Starting phenix.real_space_refine on Sat Feb 24 17:57:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981_neut_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf8_29981/02_2024/8gf8_29981_neut_trim_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= 0.021 sd= 0.104 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: 7 Type Number sf(0) Gaussians P 36 5.49 5 S 136 5.16 5 Na 2 4.78 5 C 14780 2.51 5 N 3340 2.21 5 O 3992 1.98 5 H 20452 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 213": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 410": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 575": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 654": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 740": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 744": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42738 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "B" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "C" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "D" Number of atoms: 10196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 10196 Classifications: {'peptide': 630} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 613} Chain breaks: 1 Chain: "A" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 490 Unusual residues: {' NA': 2, '8IJ': 1, 'POV': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 592 Unusual residues: {'8IJ': 1, 'POV': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 488 Unusual residues: {'8IJ': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 384 Unusual residues: {'8IJ': 1, 'POV': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 18.15, per 1000 atoms: 0.42 Number of scatterers: 42738 At special positions: 0 Unit cell: (129.525, 129.525, 117.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 136 16.00 P 36 15.00 Na 2 11.00 O 3992 8.00 N 3340 7.00 C 14780 6.00 H 20452 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 391 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 391 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.42 Conformation dependent library (CDL) restraints added in 3.8 seconds 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 4 sheets defined 53.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.03 Creating SS restraints... Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.502A pdb=" N GLN A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 3.904A pdb=" N ASN A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.819A pdb=" N THR A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 262 through 269 removed outlier: 3.513A pdb=" N LEU A 269 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 300 through 320 removed outlier: 3.831A pdb=" N SER A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 328 No H-bonds generated for 'chain 'A' and resid 326 through 328' Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 419 through 429 removed outlier: 3.513A pdb=" N GLN A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 454 Processing helix chain 'A' and resid 469 through 493 removed outlier: 3.681A pdb=" N PHE A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 503 through 506 No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 513 through 531 removed outlier: 3.752A pdb=" N VAL A 527 " --> pdb=" O MET A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 558 removed outlier: 3.666A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLY A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 596 removed outlier: 3.917A pdb=" N MET A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 638 removed outlier: 3.728A pdb=" N GLU A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'A' and resid 675 through 689 Processing helix chain 'A' and resid 692 through 712 removed outlier: 3.684A pdb=" N ILE A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 123 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.501A pdb=" N GLN B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 149 removed outlier: 3.903A pdb=" N ASN B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 164 Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 188 through 191 No H-bonds generated for 'chain 'B' and resid 188 through 191' Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.820A pdb=" N THR B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.513A pdb=" N LEU B 269 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 300 through 320 removed outlier: 3.831A pdb=" N SER B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 312 " --> pdb=" O SER B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 328 No H-bonds generated for 'chain 'B' and resid 326 through 328' Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 419 through 429 removed outlier: 3.514A pdb=" N GLN B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 454 Processing helix chain 'B' and resid 469 through 493 removed outlier: 3.681A pdb=" N PHE B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 503 through 506 No H-bonds generated for 'chain 'B' and resid 503 through 506' Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.751A pdb=" N VAL B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.666A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 556 " --> pdb=" O MET B 552 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 596 removed outlier: 3.918A pdb=" N MET B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 582 " --> pdb=" O CYS B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.729A pdb=" N GLU B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 671 Processing helix chain 'B' and resid 675 through 689 Processing helix chain 'B' and resid 692 through 712 removed outlier: 3.683A pdb=" N ILE B 697 " --> pdb=" O GLU B 693 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 123 Processing helix chain 'C' and resid 127 through 139 removed outlier: 3.502A pdb=" N GLN C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 149 removed outlier: 3.904A pdb=" N ASN C 147 " --> pdb=" O HIS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 174 through 183 Processing helix chain 'C' and resid 188 through 191 No H-bonds generated for 'chain 'C' and resid 188 through 191' Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 223 removed outlier: 3.819A pdb=" N THR C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 262 through 269 removed outlier: 3.513A pdb=" N LEU C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 300 through 320 removed outlier: 3.831A pdb=" N SER C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN C 311 " --> pdb=" O THR C 307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 312 " --> pdb=" O SER C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 328 No H-bonds generated for 'chain 'C' and resid 326 through 328' Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 419 through 429 removed outlier: 3.514A pdb=" N GLN C 424 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 454 Processing helix chain 'C' and resid 469 through 493 removed outlier: 3.682A pdb=" N PHE C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 503 through 506 No H-bonds generated for 'chain 'C' and resid 503 through 506' Processing helix chain 'C' and resid 513 through 531 removed outlier: 3.752A pdb=" N VAL C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 558 removed outlier: 3.666A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 596 removed outlier: 3.918A pdb=" N MET C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 638 removed outlier: 3.729A pdb=" N GLU C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 671 Processing helix chain 'C' and resid 675 through 689 Processing helix chain 'C' and resid 692 through 712 removed outlier: 3.683A pdb=" N ILE C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 700 " --> pdb=" O ASN C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 123 Processing helix chain 'D' and resid 127 through 139 removed outlier: 3.503A pdb=" N GLN D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 149 removed outlier: 3.904A pdb=" N ASN D 147 " --> pdb=" O HIS D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 174 through 183 Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 223 removed outlier: 3.819A pdb=" N THR D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 220 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 262 through 269 removed outlier: 3.513A pdb=" N LEU D 269 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 300 through 320 removed outlier: 3.831A pdb=" N SER D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 311 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 312 " --> pdb=" O SER D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 328 No H-bonds generated for 'chain 'D' and resid 326 through 328' Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 419 through 429 removed outlier: 3.514A pdb=" N GLN D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 454 Processing helix chain 'D' and resid 469 through 493 removed outlier: 3.681A pdb=" N PHE D 473 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 513 through 531 removed outlier: 3.751A pdb=" N VAL D 527 " --> pdb=" O MET D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 558 removed outlier: 3.665A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 596 removed outlier: 3.916A pdb=" N MET D 572 " --> pdb=" O MET D 568 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 582 " --> pdb=" O CYS D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 638 removed outlier: 3.728A pdb=" N GLU D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 671 Processing helix chain 'D' and resid 675 through 689 Processing helix chain 'D' and resid 692 through 712 removed outlier: 3.683A pdb=" N ILE D 697 " --> pdb=" O GLU D 693 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 700 " --> pdb=" O ASN D 696 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 369 through 371 removed outlier: 3.678A pdb=" N PHE A 370 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 369 through 371 removed outlier: 3.679A pdb=" N PHE B 370 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 369 through 371 removed outlier: 3.679A pdb=" N PHE C 370 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 369 through 371 removed outlier: 3.679A pdb=" N PHE D 370 " --> pdb=" O LEU D 382 " (cutoff:3.500A) 836 hydrogen bonds defined for protein. 2484 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.01 Time building geometry restraints manager: 35.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 20412 1.03 - 1.23: 475 1.23 - 1.43: 8629 1.43 - 1.63: 13408 1.63 - 1.83: 224 Bond restraints: 43148 Sorted by residual: bond pdb=" C41 8IJ A1202 " pdb=" O40 8IJ A1202 " ideal model delta sigma weight residual 1.403 1.339 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C41 8IJ B1205 " pdb=" O40 8IJ B1205 " ideal model delta sigma weight residual 1.403 1.339 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C41 8IJ D1202 " pdb=" O40 8IJ D1202 " ideal model delta sigma weight residual 1.403 1.340 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O12 POV B1204 " pdb=" P POV B1204 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C41 8IJ C1203 " pdb=" O40 8IJ C1203 " ideal model delta sigma weight residual 1.403 1.340 0.063 2.00e-02 2.50e+03 9.91e+00 ... (remaining 43143 not shown) Histogram of bond angle deviations from ideal: 97.08 - 104.53: 340 104.53 - 111.98: 46615 111.98 - 119.42: 12299 119.42 - 126.87: 17151 126.87 - 134.31: 251 Bond angle restraints: 76656 Sorted by residual: angle pdb=" CA LEU A 675 " pdb=" CB LEU A 675 " pdb=" CG LEU A 675 " ideal model delta sigma weight residual 116.30 131.61 -15.31 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU D 675 " pdb=" CB LEU D 675 " pdb=" CG LEU D 675 " ideal model delta sigma weight residual 116.30 131.60 -15.30 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU B 675 " pdb=" CB LEU B 675 " pdb=" CG LEU B 675 " ideal model delta sigma weight residual 116.30 131.59 -15.29 3.50e+00 8.16e-02 1.91e+01 angle pdb=" CA LEU C 675 " pdb=" CB LEU C 675 " pdb=" CG LEU C 675 " ideal model delta sigma weight residual 116.30 131.56 -15.26 3.50e+00 8.16e-02 1.90e+01 angle pdb=" O16 8IJ A1202 " pdb=" P2 8IJ A1202 " pdb=" O4 8IJ A1202 " ideal model delta sigma weight residual 109.49 97.16 12.33 3.00e+00 1.11e-01 1.69e+01 ... (remaining 76651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 20071 34.58 - 69.16: 715 69.16 - 103.74: 109 103.74 - 138.32: 45 138.32 - 172.89: 20 Dihedral angle restraints: 20960 sinusoidal: 11936 harmonic: 9024 Sorted by residual: dihedral pdb=" CA SER D 272 " pdb=" C SER D 272 " pdb=" N TRP D 273 " pdb=" CA TRP D 273 " ideal model delta harmonic sigma weight residual -180.00 -145.92 -34.08 0 5.00e+00 4.00e-02 4.65e+01 dihedral pdb=" CA SER A 272 " pdb=" C SER A 272 " pdb=" N TRP A 273 " pdb=" CA TRP A 273 " ideal model delta harmonic sigma weight residual -180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA SER C 272 " pdb=" C SER C 272 " pdb=" N TRP C 273 " pdb=" CA TRP C 273 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 20957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 3240 1.003 - 2.006: 0 2.006 - 3.010: 0 3.010 - 4.013: 0 4.013 - 5.016: 4 Chirality restraints: 3244 Sorted by residual: chirality pdb=" C5 8IJ B1205 " pdb=" C14 8IJ B1205 " pdb=" C6 8IJ B1205 " pdb=" O4 8IJ B1205 " both_signs ideal model delta sigma weight residual False 2.50 -2.52 5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C5 8IJ C1203 " pdb=" C14 8IJ C1203 " pdb=" C6 8IJ C1203 " pdb=" O4 8IJ C1203 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C5 8IJ A1202 " pdb=" C14 8IJ A1202 " pdb=" C6 8IJ A1202 " pdb=" O4 8IJ A1202 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.29e+02 ... (remaining 3241 not shown) Planarity restraints: 6064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 420 " -0.093 2.00e-02 2.50e+03 1.00e-01 1.51e+02 pdb=" CG ASN C 420 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 420 " 0.086 2.00e-02 2.50e+03 pdb=" ND2 ASN C 420 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN C 420 " 0.143 2.00e-02 2.50e+03 pdb="HD22 ASN C 420 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 420 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.50e+02 pdb=" CG ASN B 420 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 420 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN B 420 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 420 " -0.142 2.00e-02 2.50e+03 pdb="HD22 ASN B 420 " 0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 420 " 0.093 2.00e-02 2.50e+03 1.00e-01 1.50e+02 pdb=" CG ASN A 420 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 420 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN A 420 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 420 " -0.142 2.00e-02 2.50e+03 pdb="HD22 ASN A 420 " 0.153 2.00e-02 2.50e+03 ... (remaining 6061 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 4949 2.27 - 2.85: 97587 2.85 - 3.43: 113079 3.43 - 4.02: 157700 4.02 - 4.60: 243288 Nonbonded interactions: 616603 Sorted by model distance: nonbonded pdb=" O ARG C 356 " pdb=" H ARG C 368 " model vdw 1.684 1.850 nonbonded pdb=" O ARG D 356 " pdb=" H ARG D 368 " model vdw 1.684 1.850 nonbonded pdb=" O ARG B 356 " pdb=" H ARG B 368 " model vdw 1.684 1.850 nonbonded pdb=" O ARG A 356 " pdb=" H ARG A 368 " model vdw 1.685 1.850 nonbonded pdb=" O GLU C 398 " pdb=" H TYR C 402 " model vdw 1.690 1.850 ... (remaining 616598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 115 through 769 or resid 1201 or resid 1204 or (resid 1206 \ and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name \ C316)) or resid 1207 or (resid 1208 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C310 or name C311 or name C312 or name C3 \ 13 or name C314 or name C315 or name C316)))) selection = (chain 'B' and (resid 115 through 769 or resid 1201 or resid 1204 or (resid 1206 \ and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name \ C316)) or resid 1207 through 1208)) selection = (chain 'C' and (resid 115 through 769 or resid 1201 or resid 1204 or resid 1206 \ through 1207 or (resid 1208 and (name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C310 or name C311 or name C312 or name C313 or nam \ e C314 or name C315 or name C316)))) selection = (chain 'D' and (resid 115 through 769 or resid 1201 or resid 1204 or (resid 1206 \ and (name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C310 or name C311 or name C312 or name C313 or name C314 or name C315 or name \ C316)) or resid 1207 or (resid 1208 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C310 or name C311 or name C312 or name C3 \ 13 or name C314 or name C315 or name C316)))) } 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: 1.190 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: 0.630 Extract box with map and model: 6.470 Check model and map are aligned: 0.660 Set scattering table: 0.420 Process input model: 133.330 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.220 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:15.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.008 0.064 22696 Z= 0.482 Angle : 1.113 15.311 30328 Z= 0.513 Chirality : 0.182 5.016 3244 Planarity : 0.005 0.046 3616 Dihedral : 20.865 172.895 9160 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.42 % Favored : 88.58 % Rotamer: Outliers : 0.18 % Allowed : 3.96 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -5.60 (0.12), residues: 2504 helix: -3.55 (0.09), residues: 1460 sheet: -3.99 (0.43), residues: 92 loop : -3.73 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 698 HIS 0.010 0.002 HIS B 233 PHE 0.026 0.003 PHE B 721 TYR 0.022 0.003 TYR B 739 ARG 0.009 0.001 ARG D 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 506 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 HIS cc_start: 0.5396 (p90) cc_final: 0.4819 (p90) REVERT: A 340 LEU cc_start: 0.8042 (tp) cc_final: 0.7785 (tp) REVERT: A 523 MET cc_start: 0.7674 (tpt) cc_final: 0.7338 (tpt) REVERT: A 599 ILE cc_start: 0.8337 (mt) cc_final: 0.8011 (mp) REVERT: A 753 TRP cc_start: 0.3020 (m100) cc_final: 0.2516 (p-90) REVERT: B 233 HIS cc_start: 0.5392 (p90) cc_final: 0.4765 (p90) REVERT: B 340 LEU cc_start: 0.8037 (tp) cc_final: 0.7761 (tp) REVERT: B 523 MET cc_start: 0.7672 (tpt) cc_final: 0.7384 (tpt) REVERT: B 753 TRP cc_start: 0.3090 (m100) cc_final: 0.2493 (p-90) REVERT: C 340 LEU cc_start: 0.8064 (tp) cc_final: 0.7797 (tp) REVERT: C 753 TRP cc_start: 0.3049 (m100) cc_final: 0.2491 (p-90) REVERT: D 233 HIS cc_start: 0.5409 (p90) cc_final: 0.4805 (p90) REVERT: D 340 LEU cc_start: 0.8073 (tp) cc_final: 0.7808 (tp) REVERT: D 523 MET cc_start: 0.7689 (tpt) cc_final: 0.7341 (tpt) REVERT: D 753 TRP cc_start: 0.2966 (m100) cc_final: 0.2397 (p-90) outliers start: 4 outliers final: 0 residues processed: 510 average time/residue: 2.6737 time to fit residues: 1570.6921 Evaluate side-chains 282 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 561 GLN B 165 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 GLN B 561 GLN B 629 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN C 561 GLN C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 355 GLN D 561 GLN D 629 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22696 Z= 0.228 Angle : 0.622 7.112 30328 Z= 0.318 Chirality : 0.037 0.323 3244 Planarity : 0.004 0.037 3616 Dihedral : 24.052 179.362 4332 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 2.52 % Allowed : 13.04 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.15), residues: 2504 helix: -1.76 (0.12), residues: 1512 sheet: -3.68 (0.45), residues: 92 loop : -3.25 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 698 HIS 0.012 0.001 HIS B 167 PHE 0.013 0.001 PHE C 305 TYR 0.016 0.002 TYR B 584 ARG 0.007 0.001 ARG C 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 307 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6842 (ttp) REVERT: A 295 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7607 (m) REVERT: A 523 MET cc_start: 0.7906 (tpt) cc_final: 0.7322 (tpt) REVERT: A 753 TRP cc_start: 0.2911 (m100) cc_final: 0.2191 (p-90) REVERT: B 163 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6702 (ttp) REVERT: B 233 HIS cc_start: 0.5473 (p90) cc_final: 0.4891 (p-80) REVERT: B 305 PHE cc_start: 0.7704 (t80) cc_final: 0.7230 (t80) REVERT: B 326 LEU cc_start: 0.8423 (tp) cc_final: 0.8176 (mt) REVERT: B 523 MET cc_start: 0.7862 (tpt) cc_final: 0.7358 (tpt) REVERT: B 753 TRP cc_start: 0.2893 (m100) cc_final: 0.2185 (p-90) REVERT: C 163 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6752 (ttm) REVERT: C 523 MET cc_start: 0.7658 (tpt) cc_final: 0.7302 (tpt) REVERT: D 163 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6632 (ttp) REVERT: D 295 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7677 (m) REVERT: D 523 MET cc_start: 0.7875 (tpt) cc_final: 0.7338 (tpt) outliers start: 56 outliers final: 4 residues processed: 338 average time/residue: 2.2882 time to fit residues: 911.0393 Evaluate side-chains 271 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 261 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 63 optimal weight: 50.0000 chunk 229 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN A 355 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 355 GLN B 629 ASN ** B 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 355 GLN ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 355 GLN ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 22696 Z= 0.354 Angle : 0.627 6.195 30328 Z= 0.325 Chirality : 0.038 0.215 3244 Planarity : 0.004 0.046 3616 Dihedral : 23.776 179.074 4332 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 2.29 % Allowed : 12.72 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.15), residues: 2504 helix: -0.99 (0.12), residues: 1504 sheet: -3.86 (0.39), residues: 92 loop : -3.09 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 698 HIS 0.004 0.001 HIS C 233 PHE 0.023 0.002 PHE A 439 TYR 0.012 0.002 TYR A 584 ARG 0.009 0.001 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 285 time to evaluate : 3.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7060 (mtm) cc_final: 0.6765 (ttp) REVERT: A 295 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7979 (t) REVERT: A 305 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7356 (t80) REVERT: A 326 LEU cc_start: 0.8469 (tp) cc_final: 0.8221 (mt) REVERT: A 685 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7047 (tp30) REVERT: B 163 MET cc_start: 0.7007 (OUTLIER) cc_final: 0.6746 (ttp) REVERT: B 305 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7082 (t80) REVERT: B 523 MET cc_start: 0.8126 (tpt) cc_final: 0.7548 (tpt) REVERT: B 685 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6985 (tp30) REVERT: C 305 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7569 (t80) REVERT: C 523 MET cc_start: 0.7954 (tpt) cc_final: 0.7423 (tpt) REVERT: D 163 MET cc_start: 0.6982 (mtm) cc_final: 0.6683 (ttp) REVERT: D 215 MET cc_start: 0.6401 (ttp) cc_final: 0.6180 (ttp) REVERT: D 295 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7948 (t) REVERT: D 305 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7326 (t80) REVERT: D 685 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7023 (tp30) outliers start: 51 outliers final: 12 residues processed: 320 average time/residue: 2.3569 time to fit residues: 887.5563 Evaluate side-chains 261 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 230 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22696 Z= 0.258 Angle : 0.546 5.390 30328 Z= 0.284 Chirality : 0.036 0.213 3244 Planarity : 0.004 0.048 3616 Dihedral : 22.090 179.803 4332 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.61 % Allowed : 14.75 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2504 helix: -0.41 (0.13), residues: 1500 sheet: -3.46 (0.43), residues: 92 loop : -3.01 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 698 HIS 0.003 0.001 HIS C 233 PHE 0.018 0.001 PHE A 439 TYR 0.013 0.002 TYR C 584 ARG 0.004 0.001 ARG B 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 256 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6701 (ttp) REVERT: A 294 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8288 (mm-30) REVERT: A 295 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7995 (t) REVERT: A 523 MET cc_start: 0.7590 (mmm) cc_final: 0.7175 (tpt) REVERT: A 572 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7166 (mpp) REVERT: B 163 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6648 (ttp) REVERT: B 326 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7992 (tp) REVERT: B 523 MET cc_start: 0.7977 (tpt) cc_final: 0.7456 (tpt) REVERT: D 163 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6551 (ttp) REVERT: D 215 MET cc_start: 0.6437 (ttp) cc_final: 0.6225 (ttp) REVERT: D 295 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8019 (t) REVERT: D 523 MET cc_start: 0.7550 (mmm) cc_final: 0.7131 (tpt) REVERT: D 572 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7154 (mpp) outliers start: 58 outliers final: 19 residues processed: 284 average time/residue: 2.1170 time to fit residues: 717.1536 Evaluate side-chains 265 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 238 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 3 optimal weight: 30.0000 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 124 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22696 Z= 0.325 Angle : 0.570 5.804 30328 Z= 0.294 Chirality : 0.037 0.202 3244 Planarity : 0.004 0.037 3616 Dihedral : 21.608 168.273 4332 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.97 % Allowed : 14.93 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2504 helix: -0.36 (0.13), residues: 1524 sheet: -3.51 (0.42), residues: 92 loop : -3.10 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 698 HIS 0.003 0.001 HIS C 233 PHE 0.021 0.002 PHE A 439 TYR 0.013 0.002 TYR D 310 ARG 0.003 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 250 time to evaluate : 3.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6690 (ttp) REVERT: A 295 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7952 (t) REVERT: A 326 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8060 (mt) REVERT: B 163 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6776 (ttp) REVERT: B 523 MET cc_start: 0.8009 (tpt) cc_final: 0.7449 (tpt) REVERT: C 163 MET cc_start: 0.6960 (mtm) cc_final: 0.6638 (ttp) REVERT: D 163 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6599 (ttp) REVERT: D 295 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7973 (t) outliers start: 66 outliers final: 23 residues processed: 291 average time/residue: 2.0459 time to fit residues: 716.5434 Evaluate side-chains 261 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 232 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 749 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22696 Z= 0.273 Angle : 0.542 4.799 30328 Z= 0.282 Chirality : 0.036 0.203 3244 Planarity : 0.003 0.037 3616 Dihedral : 20.635 158.556 4332 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.06 % Allowed : 15.74 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.16), residues: 2504 helix: -0.14 (0.13), residues: 1524 sheet: -3.25 (0.44), residues: 92 loop : -2.96 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 698 HIS 0.003 0.001 HIS B 321 PHE 0.013 0.001 PHE A 439 TYR 0.017 0.002 TYR D 310 ARG 0.003 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 242 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7014 (mtm) cc_final: 0.6738 (ttp) REVERT: A 523 MET cc_start: 0.7677 (mmm) cc_final: 0.7107 (tpt) REVERT: A 572 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7198 (mpp) REVERT: B 163 MET cc_start: 0.7012 (mtm) cc_final: 0.6798 (ttp) REVERT: B 326 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8065 (mt) REVERT: B 523 MET cc_start: 0.7957 (tpt) cc_final: 0.7409 (tpt) REVERT: C 163 MET cc_start: 0.6904 (mtm) cc_final: 0.6613 (ttp) REVERT: C 523 MET cc_start: 0.7879 (tpt) cc_final: 0.7309 (tpt) REVERT: D 163 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6635 (ttp) REVERT: D 523 MET cc_start: 0.7655 (mmm) cc_final: 0.7017 (tpt) outliers start: 68 outliers final: 23 residues processed: 284 average time/residue: 1.9519 time to fit residues: 669.8159 Evaluate side-chains 254 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 205 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 749 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS B 629 ASN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22696 Z= 0.183 Angle : 0.502 4.710 30328 Z= 0.261 Chirality : 0.035 0.200 3244 Planarity : 0.003 0.035 3616 Dihedral : 19.513 152.779 4332 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.79 % Allowed : 16.14 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2504 helix: 0.29 (0.13), residues: 1504 sheet: -2.92 (0.48), residues: 92 loop : -2.63 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 753 HIS 0.004 0.001 HIS A 321 PHE 0.009 0.001 PHE B 496 TYR 0.018 0.001 TYR A 310 ARG 0.003 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 241 time to evaluate : 3.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6999 (mtm) cc_final: 0.6755 (ttp) REVERT: A 206 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7247 (tt) REVERT: A 326 LEU cc_start: 0.8318 (tt) cc_final: 0.8039 (mt) REVERT: B 206 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7201 (tt) REVERT: B 326 LEU cc_start: 0.8325 (tt) cc_final: 0.8043 (mt) REVERT: B 523 MET cc_start: 0.7874 (tpt) cc_final: 0.7299 (tpt) REVERT: C 163 MET cc_start: 0.6887 (mtm) cc_final: 0.6629 (ttp) REVERT: C 372 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6502 (tp30) REVERT: C 523 MET cc_start: 0.7753 (tpt) cc_final: 0.7182 (tpt) REVERT: D 163 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6504 (ttp) REVERT: D 206 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7222 (tt) REVERT: D 372 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6584 (tp30) outliers start: 62 outliers final: 24 residues processed: 283 average time/residue: 2.0882 time to fit residues: 715.5297 Evaluate side-chains 262 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 232 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain A residue 749 ASN Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 372 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 692 GLN A 749 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 692 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 692 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22696 Z= 0.235 Angle : 0.517 4.677 30328 Z= 0.268 Chirality : 0.035 0.200 3244 Planarity : 0.003 0.041 3616 Dihedral : 19.425 146.100 4332 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.29 % Allowed : 17.22 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2504 helix: 0.22 (0.13), residues: 1528 sheet: -2.72 (0.51), residues: 92 loop : -2.77 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 750 HIS 0.004 0.001 HIS A 321 PHE 0.011 0.001 PHE A 439 TYR 0.017 0.001 TYR B 310 ARG 0.003 0.000 ARG C 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 236 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6773 (ttp) REVERT: A 206 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7238 (tt) REVERT: A 294 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 206 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7162 (tt) REVERT: B 326 LEU cc_start: 0.8330 (tt) cc_final: 0.8059 (mt) REVERT: C 163 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6642 (ttp) REVERT: C 523 MET cc_start: 0.7810 (tpt) cc_final: 0.7240 (tpt) REVERT: D 163 MET cc_start: 0.6834 (mtm) cc_final: 0.6549 (ttp) REVERT: D 206 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7221 (tt) REVERT: D 372 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6610 (tp30) outliers start: 51 outliers final: 26 residues processed: 272 average time/residue: 2.0858 time to fit residues: 680.3756 Evaluate side-chains 265 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 98 optimal weight: 0.3980 chunk 177 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 204 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 629 ASN B 692 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 692 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22696 Z= 0.294 Angle : 0.545 6.037 30328 Z= 0.282 Chirality : 0.037 0.202 3244 Planarity : 0.003 0.038 3616 Dihedral : 19.663 140.289 4332 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 2.25 % Allowed : 17.31 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2504 helix: 0.12 (0.13), residues: 1532 sheet: -2.70 (0.51), residues: 92 loop : -2.80 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 698 HIS 0.006 0.001 HIS A 321 PHE 0.015 0.002 PHE A 439 TYR 0.021 0.002 TYR B 310 ARG 0.004 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6779 (ttp) REVERT: A 206 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7250 (tt) REVERT: A 326 LEU cc_start: 0.8348 (tt) cc_final: 0.8023 (mt) REVERT: A 523 MET cc_start: 0.7740 (mmm) cc_final: 0.7023 (tpt) REVERT: B 206 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7184 (tt) REVERT: B 523 MET cc_start: 0.7656 (mmm) cc_final: 0.7163 (tpt) REVERT: C 163 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6591 (ttp) REVERT: C 523 MET cc_start: 0.7843 (tpt) cc_final: 0.7281 (tpt) REVERT: D 163 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6537 (ttp) REVERT: D 206 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7226 (tt) outliers start: 50 outliers final: 28 residues processed: 266 average time/residue: 2.2811 time to fit residues: 727.9499 Evaluate side-chains 263 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 310 TYR Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 199 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 692 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 692 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 692 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22696 Z= 0.199 Angle : 0.505 4.886 30328 Z= 0.262 Chirality : 0.035 0.199 3244 Planarity : 0.003 0.036 3616 Dihedral : 18.980 134.596 4332 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 1.84 % Allowed : 17.94 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2504 helix: 0.33 (0.13), residues: 1528 sheet: -2.51 (0.53), residues: 92 loop : -2.59 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 549 HIS 0.005 0.001 HIS A 321 PHE 0.008 0.001 PHE D 650 TYR 0.016 0.001 TYR A 310 ARG 0.004 0.000 ARG B 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5008 Ramachandran restraints generated. 2504 Oldfield, 0 Emsley, 2504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 235 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6977 (mtm) cc_final: 0.6731 (ttp) REVERT: A 206 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7256 (tt) REVERT: A 326 LEU cc_start: 0.8339 (tt) cc_final: 0.7882 (mt) REVERT: A 372 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6485 (tp30) REVERT: A 523 MET cc_start: 0.7738 (mmm) cc_final: 0.7008 (tpt) REVERT: B 206 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7158 (tt) REVERT: B 326 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 523 MET cc_start: 0.7690 (mmm) cc_final: 0.7006 (tpt) REVERT: C 163 MET cc_start: 0.6806 (mtm) cc_final: 0.6564 (ttp) REVERT: C 523 MET cc_start: 0.7753 (tpt) cc_final: 0.7193 (tpt) REVERT: D 163 MET cc_start: 0.6809 (mtm) cc_final: 0.6534 (ttp) REVERT: D 206 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7208 (tt) REVERT: D 372 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6511 (tp30) REVERT: D 523 MET cc_start: 0.7672 (mmm) cc_final: 0.6921 (tpt) outliers start: 41 outliers final: 23 residues processed: 262 average time/residue: 2.3191 time to fit residues: 716.0189 Evaluate side-chains 256 residues out of total 2224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 740 ARG Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 740 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 740 ARG Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 740 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN A 692 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 ASN B 692 GLN ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 ASN ** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 ASN D 692 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.217242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.174343 restraints weight = 65682.453| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.91 r_work: 0.3654 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22696 Z= 0.212 Angle : 0.507 4.623 30328 Z= 0.264 Chirality : 0.035 0.201 3244 Planarity : 0.003 0.037 3616 Dihedral : 18.882 131.001 4332 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 23.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 2.02 % Allowed : 18.03 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2504 helix: 0.39 (0.13), residues: 1536 sheet: -2.49 (0.54), residues: 92 loop : -2.52 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 698 HIS 0.005 0.001 HIS A 321 PHE 0.010 0.001 PHE A 439 TYR 0.016 0.001 TYR B 310 ARG 0.003 0.000 ARG C 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13409.00 seconds wall clock time: 236 minutes 55.32 seconds (14215.32 seconds total)