Starting phenix.real_space_refine on Sat Feb 17 23:30:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t37_25650/02_2024/7t37_25650_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t37_25650/02_2024/7t37_25650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t37_25650/02_2024/7t37_25650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t37_25650/02_2024/7t37_25650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t37_25650/02_2024/7t37_25650_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t37_25650/02_2024/7t37_25650_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 116 5.16 5 B 4 2.79 5 C 13224 2.51 5 N 3388 2.21 5 O 3444 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "D PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 670": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20176 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "C" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 5004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 5004 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 594} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'FZ4': 1, 'P0T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.08, per 1000 atoms: 0.55 Number of scatterers: 20176 At special positions: 0 Unit cell: (140.17, 140.17, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 116 16.00 O 3444 8.00 N 3388 7.00 C 13224 6.00 B 4 5.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 8.70 Conformation dependent library (CDL) restraints added in 3.3 seconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 56.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 249 through 255 removed outlier: 3.623A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.659A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 379 through 412 removed outlier: 3.532A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 458 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 472 through 492 removed outlier: 3.868A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 483 " --> pdb=" O GLN A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 3.540A pdb=" N LEU A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.774A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 558 Processing helix chain 'A' and resid 593 through 605 removed outlier: 4.527A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 649 removed outlier: 3.635A pdb=" N VAL A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 3.801A pdb=" N TRP A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A 672 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 673 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 255 removed outlier: 3.911A pdb=" N VAL B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.678A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 379 through 412 removed outlier: 3.530A pdb=" N ARG B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 458 Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 472 through 492 removed outlier: 3.919A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B 483 " --> pdb=" O GLN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 518 removed outlier: 3.530A pdb=" N LEU B 501 " --> pdb=" O TYR B 497 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 529 removed outlier: 3.788A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 558 Processing helix chain 'B' and resid 593 through 605 removed outlier: 4.526A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 605 " --> pdb=" O PHE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 649 removed outlier: 3.636A pdb=" N VAL B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 3.806A pdb=" N TRP B 657 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 672 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.534A pdb=" N LEU C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.683A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 379 through 412 removed outlier: 3.530A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 458 Processing helix chain 'C' and resid 468 through 470 No H-bonds generated for 'chain 'C' and resid 468 through 470' Processing helix chain 'C' and resid 472 through 492 removed outlier: 3.847A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR C 483 " --> pdb=" O GLN C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 518 removed outlier: 3.532A pdb=" N LEU C 501 " --> pdb=" O TYR C 497 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.787A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 558 Processing helix chain 'C' and resid 593 through 605 removed outlier: 4.523A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 649 removed outlier: 3.637A pdb=" N VAL C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 673 removed outlier: 3.809A pdb=" N TRP C 657 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 672 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 673 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 249 through 255 removed outlier: 3.913A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 281 removed outlier: 3.683A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 379 through 412 removed outlier: 3.530A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 458 Processing helix chain 'D' and resid 468 through 470 No H-bonds generated for 'chain 'D' and resid 468 through 470' Processing helix chain 'D' and resid 472 through 492 removed outlier: 3.847A pdb=" N PHE D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR D 483 " --> pdb=" O GLN D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 518 removed outlier: 3.532A pdb=" N LEU D 501 " --> pdb=" O TYR D 497 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ARG D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY D 518 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 529 removed outlier: 3.786A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 558 Processing helix chain 'D' and resid 593 through 605 removed outlier: 4.528A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 605 " --> pdb=" O PHE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 649 removed outlier: 3.632A pdb=" N VAL D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 673 removed outlier: 3.782A pdb=" N TRP D 657 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU D 672 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 673 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 Processing sheet with id= A, first strand: chain 'A' and resid 687 through 690 removed outlier: 3.635A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 687 through 690 removed outlier: 3.634A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 687 through 690 removed outlier: 3.633A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 687 through 690 removed outlier: 3.638A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 9.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6264 1.34 - 1.46: 4694 1.46 - 1.58: 9546 1.58 - 1.70: 0 1.70 - 1.81: 180 Bond restraints: 20684 Sorted by residual: bond pdb=" C12 P0T D 802 " pdb=" O02 P0T D 802 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" C12 P0T A1001 " pdb=" O02 P0T A1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" C12 P0T C1001 " pdb=" O02 P0T C1001 " ideal model delta sigma weight residual 1.352 1.404 -0.052 2.00e-02 2.50e+03 6.71e+00 bond pdb=" C12 P0T B1001 " pdb=" O02 P0T B1001 " ideal model delta sigma weight residual 1.352 1.403 -0.051 2.00e-02 2.50e+03 6.57e+00 bond pdb=" C15 P0T B1001 " pdb=" C18 P0T B1001 " ideal model delta sigma weight residual 1.503 1.554 -0.051 2.00e-02 2.50e+03 6.47e+00 ... (remaining 20679 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.73: 384 105.73 - 112.83: 11023 112.83 - 119.92: 7270 119.92 - 127.02: 9075 127.02 - 134.11: 292 Bond angle restraints: 28044 Sorted by residual: angle pdb=" CA VAL B 190 " pdb=" CB VAL B 190 " pdb=" CG1 VAL B 190 " ideal model delta sigma weight residual 110.40 117.27 -6.87 1.70e+00 3.46e-01 1.63e+01 angle pdb=" CA VAL A 190 " pdb=" CB VAL A 190 " pdb=" CG1 VAL A 190 " ideal model delta sigma weight residual 110.40 117.25 -6.85 1.70e+00 3.46e-01 1.62e+01 angle pdb=" CA VAL D 190 " pdb=" CB VAL D 190 " pdb=" CG1 VAL D 190 " ideal model delta sigma weight residual 110.40 117.21 -6.81 1.70e+00 3.46e-01 1.61e+01 angle pdb=" CA VAL C 190 " pdb=" CB VAL C 190 " pdb=" CG1 VAL C 190 " ideal model delta sigma weight residual 110.40 117.10 -6.70 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CB MET C 404 " pdb=" CG MET C 404 " pdb=" SD MET C 404 " ideal model delta sigma weight residual 112.70 101.75 10.95 3.00e+00 1.11e-01 1.33e+01 ... (remaining 28039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 11310 19.02 - 38.04: 769 38.04 - 57.05: 97 57.05 - 76.07: 16 76.07 - 95.09: 12 Dihedral angle restraints: 12204 sinusoidal: 4964 harmonic: 7240 Sorted by residual: dihedral pdb=" CA ALA C 480 " pdb=" C ALA C 480 " pdb=" N LEU C 481 " pdb=" CA LEU C 481 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA D 480 " pdb=" C ALA D 480 " pdb=" N LEU D 481 " pdb=" CA LEU D 481 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ALA B 480 " pdb=" C ALA B 480 " pdb=" N LEU B 481 " pdb=" CA LEU B 481 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2013 0.040 - 0.080: 871 0.080 - 0.120: 213 0.120 - 0.159: 39 0.159 - 0.199: 8 Chirality restraints: 3144 Sorted by residual: chirality pdb=" CB VAL B 190 " pdb=" CA VAL B 190 " pdb=" CG1 VAL B 190 " pdb=" CG2 VAL B 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CB VAL D 190 " pdb=" CA VAL D 190 " pdb=" CG1 VAL D 190 " pdb=" CG2 VAL D 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB VAL C 190 " pdb=" CA VAL C 190 " pdb=" CG1 VAL C 190 " pdb=" CG2 VAL C 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.40e-01 ... (remaining 3141 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 484 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.83e+00 pdb=" C VAL D 484 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL D 484 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU D 485 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 484 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C VAL B 484 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 484 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 485 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 484 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C VAL A 484 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL A 484 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU A 485 " 0.014 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4486 2.78 - 3.31: 18398 3.31 - 3.84: 32066 3.84 - 4.37: 35775 4.37 - 4.90: 63635 Nonbonded interactions: 154360 Sorted by model distance: nonbonded pdb=" OH TYR A 455 " pdb=" OE1 GLU A 473 " model vdw 2.247 2.440 nonbonded pdb=" NH2 ARG C 706 " pdb=" OE1 GLN D 40 " model vdw 2.323 2.520 nonbonded pdb=" NH2 ARG B 706 " pdb=" OE1 GLN C 40 " model vdw 2.324 2.520 nonbonded pdb=" NH2 ARG A 706 " pdb=" OE1 GLN B 40 " model vdw 2.325 2.520 nonbonded pdb=" OE1 GLN A 40 " pdb=" NH2 ARG D 706 " model vdw 2.329 2.520 ... (remaining 154355 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 31 through 720) selection = (chain 'B' and resid 31 through 720) selection = (chain 'C' and resid 31 through 720) selection = (chain 'D' and resid 31 through 720) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.760 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 54.290 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.120 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 20684 Z= 0.415 Angle : 0.847 10.948 28044 Z= 0.429 Chirality : 0.046 0.199 3144 Planarity : 0.006 0.051 3460 Dihedral : 13.204 95.088 7516 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.15), residues: 2428 helix: -0.34 (0.13), residues: 1420 sheet: -0.34 (0.66), residues: 68 loop : -1.86 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 333 HIS 0.007 0.002 HIS D 651 PHE 0.020 0.003 PHE C 394 TYR 0.027 0.002 TYR B 335 ARG 0.003 0.001 ARG A 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.383 Fit side-chains REVERT: A 42 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6800 (mm-30) REVERT: A 529 ILE cc_start: 0.9180 (tp) cc_final: 0.8947 (tp) REVERT: B 42 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6794 (mm-30) REVERT: B 529 ILE cc_start: 0.9184 (tp) cc_final: 0.8948 (tp) REVERT: C 42 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 529 ILE cc_start: 0.9195 (tp) cc_final: 0.8957 (tp) REVERT: D 42 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6839 (mm-30) REVERT: D 529 ILE cc_start: 0.9181 (tp) cc_final: 0.8949 (tp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2804 time to fit residues: 80.2889 Evaluate side-chains 141 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS B 370 HIS B 452 GLN C 370 HIS D 370 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20684 Z= 0.325 Angle : 0.586 6.988 28044 Z= 0.294 Chirality : 0.037 0.126 3144 Planarity : 0.004 0.035 3460 Dihedral : 6.649 79.504 2812 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.74 % Allowed : 6.76 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.17), residues: 2428 helix: 0.73 (0.14), residues: 1416 sheet: 0.01 (0.69), residues: 68 loop : -1.56 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 333 HIS 0.005 0.002 HIS B 413 PHE 0.011 0.002 PHE B 540 TYR 0.016 0.002 TYR A 98 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 2.204 Fit side-chains REVERT: A 42 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7021 (mm-30) REVERT: A 503 LEU cc_start: 0.8074 (tp) cc_final: 0.7844 (tt) REVERT: B 42 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7023 (mm-30) REVERT: B 503 LEU cc_start: 0.8083 (tp) cc_final: 0.7827 (tt) REVERT: C 277 MET cc_start: 0.8260 (mtp) cc_final: 0.8026 (mtt) REVERT: D 277 MET cc_start: 0.8258 (mtp) cc_final: 0.8016 (mtt) REVERT: D 503 LEU cc_start: 0.8070 (tp) cc_final: 0.7843 (tt) outliers start: 16 outliers final: 12 residues processed: 157 average time/residue: 0.2572 time to fit residues: 67.6132 Evaluate side-chains 158 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 184 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 487 GLN B 487 GLN C 487 GLN D 487 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20684 Z= 0.124 Angle : 0.426 6.340 28044 Z= 0.214 Chirality : 0.033 0.113 3144 Planarity : 0.003 0.033 3460 Dihedral : 5.861 73.683 2812 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2428 helix: 1.43 (0.14), residues: 1416 sheet: 0.01 (0.68), residues: 68 loop : -1.41 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 333 HIS 0.003 0.001 HIS D 651 PHE 0.007 0.001 PHE D 551 TYR 0.021 0.001 TYR A 98 ARG 0.001 0.000 ARG B 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.504 Fit side-chains REVERT: A 42 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7095 (mm-30) REVERT: A 221 LYS cc_start: 0.8705 (tttt) cc_final: 0.8103 (tptt) REVERT: A 494 THR cc_start: 0.8877 (t) cc_final: 0.8614 (t) REVERT: A 503 LEU cc_start: 0.8042 (tp) cc_final: 0.7700 (tt) REVERT: A 529 ILE cc_start: 0.9188 (tp) cc_final: 0.8802 (tp) REVERT: A 640 MET cc_start: 0.7780 (tmm) cc_final: 0.7520 (tmm) REVERT: B 98 TYR cc_start: 0.7776 (t80) cc_final: 0.7503 (t80) REVERT: B 221 LYS cc_start: 0.8711 (tttt) cc_final: 0.8118 (tptt) REVERT: B 494 THR cc_start: 0.8888 (t) cc_final: 0.8642 (t) REVERT: B 503 LEU cc_start: 0.8046 (tp) cc_final: 0.7708 (tt) REVERT: B 529 ILE cc_start: 0.9220 (tp) cc_final: 0.8842 (tp) REVERT: B 640 MET cc_start: 0.7779 (tmm) cc_final: 0.7525 (tmm) REVERT: C 98 TYR cc_start: 0.7779 (t80) cc_final: 0.7543 (t80) REVERT: C 494 THR cc_start: 0.8876 (t) cc_final: 0.8641 (t) REVERT: C 503 LEU cc_start: 0.7980 (tp) cc_final: 0.7667 (tt) REVERT: C 529 ILE cc_start: 0.9201 (tp) cc_final: 0.8809 (tp) REVERT: C 640 MET cc_start: 0.7788 (tmm) cc_final: 0.7538 (tmm) REVERT: D 98 TYR cc_start: 0.7790 (t80) cc_final: 0.7559 (t80) REVERT: D 221 LYS cc_start: 0.8737 (tttt) cc_final: 0.8135 (tptt) REVERT: D 494 THR cc_start: 0.8852 (t) cc_final: 0.8598 (t) REVERT: D 503 LEU cc_start: 0.7999 (tp) cc_final: 0.7695 (tt) REVERT: D 529 ILE cc_start: 0.9218 (tp) cc_final: 0.8832 (tp) REVERT: D 640 MET cc_start: 0.7760 (tmm) cc_final: 0.7484 (tmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2686 time to fit residues: 74.9438 Evaluate side-chains 161 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 222 optimal weight: 0.8980 chunk 235 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN C 247 ASN C 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20684 Z= 0.180 Angle : 0.448 6.288 28044 Z= 0.224 Chirality : 0.034 0.117 3144 Planarity : 0.003 0.030 3460 Dihedral : 5.784 73.813 2812 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.83 % Allowed : 9.95 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.17), residues: 2428 helix: 1.65 (0.14), residues: 1412 sheet: 0.16 (0.68), residues: 68 loop : -1.33 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 333 HIS 0.003 0.001 HIS A 313 PHE 0.008 0.001 PHE C 519 TYR 0.018 0.001 TYR A 98 ARG 0.001 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 2.496 Fit side-chains REVERT: A 221 LYS cc_start: 0.8680 (tttt) cc_final: 0.8105 (tptt) REVERT: A 494 THR cc_start: 0.8861 (t) cc_final: 0.8577 (t) REVERT: A 640 MET cc_start: 0.7788 (tmm) cc_final: 0.7486 (tmm) REVERT: B 221 LYS cc_start: 0.8725 (tttt) cc_final: 0.8142 (tptt) REVERT: B 494 THR cc_start: 0.8884 (t) cc_final: 0.8630 (t) REVERT: B 640 MET cc_start: 0.7833 (tmm) cc_final: 0.7527 (tmm) REVERT: C 98 TYR cc_start: 0.7776 (t80) cc_final: 0.7556 (t80) REVERT: C 221 LYS cc_start: 0.8674 (tttt) cc_final: 0.8071 (tptt) REVERT: C 494 THR cc_start: 0.8894 (t) cc_final: 0.8629 (t) REVERT: C 640 MET cc_start: 0.7850 (tmm) cc_final: 0.7544 (tmm) REVERT: D 98 TYR cc_start: 0.7775 (t80) cc_final: 0.7548 (t80) REVERT: D 221 LYS cc_start: 0.8707 (tttt) cc_final: 0.8131 (tptt) REVERT: D 494 THR cc_start: 0.8864 (t) cc_final: 0.8581 (t) REVERT: D 640 MET cc_start: 0.7849 (tmm) cc_final: 0.7544 (tmm) outliers start: 18 outliers final: 11 residues processed: 169 average time/residue: 0.2856 time to fit residues: 80.1632 Evaluate side-chains 165 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 483 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 10.0000 chunk 133 optimal weight: 0.1980 chunk 3 optimal weight: 8.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 201 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 368 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20684 Z= 0.163 Angle : 0.438 6.293 28044 Z= 0.217 Chirality : 0.034 0.116 3144 Planarity : 0.003 0.029 3460 Dihedral : 5.637 73.500 2812 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.20 % Allowed : 10.46 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2428 helix: 1.83 (0.14), residues: 1412 sheet: 0.20 (0.68), residues: 68 loop : -1.31 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 333 HIS 0.003 0.001 HIS D 313 PHE 0.007 0.001 PHE D 476 TYR 0.019 0.001 TYR B 98 ARG 0.001 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 159 time to evaluate : 2.350 Fit side-chains REVERT: A 221 LYS cc_start: 0.8734 (tttt) cc_final: 0.8165 (tptt) REVERT: A 494 THR cc_start: 0.8825 (t) cc_final: 0.8561 (t) REVERT: A 640 MET cc_start: 0.7828 (tmm) cc_final: 0.7503 (tmm) REVERT: B 98 TYR cc_start: 0.7787 (t80) cc_final: 0.7510 (t80) REVERT: B 221 LYS cc_start: 0.8718 (tttt) cc_final: 0.8141 (tptt) REVERT: B 494 THR cc_start: 0.8829 (t) cc_final: 0.8562 (t) REVERT: B 640 MET cc_start: 0.7829 (tmm) cc_final: 0.7504 (tmm) REVERT: C 221 LYS cc_start: 0.8663 (tttt) cc_final: 0.8095 (tptt) REVERT: C 494 THR cc_start: 0.8823 (t) cc_final: 0.8569 (t) REVERT: C 640 MET cc_start: 0.7836 (tmm) cc_final: 0.7503 (tmm) REVERT: D 98 TYR cc_start: 0.7776 (t80) cc_final: 0.7547 (t80) REVERT: D 221 LYS cc_start: 0.8743 (tttt) cc_final: 0.8130 (tptt) REVERT: D 494 THR cc_start: 0.8831 (t) cc_final: 0.8565 (t) REVERT: D 640 MET cc_start: 0.7841 (tmm) cc_final: 0.7514 (tmm) outliers start: 26 outliers final: 20 residues processed: 179 average time/residue: 0.2657 time to fit residues: 79.6891 Evaluate side-chains 178 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 236 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 123 optimal weight: 20.0000 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 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20684 Z= 0.288 Angle : 0.534 7.161 28044 Z= 0.264 Chirality : 0.037 0.124 3144 Planarity : 0.003 0.028 3460 Dihedral : 5.910 74.018 2812 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.30 % Allowed : 11.44 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.17), residues: 2428 helix: 1.68 (0.14), residues: 1408 sheet: 0.15 (0.69), residues: 68 loop : -1.35 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 333 HIS 0.004 0.001 HIS D 313 PHE 0.010 0.002 PHE C 519 TYR 0.018 0.002 TYR C 98 ARG 0.002 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 2.468 Fit side-chains REVERT: A 98 TYR cc_start: 0.7868 (t80) cc_final: 0.7609 (t80) REVERT: A 221 LYS cc_start: 0.8806 (tttt) cc_final: 0.8329 (tptt) REVERT: A 494 THR cc_start: 0.8897 (t) cc_final: 0.8621 (t) REVERT: A 640 MET cc_start: 0.7815 (tmm) cc_final: 0.7490 (tmm) REVERT: B 221 LYS cc_start: 0.8846 (tttt) cc_final: 0.8303 (tptt) REVERT: B 494 THR cc_start: 0.8918 (t) cc_final: 0.8631 (t) REVERT: B 640 MET cc_start: 0.7820 (tmm) cc_final: 0.7499 (tmm) REVERT: C 221 LYS cc_start: 0.8805 (tttt) cc_final: 0.8271 (tptt) REVERT: C 494 THR cc_start: 0.8898 (t) cc_final: 0.8616 (t) REVERT: C 640 MET cc_start: 0.7822 (tmm) cc_final: 0.7503 (tmm) REVERT: D 98 TYR cc_start: 0.7919 (t80) cc_final: 0.7712 (t80) REVERT: D 221 LYS cc_start: 0.8849 (tttt) cc_final: 0.8300 (tptt) REVERT: D 494 THR cc_start: 0.8901 (t) cc_final: 0.8613 (t) REVERT: D 640 MET cc_start: 0.7831 (tmm) cc_final: 0.7508 (tmm) outliers start: 28 outliers final: 28 residues processed: 172 average time/residue: 0.2638 time to fit residues: 75.7384 Evaluate side-chains 177 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 131 optimal weight: 0.0020 chunk 235 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20684 Z= 0.215 Angle : 0.481 7.138 28044 Z= 0.239 Chirality : 0.035 0.120 3144 Planarity : 0.003 0.027 3460 Dihedral : 5.767 73.245 2812 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.48 % Allowed : 12.73 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2428 helix: 1.80 (0.14), residues: 1408 sheet: 0.18 (0.68), residues: 68 loop : -1.30 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS D 313 PHE 0.010 0.001 PHE C 519 TYR 0.018 0.001 TYR B 98 ARG 0.001 0.000 ARG D 369 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.401 Fit side-chains REVERT: A 98 TYR cc_start: 0.7768 (t80) cc_final: 0.7422 (t80) REVERT: A 221 LYS cc_start: 0.8793 (tttt) cc_final: 0.8345 (tptt) REVERT: A 494 THR cc_start: 0.8879 (t) cc_final: 0.8611 (t) REVERT: A 640 MET cc_start: 0.7864 (tmm) cc_final: 0.7517 (tmm) REVERT: B 221 LYS cc_start: 0.8838 (tttt) cc_final: 0.8294 (tptt) REVERT: B 494 THR cc_start: 0.8876 (t) cc_final: 0.8607 (t) REVERT: B 640 MET cc_start: 0.7829 (tmm) cc_final: 0.7488 (tmm) REVERT: C 98 TYR cc_start: 0.7851 (t80) cc_final: 0.7428 (t80) REVERT: C 221 LYS cc_start: 0.8820 (tttt) cc_final: 0.8331 (tptt) REVERT: C 494 THR cc_start: 0.8870 (t) cc_final: 0.8612 (t) REVERT: C 640 MET cc_start: 0.7874 (tmm) cc_final: 0.7529 (tmm) REVERT: D 98 TYR cc_start: 0.7869 (t80) cc_final: 0.7659 (t80) REVERT: D 221 LYS cc_start: 0.8836 (tttt) cc_final: 0.8338 (tptt) REVERT: D 494 THR cc_start: 0.8882 (t) cc_final: 0.8614 (t) REVERT: D 640 MET cc_start: 0.7823 (tmm) cc_final: 0.7481 (tmm) outliers start: 32 outliers final: 32 residues processed: 181 average time/residue: 0.2747 time to fit residues: 82.5030 Evaluate side-chains 187 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 0.0980 chunk 70 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20684 Z= 0.107 Angle : 0.414 6.564 28044 Z= 0.207 Chirality : 0.033 0.111 3144 Planarity : 0.003 0.030 3460 Dihedral : 5.301 70.369 2812 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.11 % Allowed : 13.01 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.24 (0.18), residues: 2428 helix: 2.09 (0.14), residues: 1416 sheet: 0.34 (0.67), residues: 68 loop : -1.18 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 333 HIS 0.002 0.000 HIS D 370 PHE 0.007 0.001 PHE C 519 TYR 0.021 0.001 TYR B 98 ARG 0.001 0.000 ARG C 706 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 2.495 Fit side-chains REVERT: A 98 TYR cc_start: 0.7627 (t80) cc_final: 0.7186 (t80) REVERT: A 221 LYS cc_start: 0.8712 (tttt) cc_final: 0.8196 (tptt) REVERT: A 494 THR cc_start: 0.8798 (t) cc_final: 0.8558 (t) REVERT: A 640 MET cc_start: 0.7889 (tmm) cc_final: 0.7511 (tmm) REVERT: B 98 TYR cc_start: 0.7674 (t80) cc_final: 0.7139 (t80) REVERT: B 221 LYS cc_start: 0.8760 (tttt) cc_final: 0.8202 (tptt) REVERT: B 494 THR cc_start: 0.8792 (t) cc_final: 0.8552 (t) REVERT: B 640 MET cc_start: 0.7902 (tmm) cc_final: 0.7532 (tmm) REVERT: C 98 TYR cc_start: 0.7662 (t80) cc_final: 0.7035 (t80) REVERT: C 221 LYS cc_start: 0.8739 (tttt) cc_final: 0.8195 (tptt) REVERT: C 494 THR cc_start: 0.8786 (t) cc_final: 0.8547 (t) REVERT: C 640 MET cc_start: 0.7915 (tmm) cc_final: 0.7537 (tmm) REVERT: D 111 TYR cc_start: 0.8141 (m-80) cc_final: 0.7845 (m-10) REVERT: D 221 LYS cc_start: 0.8775 (tttt) cc_final: 0.8241 (tptt) REVERT: D 494 THR cc_start: 0.8800 (t) cc_final: 0.8559 (t) REVERT: D 640 MET cc_start: 0.7913 (tmm) cc_final: 0.7539 (tmm) outliers start: 24 outliers final: 23 residues processed: 182 average time/residue: 0.2696 time to fit residues: 82.1009 Evaluate side-chains 180 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 219 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20684 Z= 0.297 Angle : 0.537 7.005 28044 Z= 0.264 Chirality : 0.037 0.124 3144 Planarity : 0.003 0.029 3460 Dihedral : 5.712 73.025 2812 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 13.33 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.18), residues: 2428 helix: 1.93 (0.14), residues: 1408 sheet: 0.37 (0.68), residues: 68 loop : -1.26 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 333 HIS 0.005 0.001 HIS A 313 PHE 0.010 0.002 PHE A 519 TYR 0.018 0.002 TYR D 98 ARG 0.002 0.000 ARG D 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 156 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7833 (t80) cc_final: 0.7479 (t80) REVERT: A 221 LYS cc_start: 0.8836 (tttt) cc_final: 0.8248 (tptt) REVERT: A 494 THR cc_start: 0.8887 (t) cc_final: 0.8609 (t) REVERT: A 640 MET cc_start: 0.7868 (tmm) cc_final: 0.7636 (tmm) REVERT: B 98 TYR cc_start: 0.7843 (t80) cc_final: 0.7404 (t80) REVERT: B 221 LYS cc_start: 0.8849 (tttt) cc_final: 0.8260 (tptt) REVERT: B 494 THR cc_start: 0.8886 (t) cc_final: 0.8608 (t) REVERT: B 640 MET cc_start: 0.7870 (tmm) cc_final: 0.7636 (tmm) REVERT: C 98 TYR cc_start: 0.7865 (t80) cc_final: 0.7442 (t80) REVERT: C 221 LYS cc_start: 0.8857 (tttt) cc_final: 0.8250 (tptt) REVERT: C 494 THR cc_start: 0.8881 (t) cc_final: 0.8605 (t) REVERT: C 640 MET cc_start: 0.7867 (tmm) cc_final: 0.7634 (tmm) REVERT: D 98 TYR cc_start: 0.7888 (t80) cc_final: 0.7433 (t80) REVERT: D 221 LYS cc_start: 0.8860 (tttt) cc_final: 0.8353 (tptt) REVERT: D 494 THR cc_start: 0.8889 (t) cc_final: 0.8637 (t) REVERT: D 640 MET cc_start: 0.7875 (tmm) cc_final: 0.7643 (tmm) outliers start: 28 outliers final: 23 residues processed: 179 average time/residue: 0.2732 time to fit residues: 81.4245 Evaluate side-chains 179 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 223 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20684 Z= 0.125 Angle : 0.435 7.182 28044 Z= 0.216 Chirality : 0.033 0.112 3144 Planarity : 0.003 0.029 3460 Dihedral : 5.323 70.437 2812 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.16 % Allowed : 13.29 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.28 (0.18), residues: 2428 helix: 2.13 (0.14), residues: 1412 sheet: 0.45 (0.67), residues: 68 loop : -1.17 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 333 HIS 0.002 0.001 HIS D 370 PHE 0.007 0.001 PHE A 519 TYR 0.019 0.001 TYR D 98 ARG 0.001 0.000 ARG A 706 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 161 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7644 (t80) cc_final: 0.7243 (t80) REVERT: A 221 LYS cc_start: 0.8731 (tttt) cc_final: 0.8204 (tptt) REVERT: A 491 PHE cc_start: 0.7318 (m-80) cc_final: 0.6892 (m-10) REVERT: A 494 THR cc_start: 0.8799 (t) cc_final: 0.8564 (t) REVERT: A 640 MET cc_start: 0.7904 (tmm) cc_final: 0.7524 (tmm) REVERT: B 98 TYR cc_start: 0.7678 (t80) cc_final: 0.7197 (t80) REVERT: B 221 LYS cc_start: 0.8736 (tttt) cc_final: 0.8226 (tptt) REVERT: B 494 THR cc_start: 0.8809 (t) cc_final: 0.8575 (t) REVERT: B 640 MET cc_start: 0.7916 (tmm) cc_final: 0.7538 (tmm) REVERT: C 98 TYR cc_start: 0.7675 (t80) cc_final: 0.7215 (t80) REVERT: C 221 LYS cc_start: 0.8751 (tttt) cc_final: 0.8218 (tptt) REVERT: C 491 PHE cc_start: 0.7320 (m-80) cc_final: 0.6884 (m-10) REVERT: C 494 THR cc_start: 0.8812 (t) cc_final: 0.8590 (t) REVERT: C 640 MET cc_start: 0.7925 (tmm) cc_final: 0.7546 (tmm) REVERT: D 98 TYR cc_start: 0.7701 (t80) cc_final: 0.7192 (t80) REVERT: D 221 LYS cc_start: 0.8765 (tttt) cc_final: 0.8237 (tptt) REVERT: D 491 PHE cc_start: 0.7352 (m-80) cc_final: 0.6912 (m-10) REVERT: D 494 THR cc_start: 0.8825 (t) cc_final: 0.8563 (t) REVERT: D 640 MET cc_start: 0.7940 (tmm) cc_final: 0.7556 (tmm) outliers start: 25 outliers final: 24 residues processed: 182 average time/residue: 0.2781 time to fit residues: 84.4121 Evaluate side-chains 185 residues out of total 2208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 456 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 710 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 6.9990 chunk 206 optimal weight: 0.0670 chunk 59 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN D 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085822 restraints weight = 38772.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.088654 restraints weight = 22488.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.090576 restraints weight = 15832.980| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20684 Z= 0.182 Angle : 0.462 6.512 28044 Z= 0.230 Chirality : 0.035 0.117 3144 Planarity : 0.003 0.027 3460 Dihedral : 5.401 71.097 2812 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.25 % Allowed : 13.19 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.18), residues: 2428 helix: 2.14 (0.14), residues: 1408 sheet: 0.54 (0.68), residues: 68 loop : -1.14 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 333 HIS 0.003 0.001 HIS A 313 PHE 0.009 0.001 PHE D 519 TYR 0.018 0.001 TYR D 98 ARG 0.001 0.000 ARG A 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2938.83 seconds wall clock time: 55 minutes 22.16 seconds (3322.16 seconds total)