Starting phenix.real_space_refine on Thu Feb 15 10:08:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/02_2024/7yvb_34122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/02_2024/7yvb_34122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/02_2024/7yvb_34122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/02_2024/7yvb_34122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/02_2024/7yvb_34122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/02_2024/7yvb_34122_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 7530 2.51 5 N 1974 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 529": "NH1" <-> "NH2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B ARG 186": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 361": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 529": "NH1" <-> "NH2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B GLU 574": "OE1" <-> "OE2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 361": "NH1" <-> "NH2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ARG 461": "NH1" <-> "NH2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C ARG 529": "NH1" <-> "NH2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C GLU 574": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11889 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3781 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 449} Chain breaks: 1 Chain: "B" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3781 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 449} Chain breaks: 1 Chain: "C" Number of atoms: 3781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3781 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 449} Chain breaks: 1 Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.55, per 1000 atoms: 0.55 Number of scatterers: 11889 At special positions: 0 Unit cell: (104.86, 113.42, 135.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 2304 8.00 N 1974 7.00 C 7530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 233 " distance=2.03 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 435 " distance=2.04 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 233 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 435 " distance=2.04 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 354 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 435 " distance=2.04 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 354 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 381 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 701 " - " ASN A 401 " " NAG A 702 " - " ASN A 377 " " NAG B 701 " - " ASN B 377 " " NAG B 702 " - " ASN B 401 " " NAG C 701 " - " ASN C 377 " " NAG C 702 " - " ASN C 401 " " NAG D 1 " - " ASN A 393 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 169 " " NAG G 1 " - " ASN A 221 " " NAG H 1 " - " ASN B 393 " " NAG I 1 " - " ASN B 331 " " NAG J 1 " - " ASN B 169 " " NAG K 1 " - " ASN B 221 " " NAG L 1 " - " ASN C 393 " " NAG M 1 " - " ASN C 331 " " NAG N 1 " - " ASN C 169 " " NAG O 1 " - " ASN C 221 " Time building additional restraints: 5.48 Conformation dependent library (CDL) restraints added in 2.5 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 37.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 149 through 157 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 193 through 199 Processing helix chain 'A' and resid 203 through 206 No H-bonds generated for 'chain 'A' and resid 203 through 206' Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 424 through 427 Processing helix chain 'A' and resid 455 through 466 removed outlier: 3.565A pdb=" N ARG A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 510 through 526 Processing helix chain 'A' and resid 550 through 576 removed outlier: 5.204A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 566 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 118 Processing helix chain 'B' and resid 149 through 157 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.518A pdb=" N THR B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 182 No H-bonds generated for 'chain 'B' and resid 179 through 182' Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 193 through 199 Processing helix chain 'B' and resid 203 through 206 No H-bonds generated for 'chain 'B' and resid 203 through 206' Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 347 through 362 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 407 through 420 Processing helix chain 'B' and resid 424 through 427 Processing helix chain 'B' and resid 455 through 466 removed outlier: 3.565A pdb=" N ARG B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 510 through 526 Processing helix chain 'B' and resid 550 through 576 removed outlier: 5.204A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 563 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 118 Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 179 through 182 No H-bonds generated for 'chain 'C' and resid 179 through 182' Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 193 through 199 Processing helix chain 'C' and resid 203 through 206 No H-bonds generated for 'chain 'C' and resid 203 through 206' Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 347 through 362 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 407 through 420 Processing helix chain 'C' and resid 424 through 427 Processing helix chain 'C' and resid 455 through 466 removed outlier: 3.565A pdb=" N ARG C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 486 Processing helix chain 'C' and resid 510 through 526 Processing helix chain 'C' and resid 550 through 576 removed outlier: 5.204A pdb=" N GLY C 559 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N THR C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU C 563 " --> pdb=" O GLY C 559 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY C 566 " --> pdb=" O GLY C 562 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 122 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.197A pdb=" N ASN A 232 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN A 143 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 215 through 217 removed outlier: 3.928A pdb=" N CYS A 210 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 259 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS A 210 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER A 257 " --> pdb=" O CYS A 210 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER A 313 " --> pdb=" O ASN A 531 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TYR A 533 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 315 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU A 535 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 317 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 122 through 129 Processing sheet with id= E, first strand: chain 'B' and resid 222 through 226 removed outlier: 6.197A pdb=" N ASN B 232 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 143 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 215 through 217 removed outlier: 3.928A pdb=" N CYS B 210 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 259 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS B 210 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER B 257 " --> pdb=" O CYS B 210 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER B 313 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR B 533 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 315 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B 535 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 317 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 122 through 129 Processing sheet with id= H, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.197A pdb=" N ASN C 232 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN C 143 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 215 through 217 removed outlier: 3.928A pdb=" N CYS C 210 " --> pdb=" O CYS C 217 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE C 259 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS C 210 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER C 257 " --> pdb=" O CYS C 210 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N SER C 313 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N TYR C 533 " --> pdb=" O SER C 313 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 315 " --> pdb=" O TYR C 533 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU C 535 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU C 317 " --> pdb=" O GLU C 535 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1425 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: 3.64 Time building geometry restraints manager: 5.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3780 1.34 - 1.46: 2845 1.46 - 1.58: 5393 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 12138 Sorted by residual: bond pdb=" C PRO A 434 " pdb=" N CYS A 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C PRO C 434 " pdb=" N CYS C 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C PRO B 434 " pdb=" N CYS B 435 " ideal model delta sigma weight residual 1.335 1.482 -0.147 1.30e-02 5.92e+03 1.27e+02 bond pdb=" C GLN B 472 " pdb=" N HIS B 473 " ideal model delta sigma weight residual 1.331 1.477 -0.146 1.51e-02 4.39e+03 9.37e+01 bond pdb=" C GLN A 472 " pdb=" N HIS A 473 " ideal model delta sigma weight residual 1.331 1.477 -0.146 1.51e-02 4.39e+03 9.34e+01 ... (remaining 12133 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.22: 211 105.22 - 112.42: 6335 112.42 - 119.62: 3776 119.62 - 126.82: 5964 126.82 - 134.02: 127 Bond angle restraints: 16413 Sorted by residual: angle pdb=" C MET C 475 " pdb=" N LYS C 476 " pdb=" CA LYS C 476 " ideal model delta sigma weight residual 120.29 111.96 8.33 1.42e+00 4.96e-01 3.44e+01 angle pdb=" C MET B 475 " pdb=" N LYS B 476 " pdb=" CA LYS B 476 " ideal model delta sigma weight residual 120.29 111.96 8.33 1.42e+00 4.96e-01 3.44e+01 angle pdb=" C MET A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta sigma weight residual 120.29 112.00 8.29 1.42e+00 4.96e-01 3.41e+01 angle pdb=" C GLY C 228 " pdb=" N ASN C 229 " pdb=" CA ASN C 229 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C GLY B 228 " pdb=" N ASN B 229 " pdb=" CA ASN B 229 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 ... (remaining 16408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 6859 17.69 - 35.39: 676 35.39 - 53.08: 166 53.08 - 70.77: 36 70.77 - 88.46: 12 Dihedral angle restraints: 7749 sinusoidal: 3567 harmonic: 4182 Sorted by residual: dihedral pdb=" CB CYS A 354 " pdb=" SG CYS A 354 " pdb=" SG CYS A 429 " pdb=" CB CYS A 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.44 -63.56 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS B 354 " pdb=" SG CYS B 354 " pdb=" SG CYS B 429 " pdb=" CB CYS B 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.70 -63.30 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CB CYS C 354 " pdb=" SG CYS C 354 " pdb=" SG CYS C 429 " pdb=" CB CYS C 429 " ideal model delta sinusoidal sigma weight residual -86.00 -22.74 -63.26 1 1.00e+01 1.00e-02 5.28e+01 ... (remaining 7746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1318 0.044 - 0.088: 401 0.088 - 0.132: 144 0.132 - 0.176: 24 0.176 - 0.220: 3 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CB ILE A 208 " pdb=" CA ILE A 208 " pdb=" CG1 ILE A 208 " pdb=" CG2 ILE A 208 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE C 208 " pdb=" CA ILE C 208 " pdb=" CG1 ILE C 208 " pdb=" CG2 ILE C 208 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 208 " pdb=" CA ILE B 208 " pdb=" CG1 ILE B 208 " pdb=" CG2 ILE B 208 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1887 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 462 " 0.016 2.00e-02 2.50e+03 1.96e-02 6.76e+00 pdb=" CG PHE C 462 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 462 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 462 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 462 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 462 " 0.016 2.00e-02 2.50e+03 1.95e-02 6.69e+00 pdb=" CG PHE A 462 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 462 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 462 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 462 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 462 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 462 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 462 " -0.016 2.00e-02 2.50e+03 1.95e-02 6.67e+00 pdb=" CG PHE B 462 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 462 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 462 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE B 462 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 462 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 462 " -0.001 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1814 2.75 - 3.29: 11815 3.29 - 3.83: 20693 3.83 - 4.36: 24808 4.36 - 4.90: 41712 Nonbonded interactions: 100842 Sorted by model distance: nonbonded pdb=" OG SER A 284 " pdb=" OG SER B 447 " model vdw 2.215 2.440 nonbonded pdb=" OG SER A 447 " pdb=" OG SER C 284 " model vdw 2.215 2.440 nonbonded pdb=" OG SER B 284 " pdb=" OG SER C 447 " model vdw 2.215 2.440 nonbonded pdb=" O GLY C 295 " pdb=" N ARG C 344 " model vdw 2.225 2.520 nonbonded pdb=" O GLY A 295 " pdb=" N ARG A 344 " model vdw 2.225 2.520 ... (remaining 100837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 4.410 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 35.310 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.007 0.147 12138 Z= 0.436 Angle : 0.784 9.219 16413 Z= 0.441 Chirality : 0.048 0.220 1890 Planarity : 0.005 0.063 2076 Dihedral : 14.818 88.463 4998 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.17 % Allowed : 1.40 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: -0.41 (0.22), residues: 1404 helix: 0.35 (0.21), residues: 591 sheet: 0.08 (0.33), residues: 213 loop : -0.95 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 564 HIS 0.003 0.001 HIS B 283 PHE 0.045 0.002 PHE C 462 TYR 0.018 0.002 TYR A 448 ARG 0.008 0.000 ARG B 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.388 Fit side-chains REVERT: A 121 GLN cc_start: 0.7953 (mm110) cc_final: 0.7741 (mm110) REVERT: B 576 MET cc_start: 0.3038 (pmm) cc_final: 0.2711 (pmm) REVERT: C 121 GLN cc_start: 0.8025 (mm110) cc_final: 0.7765 (mm110) REVERT: C 576 MET cc_start: 0.3654 (pmm) cc_final: 0.3242 (pmm) REVERT: P 2 MET cc_start: 0.9176 (ptt) cc_final: 0.8943 (ptt) REVERT: Q 3 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7809 (mtt90) outliers start: 15 outliers final: 0 residues processed: 160 average time/residue: 1.3988 time to fit residues: 241.0181 Evaluate side-chains 100 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 3 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 322 HIS B 191 ASN C 172 GLN C 191 ASN C 322 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12138 Z= 0.213 Angle : 0.601 9.312 16413 Z= 0.304 Chirality : 0.043 0.257 1890 Planarity : 0.004 0.058 2076 Dihedral : 8.208 56.806 2188 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.64 % Allowed : 9.11 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.03 (0.22), residues: 1404 helix: 0.83 (0.21), residues: 600 sheet: 0.15 (0.33), residues: 213 loop : -0.79 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.029 0.002 PHE B 462 TYR 0.017 0.001 TYR B 448 ARG 0.008 0.001 ARG C 543 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.372 Fit side-chains REVERT: A 121 GLN cc_start: 0.7955 (mm110) cc_final: 0.7739 (mm110) REVERT: A 182 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7838 (mmm) REVERT: A 341 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: A 515 MET cc_start: 0.8498 (mtm) cc_final: 0.8256 (mtm) REVERT: A 548 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.8161 (t80) REVERT: B 576 MET cc_start: 0.3403 (pmm) cc_final: 0.3088 (pmm) REVERT: C 98 MET cc_start: 0.5657 (ptt) cc_final: 0.5350 (ptm) REVERT: C 121 GLN cc_start: 0.8014 (mm110) cc_final: 0.7759 (mm110) REVERT: C 576 MET cc_start: 0.3765 (pmm) cc_final: 0.3446 (pmm) REVERT: R 3 ARG cc_start: 0.8511 (mtt-85) cc_final: 0.8297 (mtt-85) outliers start: 21 outliers final: 3 residues processed: 122 average time/residue: 1.2925 time to fit residues: 171.6459 Evaluate side-chains 102 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12138 Z= 0.386 Angle : 0.639 9.241 16413 Z= 0.322 Chirality : 0.045 0.236 1890 Planarity : 0.004 0.055 2076 Dihedral : 7.808 57.662 2184 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.04 % Allowed : 10.98 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.05 (0.22), residues: 1404 helix: 0.81 (0.21), residues: 600 sheet: 0.31 (0.33), residues: 213 loop : -0.81 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.006 0.001 HIS B 283 PHE 0.017 0.002 PHE B 463 TYR 0.023 0.002 TYR B 448 ARG 0.009 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 113 time to evaluate : 1.503 Fit side-chains REVERT: A 121 GLN cc_start: 0.7977 (mm110) cc_final: 0.7767 (mm110) REVERT: A 132 MET cc_start: 0.8417 (ptm) cc_final: 0.8202 (ptp) REVERT: A 163 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 182 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8114 (mtt) REVERT: A 341 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: A 515 MET cc_start: 0.8528 (mtm) cc_final: 0.8305 (mtm) REVERT: A 548 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.8170 (t80) REVERT: B 121 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7547 (mm110) REVERT: B 307 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8707 (mt) REVERT: C 98 MET cc_start: 0.5782 (ptt) cc_final: 0.5401 (ptm) REVERT: C 121 GLN cc_start: 0.8054 (mm110) cc_final: 0.7797 (mm110) REVERT: C 163 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.7917 (t0) REVERT: C 518 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 543 ARG cc_start: 0.7970 (ttp-110) cc_final: 0.7701 (mtp-110) REVERT: C 576 MET cc_start: 0.4266 (pmm) cc_final: 0.3948 (pmm) outliers start: 39 outliers final: 10 residues processed: 129 average time/residue: 1.2002 time to fit residues: 169.3866 Evaluate side-chains 119 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 128 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.186 Angle : 0.552 9.344 16413 Z= 0.276 Chirality : 0.041 0.255 1890 Planarity : 0.004 0.051 2076 Dihedral : 7.297 56.632 2184 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.34 % Allowed : 13.63 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.33 (0.23), residues: 1404 helix: 1.04 (0.22), residues: 600 sheet: 0.30 (0.32), residues: 225 loop : -0.61 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 564 HIS 0.002 0.001 HIS B 283 PHE 0.014 0.001 PHE B 554 TYR 0.014 0.001 TYR A 448 ARG 0.009 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.511 Fit side-chains REVERT: A 132 MET cc_start: 0.8303 (ptm) cc_final: 0.8065 (ptp) REVERT: A 297 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8373 (ptp) REVERT: A 515 MET cc_start: 0.8472 (mtm) cc_final: 0.8248 (mtm) REVERT: A 548 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.8097 (t80) REVERT: B 121 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: B 337 LEU cc_start: 0.8812 (mt) cc_final: 0.8526 (mt) REVERT: B 341 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: C 98 MET cc_start: 0.5839 (ptt) cc_final: 0.5444 (ptm) REVERT: C 121 GLN cc_start: 0.8079 (mm110) cc_final: 0.7811 (mm110) REVERT: C 192 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8286 (pt) REVERT: C 543 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7602 (mtp-110) REVERT: C 548 TYR cc_start: 0.8140 (t80) cc_final: 0.7873 (t80) REVERT: R 2 MET cc_start: 0.9120 (ptt) cc_final: 0.8897 (ptm) outliers start: 30 outliers final: 10 residues processed: 127 average time/residue: 1.1657 time to fit residues: 162.7619 Evaluate side-chains 120 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 12138 Z= 0.364 Angle : 0.624 9.242 16413 Z= 0.311 Chirality : 0.044 0.240 1890 Planarity : 0.004 0.049 2076 Dihedral : 7.378 57.675 2184 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.50 % Allowed : 13.71 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.23 (0.23), residues: 1404 helix: 0.93 (0.21), residues: 600 sheet: 0.17 (0.32), residues: 237 loop : -0.61 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 564 HIS 0.005 0.001 HIS B 283 PHE 0.015 0.002 PHE B 463 TYR 0.022 0.002 TYR B 448 ARG 0.011 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 104 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8359 (ptm) cc_final: 0.8153 (ptp) REVERT: A 297 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8402 (ptp) REVERT: A 346 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 515 MET cc_start: 0.8511 (mtm) cc_final: 0.8277 (mtm) REVERT: B 121 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: B 307 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8677 (mt) REVERT: B 320 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7874 (mt) REVERT: B 341 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7491 (pt0) REVERT: C 98 MET cc_start: 0.5972 (ptt) cc_final: 0.5560 (ptm) REVERT: C 121 GLN cc_start: 0.8049 (mm110) cc_final: 0.7836 (mm110) REVERT: R 3 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.8126 (mtt-85) outliers start: 45 outliers final: 20 residues processed: 130 average time/residue: 1.0790 time to fit residues: 154.4912 Evaluate side-chains 127 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12138 Z= 0.252 Angle : 0.583 9.265 16413 Z= 0.290 Chirality : 0.042 0.243 1890 Planarity : 0.004 0.049 2076 Dihedral : 7.147 56.842 2184 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.35 % Allowed : 14.88 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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 (0.23), residues: 1404 helix: 0.96 (0.21), residues: 603 sheet: 0.19 (0.32), residues: 237 loop : -0.56 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 564 HIS 0.003 0.001 HIS B 283 PHE 0.013 0.001 PHE B 463 TYR 0.017 0.001 TYR A 448 ARG 0.011 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8398 (ptp) REVERT: A 341 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: A 346 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8864 (p) REVERT: A 518 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: B 121 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: B 337 LEU cc_start: 0.8845 (mt) cc_final: 0.8546 (mt) REVERT: B 341 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: C 98 MET cc_start: 0.5897 (ptt) cc_final: 0.5489 (ptm) REVERT: C 192 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8295 (pt) outliers start: 43 outliers final: 20 residues processed: 137 average time/residue: 1.1118 time to fit residues: 167.8414 Evaluate side-chains 130 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12138 Z= 0.209 Angle : 0.584 9.302 16413 Z= 0.287 Chirality : 0.042 0.245 1890 Planarity : 0.004 0.050 2076 Dihedral : 6.973 56.953 2184 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.73 % Allowed : 15.73 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.34 (0.23), residues: 1404 helix: 1.01 (0.22), residues: 600 sheet: 0.21 (0.32), residues: 237 loop : -0.52 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 564 HIS 0.003 0.001 HIS B 283 PHE 0.012 0.001 PHE A 554 TYR 0.014 0.001 TYR A 448 ARG 0.013 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 113 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.7976 (t0) REVERT: A 297 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8386 (ptp) REVERT: A 341 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: A 346 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8876 (p) REVERT: A 518 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: B 337 LEU cc_start: 0.8836 (mt) cc_final: 0.8562 (mt) REVERT: B 341 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: C 119 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8230 (pt0) REVERT: C 192 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8275 (pt) outliers start: 35 outliers final: 19 residues processed: 134 average time/residue: 1.1672 time to fit residues: 171.2167 Evaluate side-chains 131 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.195 Angle : 0.584 9.306 16413 Z= 0.287 Chirality : 0.041 0.248 1890 Planarity : 0.004 0.066 2076 Dihedral : 6.875 56.957 2184 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.80 % Allowed : 16.28 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.45 (0.23), residues: 1404 helix: 1.05 (0.22), residues: 600 sheet: 0.49 (0.34), residues: 213 loop : -0.49 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 564 HIS 0.003 0.001 HIS B 283 PHE 0.014 0.001 PHE B 554 TYR 0.014 0.001 TYR A 448 ARG 0.013 0.001 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8377 (ptp) REVERT: A 341 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: A 346 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 518 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7175 (tt0) REVERT: B 337 LEU cc_start: 0.8824 (mt) cc_final: 0.8565 (mt) REVERT: B 341 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: C 98 MET cc_start: 0.5709 (ptt) cc_final: 0.5286 (ptm) REVERT: C 192 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8264 (pt) REVERT: C 346 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8843 (p) REVERT: R 2 MET cc_start: 0.9105 (ptt) cc_final: 0.8856 (ptm) outliers start: 36 outliers final: 19 residues processed: 130 average time/residue: 1.1461 time to fit residues: 164.2082 Evaluate side-chains 130 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.0870 chunk 130 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.165 Angle : 0.573 9.340 16413 Z= 0.280 Chirality : 0.041 0.251 1890 Planarity : 0.004 0.051 2076 Dihedral : 6.644 56.816 2184 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.34 % Allowed : 16.82 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % 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: 0.51 (0.23), residues: 1404 helix: 1.09 (0.22), residues: 600 sheet: 0.52 (0.34), residues: 213 loop : -0.43 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 564 HIS 0.002 0.001 HIS B 283 PHE 0.011 0.001 PHE B 554 TYR 0.012 0.001 TYR B 448 ARG 0.012 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8348 (ptp) REVERT: A 307 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8578 (pt) REVERT: A 341 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7421 (pt0) REVERT: A 346 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8844 (p) REVERT: B 337 LEU cc_start: 0.8803 (mt) cc_final: 0.8588 (mt) REVERT: C 98 MET cc_start: 0.5679 (ptt) cc_final: 0.5287 (ptm) REVERT: C 119 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: C 192 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8246 (pt) REVERT: C 346 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8822 (p) REVERT: C 576 MET cc_start: 0.2713 (pmm) cc_final: 0.2009 (pmm) outliers start: 30 outliers final: 18 residues processed: 134 average time/residue: 1.1268 time to fit residues: 166.3127 Evaluate side-chains 135 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 565 MET Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 550 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.200 Angle : 0.599 9.400 16413 Z= 0.293 Chirality : 0.042 0.249 1890 Planarity : 0.004 0.047 2076 Dihedral : 6.677 57.099 2184 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.87 % Allowed : 17.83 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.52 (0.23), residues: 1404 helix: 1.08 (0.22), residues: 600 sheet: 0.56 (0.34), residues: 213 loop : -0.42 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.015 0.001 PHE B 554 TYR 0.014 0.001 TYR B 448 ARG 0.012 0.001 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8387 (ptp) REVERT: A 307 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8494 (pt) REVERT: A 341 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7388 (pt0) REVERT: A 346 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8848 (p) REVERT: B 337 LEU cc_start: 0.8822 (mt) cc_final: 0.8604 (mt) REVERT: C 98 MET cc_start: 0.5676 (ptt) cc_final: 0.5285 (ptm) REVERT: C 192 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8215 (pt) REVERT: C 553 LEU cc_start: 0.7954 (tt) cc_final: 0.7747 (tt) REVERT: C 576 MET cc_start: 0.2896 (pmm) cc_final: 0.2271 (pmm) outliers start: 24 outliers final: 16 residues processed: 122 average time/residue: 1.1242 time to fit residues: 151.0816 Evaluate side-chains 127 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 354 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN B 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093726 restraints weight = 15228.117| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.20 r_work: 0.2923 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12138 Z= 0.198 Angle : 0.604 10.709 16413 Z= 0.295 Chirality : 0.042 0.247 1890 Planarity : 0.004 0.055 2076 Dihedral : 6.628 56.955 2184 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.95 % Allowed : 18.07 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.54 (0.23), residues: 1404 helix: 1.08 (0.22), residues: 600 sheet: 0.57 (0.34), residues: 213 loop : -0.38 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 564 HIS 0.003 0.001 HIS B 283 PHE 0.014 0.001 PHE C 554 TYR 0.014 0.001 TYR B 448 ARG 0.014 0.001 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.70 seconds wall clock time: 71 minutes 38.38 seconds (4298.38 seconds total)