 0.042 0.185 2644 Planarity : 0.004 0.055 2948 Dihedral : 13.737 116.889 2764 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.67 % Allowed : 18.55 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2044 helix: 1.41 (0.15), residues: 1200 sheet: 0.29 (0.46), residues: 124 loop : -1.04 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 596 HIS 0.004 0.002 HIS A 321 PHE 0.016 0.001 PHE C 138 TYR 0.012 0.001 TYR D 160 ARG 0.014 0.001 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 224 time to evaluate : 2.197 Fit side-chains REVERT: A 158 ARG cc_start: 0.7992 (ttm110) cc_final: 0.7272 (mtm180) REVERT: A 274 ARG cc_start: 0.7676 (mmm160) cc_final: 0.7449 (mmt90) REVERT: A 326 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 397 MET cc_start: 0.8295 (mmm) cc_final: 0.7978 (tpt) REVERT: A 433 GLN cc_start: 0.7884 (tt0) cc_final: 0.7536 (tt0) REVERT: A 455 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7975 (mm) REVERT: B 158 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7262 (mtm180) REVERT: B 291 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7382 (ttp-110) REVERT: B 397 MET cc_start: 0.8298 (mmm) cc_final: 0.7976 (tpt) REVERT: B 433 GLN cc_start: 0.7881 (tt0) cc_final: 0.7537 (tt0) REVERT: C 158 ARG cc_start: 0.8057 (ttm110) cc_final: 0.7291 (mtm180) REVERT: C 272 ASN cc_start: 0.8050 (t0) cc_final: 0.7846 (t0) REVERT: C 326 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8176 (tp) REVERT: C 397 MET cc_start: 0.8294 (mmm) cc_final: 0.7983 (tpt) REVERT: C 433 GLN cc_start: 0.7902 (tt0) cc_final: 0.7612 (tt0) REVERT: C 455 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7966 (mm) REVERT: D 158 ARG cc_start: 0.8088 (ttm110) cc_final: 0.7344 (mtm180) REVERT: D 326 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8008 (tp) REVERT: D 397 MET cc_start: 0.8294 (mmm) cc_final: 0.7983 (tpt) REVERT: D 433 GLN cc_start: 0.7878 (tt0) cc_final: 0.7581 (tt0) outliers start: 31 outliers final: 21 residues processed: 242 average time/residue: 1.5417 time to fit residues: 411.4436 Evaluate side-chains 248 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain D residue 228 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.0070 chunk 118 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 128 optimal weight: 0.0770 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18012 Z= 0.139 Angle : 0.504 7.097 24324 Z= 0.257 Chirality : 0.039 0.174 2644 Planarity : 0.004 0.055 2948 Dihedral : 13.266 115.024 2764 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.18 % Allowed : 19.03 % Favored : 79.78 % 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: 1.03 (0.18), residues: 2044 helix: 1.64 (0.15), residues: 1196 sheet: 0.56 (0.46), residues: 116 loop : -0.90 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.002 0.001 HIS A 321 PHE 0.010 0.001 PHE A 328 TYR 0.013 0.001 TYR D 160 ARG 0.014 0.000 ARG B 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4088 Ramachandran restraints generated. 2044 Oldfield, 0 Emsley, 2044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 2.000 Fit side-chains REVERT: A 158 ARG cc_start: 0.7978 (ttm110) cc_final: 0.7269 (mtm180) REVERT: A 326 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 397 MET cc_start: 0.8295 (mmm) cc_final: 0.7948 (tpt) REVERT: A 433 GLN cc_start: 0.7843 (tt0) cc_final: 0.7605 (tt0) REVERT: B 158 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7291 (mtm180) REVERT: B 291 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7389 (ttp-110) REVERT: B 397 MET cc_start: 0.8296 (mmm) cc_final: 0.7946 (tpt) REVERT: B 433 GLN cc_start: 0.7842 (tt0) cc_final: 0.7601 (tt0) REVERT: C 158 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7298 (mtm180) REVERT: C 397 MET cc_start: 0.8280 (mmm) cc_final: 0.7935 (tpt) REVERT: C 433 GLN cc_start: 0.7867 (tt0) cc_final: 0.7633 (tt0) REVERT: D 107 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7632 (pttt) REVERT: D 158 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7341 (mtm180) REVERT: D 288 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8214 (mtmt) REVERT: D 326 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8034 (tp) REVERT: D 397 MET cc_start: 0.8265 (mmm) cc_final: 0.7922 (tpt) REVERT: D 413 MET cc_start: 0.7434 (mtt) cc_final: 0.7146 (mtm) REVERT: D 433 GLN cc_start: 0.7836 (tt0) cc_final: 0.7596 (tt0) outliers start: 22 outliers final: 12 residues processed: 262 average time/residue: 1.4221 time to fit residues: 412.2953 Evaluate side-chains 257 residues out of total 1852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 243 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 507 LEU Chi-restraints excluded: chain D residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 166 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108319 restraints weight = 43418.352| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.74 r_work: 0.3261 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18012 Z= 0.171 Angle : 0.517 7.629 24324 Z= 0.264 Chirality : 0.040 0.175 2644 Planarity : 0.004 0.055 2948 Dihedral : 13.270 115.958 2764 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.08 % Allowed : 19.52 % Favored : 79.41 % 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: 1.08 (0.19), residues: 2044 helix: 1.67 (0.15), residues: 1196 sheet: 0.63 (0.46), residues: 116 loop : -0.88 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 124 HIS 0.003 0.001 HIS A 321 PHE 0.012 0.001 PHE B 138 TYR 0.012 0.001 TYR D 160 ARG 0.013 0.000 ARG B 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7231.71 seconds wall clock time: 129 minutes 10.85 seconds (7750.85 seconds total)