Starting phenix.real_space_refine on Sat Jul 20 20:34:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/07_2024/7yvb_34122.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/07_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_34122/07_2024/7yvb_34122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/07_2024/7yvb_34122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/07_2024/7yvb_34122.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yvb_34122/07_2024/7yvb_34122.cif" } 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-5388/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: 7.28, per 1000 atoms: 0.61 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: 5.42 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 48 helices and 24 sheets defined 43.6% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 91 through 119 removed outlier: 3.570A pdb=" N TRP A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.592A pdb=" N MET A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.837A pdb=" N PHE A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 200 removed outlier: 3.504A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 346 through 363 Processing helix chain 'A' and resid 386 through 392 Processing helix chain 'A' and resid 406 through 421 Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.565A pdb=" N ARG A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 509 through 526 Processing helix chain 'A' and resid 549 through 577 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 119 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 161 through 174 removed outlier: 3.518A pdb=" N THR B 173 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 removed outlier: 3.591A pdb=" N MET B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.838A pdb=" N PHE B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 removed outlier: 3.504A pdb=" N ALA B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 346 through 363 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 406 through 421 Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.565A pdb=" N ARG B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 487 Processing helix chain 'B' and resid 509 through 526 Processing helix chain 'B' and resid 549 through 577 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 119 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.591A pdb=" N MET C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 removed outlier: 3.837A pdb=" N PHE C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 200 removed outlier: 3.504A pdb=" N ALA C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 346 through 363 Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 406 through 421 Processing helix chain 'C' and resid 423 through 428 Processing helix chain 'C' and resid 454 through 467 removed outlier: 3.565A pdb=" N ARG C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 487 Processing helix chain 'C' and resid 509 through 526 Processing helix chain 'C' and resid 549 through 577 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=AA1, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 311 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N SER A 261 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU A 207 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 210 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL A 540 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA A 319 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR A 542 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A 321 " --> pdb=" O TYR A 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN A 544 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR A 323 " --> pdb=" O GLN A 544 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.968A pdb=" N VAL A 134 " --> pdb=" O MET A 247 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA5, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.037A pdb=" N HIS A 175 " --> pdb=" O ILE A 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 272 through 273 Processing sheet with id=AA7, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA8, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA9, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR B 311 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER B 261 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 207 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS B 210 " --> pdb=" O CYS B 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL B 540 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 319 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR B 542 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU B 321 " --> pdb=" O TYR B 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN B 544 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR B 323 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.968A pdb=" N VAL B 134 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'B' and resid 175 through 176 removed outlier: 7.037A pdb=" N HIS B 175 " --> pdb=" O ILE B 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 272 through 273 Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 337 Processing sheet with id=AB7, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR C 311 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER C 261 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU C 207 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS C 210 " --> pdb=" O CYS C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 122 through 129 removed outlier: 9.234A pdb=" N VAL C 540 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA C 319 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N TYR C 542 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU C 321 " --> pdb=" O TYR C 542 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLN C 544 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N THR C 323 " --> pdb=" O GLN C 544 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.968A pdb=" N VAL C 134 " --> pdb=" O MET C 247 " (cutoff:3.500A) Processing sheet with id=AC2, 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=AC3, first strand: chain 'C' and resid 175 through 176 removed outlier: 7.037A pdb=" N HIS C 175 " --> pdb=" O ILE C 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 272 through 273 Processing sheet with id=AC5, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AC6, first strand: chain 'C' and resid 365 through 366 622 hydrogen bonds defined for protein. 1758 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: 3.68 Time building geometry restraints manager: 5.61 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: 1802 2.75 - 3.29: 11735 3.29 - 3.83: 20550 3.83 - 4.36: 24642 4.36 - 4.90: 41705 Nonbonded interactions: 100434 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 100429 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: 0.830 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 34.740 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.080 ------------------------------------------------------------------------------- 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= 0.439 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 : 1.398 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: 1.3566 time to fit residues: 234.0415 Evaluate side-chains 100 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B 322 HIS C 172 GLN C 191 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1158 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= 0.214 Angle : 0.612 9.190 16413 Z= 0.313 Chirality : 0.043 0.265 1890 Planarity : 0.004 0.059 2076 Dihedral : 8.190 56.787 2188 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: 0.07 (0.22), residues: 1404 helix: 0.97 (0.22), residues: 600 sheet: -0.17 (0.31), residues: 228 loop : -0.76 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 564 HIS 0.003 0.001 HIS B 292 PHE 0.029 0.002 PHE B 462 TYR 0.017 0.001 TYR C 432 ARG 0.007 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 135 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 114 time to evaluate : 1.402 Fit side-chains REVERT: A 121 GLN cc_start: 0.7954 (mm110) cc_final: 0.7732 (mm110) REVERT: A 182 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: A 341 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: A 515 MET cc_start: 0.8476 (mtm) cc_final: 0.8246 (mtm) REVERT: A 548 TYR cc_start: 0.8374 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 477 ILE cc_start: 0.8614 (mt) cc_final: 0.8334 (mm) REVERT: C 98 MET cc_start: 0.5544 (ptt) cc_final: 0.5266 (ptm) REVERT: C 121 GLN cc_start: 0.8087 (mm110) cc_final: 0.7812 (mm110) REVERT: C 548 TYR cc_start: 0.8292 (t80) cc_final: 0.8079 (t80) outliers start: 21 outliers final: 3 residues processed: 119 average time/residue: 1.3117 time to fit residues: 169.7061 Evaluate side-chains 104 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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: 0.9980 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.1421 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= 0.205 Angle : 0.576 9.354 16413 Z= 0.291 Chirality : 0.042 0.247 1890 Planarity : 0.004 0.053 2076 Dihedral : 7.535 56.933 2184 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.49 % Allowed : 10.90 % Favored : 86.60 % 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: 0.21 (0.23), residues: 1404 helix: 1.15 (0.22), residues: 600 sheet: -0.28 (0.30), residues: 237 loop : -0.68 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.003 0.001 HIS B 292 PHE 0.022 0.002 PHE B 462 TYR 0.015 0.001 TYR B 448 ARG 0.009 0.000 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 142 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.381 Fit side-chains REVERT: A 121 GLN cc_start: 0.7934 (mm110) cc_final: 0.7715 (mm110) REVERT: A 163 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7925 (t0) REVERT: A 341 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7580 (pt0) REVERT: B 477 ILE cc_start: 0.8651 (mt) cc_final: 0.8420 (mm) REVERT: C 98 MET cc_start: 0.5697 (ptt) cc_final: 0.5331 (ptm) REVERT: C 121 GLN cc_start: 0.8098 (mm110) cc_final: 0.7825 (mm110) REVERT: C 192 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8372 (pt) REVERT: C 475 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7300 (mtt) REVERT: C 543 ARG cc_start: 0.7908 (ttp-110) cc_final: 0.7668 (mtp-110) REVERT: C 576 MET cc_start: 0.3753 (pmm) cc_final: 0.3349 (pmm) REVERT: R 3 ARG cc_start: 0.8375 (mtt90) cc_final: 0.7997 (mtt-85) outliers start: 32 outliers final: 8 residues processed: 122 average time/residue: 1.2459 time to fit residues: 165.5888 Evaluate side-chains 107 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 550 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 475 MET 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: 0.6980 chunk 96 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN C 119 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.182 Angle : 0.556 9.377 16413 Z= 0.279 Chirality : 0.042 0.251 1890 Planarity : 0.004 0.051 2076 Dihedral : 7.151 56.822 2184 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.79 % Allowed : 13.79 % Favored : 84.42 % 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: 0.37 (0.23), residues: 1404 helix: 1.22 (0.22), residues: 603 sheet: -0.23 (0.30), residues: 237 loop : -0.52 (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 0.015 0.002 PHE B 462 TYR 0.014 0.001 TYR B 448 ARG 0.010 0.000 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 139 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.305 Fit side-chains REVERT: A 121 GLN cc_start: 0.7999 (mm110) cc_final: 0.7790 (mm110) REVERT: C 98 MET cc_start: 0.5692 (ptt) cc_final: 0.5335 (ptm) REVERT: C 121 GLN cc_start: 0.8106 (mm110) cc_final: 0.7840 (mm110) REVERT: C 475 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7165 (mtt) REVERT: C 543 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7627 (mtp-110) REVERT: R 3 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7900 (mtt-85) outliers start: 23 outliers final: 11 residues processed: 124 average time/residue: 1.1134 time to fit residues: 151.5457 Evaluate side-chains 112 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 475 MET 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: 2.9990 chunk 77 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12138 Z= 0.256 Angle : 0.579 9.286 16413 Z= 0.291 Chirality : 0.043 0.245 1890 Planarity : 0.004 0.049 2076 Dihedral : 7.045 57.341 2184 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.49 % Allowed : 14.25 % Favored : 83.26 % 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: 0.38 (0.23), residues: 1404 helix: 1.21 (0.22), residues: 603 sheet: -0.22 (0.30), residues: 237 loop : -0.49 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 564 HIS 0.004 0.001 HIS B 283 PHE 0.012 0.002 PHE C 277 TYR 0.018 0.001 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 139 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 1.373 Fit side-chains REVERT: A 132 MET cc_start: 0.8338 (ptm) cc_final: 0.8109 (ptp) REVERT: A 182 MET cc_start: 0.8632 (mmm) cc_final: 0.8333 (mmt) REVERT: A 341 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7505 (pt0) REVERT: A 346 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8855 (p) REVERT: B 307 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8537 (pt) REVERT: C 98 MET cc_start: 0.5749 (ptt) cc_final: 0.5402 (ptm) REVERT: C 121 GLN cc_start: 0.8086 (mm110) cc_final: 0.7855 (mm110) REVERT: C 163 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.7935 (t0) REVERT: C 543 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7561 (mtp-110) REVERT: R 3 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7949 (mtt-85) outliers start: 32 outliers final: 16 residues processed: 123 average time/residue: 1.1610 time to fit residues: 157.3369 Evaluate side-chains 120 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 199 ILE 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 B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 LEU 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: 0.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12138 Z= 0.271 Angle : 0.590 9.534 16413 Z= 0.296 Chirality : 0.043 0.243 1890 Planarity : 0.004 0.049 2076 Dihedral : 7.028 57.132 2184 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.57 % Allowed : 14.80 % Favored : 82.63 % 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: 0.36 (0.23), residues: 1404 helix: 1.18 (0.22), residues: 600 sheet: -0.19 (0.30), residues: 237 loop : -0.49 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 564 HIS 0.004 0.001 HIS B 283 PHE 0.014 0.002 PHE B 554 TYR 0.018 0.001 TYR B 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 142 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 109 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 132 MET cc_start: 0.8341 (ptm) cc_final: 0.8097 (ptp) REVERT: A 182 MET cc_start: 0.8723 (mmm) cc_final: 0.8440 (mmt) REVERT: A 341 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7507 (pt0) REVERT: A 346 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8846 (p) REVERT: B 307 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8512 (pt) REVERT: C 121 GLN cc_start: 0.8098 (mm110) cc_final: 0.7859 (mm110) REVERT: C 163 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.7908 (t0) REVERT: R 3 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7897 (mtt-85) outliers start: 33 outliers final: 19 residues processed: 127 average time/residue: 1.0971 time to fit residues: 154.0494 Evaluate side-chains 124 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 199 ILE 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 B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 359 LEU 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: 0.6980 chunk 77 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 135 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 84 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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: 0.8078 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.176 Angle : 0.568 9.316 16413 Z= 0.283 Chirality : 0.041 0.249 1890 Planarity : 0.004 0.049 2076 Dihedral : 6.805 56.752 2184 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 2.49 % Allowed : 15.11 % Favored : 82.40 % 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: 0.47 (0.23), residues: 1404 helix: 1.26 (0.22), residues: 600 sheet: -0.16 (0.31), residues: 237 loop : -0.41 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 564 HIS 0.002 0.001 HIS B 283 PHE 0.011 0.001 PHE C 277 TYR 0.013 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 144 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8307 (ptm) cc_final: 0.8011 (ptp) REVERT: A 182 MET cc_start: 0.8768 (mmm) cc_final: 0.8547 (mmt) REVERT: A 341 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: A 346 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8852 (p) REVERT: B 307 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8505 (pt) REVERT: B 576 MET cc_start: 0.2376 (pmm) cc_final: 0.2080 (pmm) REVERT: C 98 MET cc_start: 0.5588 (ptt) cc_final: 0.5179 (ptm) REVERT: R 3 ARG cc_start: 0.8321 (mtt90) cc_final: 0.7852 (mtt-85) outliers start: 32 outliers final: 20 residues processed: 130 average time/residue: 1.0725 time to fit residues: 153.7569 Evaluate side-chains 122 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER 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 199 ILE 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 331 ASN 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 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 354 CYS 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: 5.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.1977 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= 0.215 Angle : 0.587 10.316 16413 Z= 0.291 Chirality : 0.042 0.245 1890 Planarity : 0.004 0.056 2076 Dihedral : 6.763 57.075 2184 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 2.26 % Allowed : 15.65 % Favored : 82.09 % 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: 0.46 (0.23), residues: 1404 helix: 1.26 (0.22), residues: 600 sheet: -0.13 (0.31), residues: 237 loop : -0.43 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.017 0.001 PHE B 554 TYR 0.015 0.001 TYR B 448 ARG 0.014 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 136 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 107 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8312 (ptm) cc_final: 0.8078 (ptp) REVERT: A 341 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: A 346 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8863 (p) REVERT: B 307 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8510 (pt) REVERT: B 576 MET cc_start: 0.2322 (pmm) cc_final: 0.1996 (pmm) REVERT: C 98 MET cc_start: 0.5670 (ptt) cc_final: 0.5264 (ptm) REVERT: R 3 ARG cc_start: 0.8344 (mtt90) cc_final: 0.7842 (mtt-85) outliers start: 29 outliers final: 23 residues processed: 123 average time/residue: 1.0868 time to fit residues: 147.2888 Evaluate side-chains 126 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER 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 199 ILE 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 331 ASN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 354 CYS 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: 0.9990 chunk 130 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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: 0.2011 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= 0.219 Angle : 0.594 9.939 16413 Z= 0.294 Chirality : 0.042 0.245 1890 Planarity : 0.004 0.054 2076 Dihedral : 6.726 56.942 2184 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.18 % Allowed : 15.81 % Favored : 82.01 % 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: 0.49 (0.23), residues: 1404 helix: 1.27 (0.22), residues: 600 sheet: -0.10 (0.31), residues: 237 loop : -0.41 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 564 HIS 0.003 0.001 HIS B 283 PHE 0.013 0.001 PHE A 462 TYR 0.015 0.001 TYR B 448 ARG 0.012 0.001 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 134 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8309 (ptm) cc_final: 0.8072 (ptp) REVERT: A 341 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: A 346 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8868 (p) REVERT: B 307 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8500 (pt) REVERT: B 576 MET cc_start: 0.2202 (pmm) cc_final: 0.1642 (pmm) REVERT: C 98 MET cc_start: 0.5662 (ptt) cc_final: 0.5262 (ptm) REVERT: R 3 ARG cc_start: 0.8375 (mtt90) cc_final: 0.7861 (mtt-85) outliers start: 28 outliers final: 21 residues processed: 123 average time/residue: 1.0796 time to fit residues: 146.9422 Evaluate side-chains 122 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER 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 199 ILE 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 331 ASN 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 199 ILE 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 354 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12138 Z= 0.238 Angle : 0.606 9.835 16413 Z= 0.300 Chirality : 0.043 0.245 1890 Planarity : 0.004 0.054 2076 Dihedral : 6.720 57.076 2184 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 1.95 % Allowed : 16.20 % Favored : 81.85 % 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: 0.47 (0.23), residues: 1404 helix: 1.23 (0.22), residues: 600 sheet: -0.09 (0.31), residues: 237 loop : -0.41 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 564 HIS 0.004 0.001 HIS B 283 PHE 0.018 0.002 PHE A 554 TYR 0.017 0.001 TYR B 448 ARG 0.014 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 130 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8313 (ptm) cc_final: 0.8073 (ptp) REVERT: A 341 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7429 (pt0) REVERT: A 346 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8861 (p) REVERT: B 307 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8511 (pt) REVERT: C 98 MET cc_start: 0.5901 (ptt) cc_final: 0.5457 (ptm) REVERT: R 3 ARG cc_start: 0.8399 (mtt90) cc_final: 0.7865 (mtt-85) outliers start: 25 outliers final: 23 residues processed: 121 average time/residue: 0.9628 time to fit residues: 129.3700 Evaluate side-chains 126 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 313 SER 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 199 ILE 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 331 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 199 ILE 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 354 CYS Chi-restraints excluded: chain C residue 359 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 115 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 6 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3660 r_free = 0.3660 target = 0.135971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100544 restraints weight = 15251.281| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.30 r_work: 0.2926 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12138 Z= 0.171 Angle : 0.587 10.238 16413 Z= 0.288 Chirality : 0.041 0.251 1890 Planarity : 0.004 0.057 2076 Dihedral : 6.569 56.791 2184 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.77 % Favored : 95.16 % Rotamer: Outliers : 2.10 % Allowed : 16.28 % Favored : 81.62 % 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: 0.60 (0.23), residues: 1404 helix: 1.32 (0.22), residues: 597 sheet: 0.04 (0.31), residues: 231 loop : -0.34 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 564 HIS 0.002 0.000 HIS A 283 PHE 0.013 0.001 PHE A 462 TYR 0.012 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: 3735.58 seconds wall clock time: 66 minutes 36.65 seconds (3996.65 seconds total)