Starting phenix.real_space_refine on Fri Mar 15 08:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iad_35300/03_2024/8iad_35300_updated.pdb" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 7198 2.51 5 N 1842 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ASP 402": "OD1" <-> "OD2" Residue "A ASP 436": "OD1" <-> "OD2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 577": "OE1" <-> "OE2" Residue "A ASP 613": "OD1" <-> "OD2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 680": "OE1" <-> "OE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B ASP 70": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ASP 330": "OD1" <-> "OD2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B ASP 402": "OD1" <-> "OD2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B TYR 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 577": "OE1" <-> "OE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B PHE 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 684": "OD1" <-> "OD2" Residue "B TYR 708": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11126 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5476 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 674} Chain breaks: 2 Chain: "B" Number of atoms: 5476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5476 Classifications: {'peptide': 704} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 674} Chain breaks: 2 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 87 Unusual residues: {' MG': 1, 'ATP': 1, 'NO3': 2, 'PIO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.43, per 1000 atoms: 0.58 Number of scatterers: 11126 At special positions: 0 Unit cell: (80.704, 104, 106.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 12 15.00 Mg 2 11.99 O 2014 8.00 N 1842 7.00 C 7198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 397 " - pdb=" SG CYS B 405 " 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: 4.73 Conformation dependent library (CDL) restraints added in 2.1 seconds 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 4 sheets defined 55.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.41 Creating SS restraints... Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 76 through 123 removed outlier: 4.119A pdb=" N TRP A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 153 removed outlier: 4.076A pdb=" N VAL A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 removed outlier: 4.256A pdb=" N ALA A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.602A pdb=" N LEU A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.236A pdb=" N TYR A 234 " --> pdb=" O TRP A 231 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 257 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 282 through 300 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 332 through 364 removed outlier: 3.718A pdb=" N LYS A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 Proline residue: A 389 - end of helix Processing helix chain 'A' and resid 435 through 442 removed outlier: 3.639A pdb=" N VAL A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 470 removed outlier: 3.911A pdb=" N ILE A 465 " --> pdb=" O GLY A 461 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 468 " --> pdb=" O CYS A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 498 removed outlier: 3.850A pdb=" N TYR A 490 " --> pdb=" O MET A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 522 Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 539 through 558 Proline residue: A 543 - end of helix removed outlier: 4.174A pdb=" N VAL A 548 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU A 550 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 554 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP A 557 " --> pdb=" O THR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.930A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 643 through 651 removed outlier: 3.620A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 670 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 716 through 726 Processing helix chain 'A' and resid 751 through 754 No H-bonds generated for 'chain 'A' and resid 751 through 754' Processing helix chain 'A' and resid 756 through 762 removed outlier: 3.655A pdb=" N GLN A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 762 " --> pdb=" O ASN A 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 76 through 123 removed outlier: 4.119A pdb=" N TRP B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 153 removed outlier: 4.076A pdb=" N VAL B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 removed outlier: 4.144A pdb=" N ALA B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 202 through 218 removed outlier: 3.602A pdb=" N LEU B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL B 207 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.235A pdb=" N TYR B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 257 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 332 through 364 removed outlier: 3.719A pdb=" N LYS B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 364 " --> pdb=" O ASN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 390 Proline residue: B 389 - end of helix Processing helix chain 'B' and resid 435 through 442 removed outlier: 3.639A pdb=" N VAL B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 470 removed outlier: 3.912A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 468 " --> pdb=" O CYS B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 498 removed outlier: 3.849A pdb=" N TYR B 490 " --> pdb=" O MET B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 522 Processing helix chain 'B' and resid 526 through 536 Processing helix chain 'B' and resid 539 through 558 Proline residue: B 543 - end of helix removed outlier: 4.175A pdb=" N VAL B 548 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 550 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 554 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP B 557 " --> pdb=" O THR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 570 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.930A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 643 through 651 removed outlier: 3.621A pdb=" N LYS B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 716 through 726 Processing helix chain 'B' and resid 751 through 754 No H-bonds generated for 'chain 'B' and resid 751 through 754' Processing helix chain 'B' and resid 756 through 762 removed outlier: 3.655A pdb=" N GLN B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 762 " --> pdb=" O ASN B 758 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 622 through 625 removed outlier: 3.868A pdb=" N GLY A 639 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 709 through 711 removed outlier: 6.517A pdb=" N LEU A 732 " --> pdb=" O VAL A 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 622 through 625 removed outlier: 3.867A pdb=" N GLY B 639 " --> pdb=" O VAL B 625 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 709 through 711 removed outlier: 6.517A pdb=" N LEU B 732 " --> pdb=" O VAL B 710 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 494 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2008 1.32 - 1.45: 2835 1.45 - 1.57: 6423 1.57 - 1.69: 18 1.69 - 1.81: 90 Bond restraints: 11374 Sorted by residual: bond pdb=" C4 ATP B 800 " pdb=" C5 ATP B 800 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP A 800 " pdb=" C5 ATP A 800 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C5 ATP B 800 " pdb=" C6 ATP B 800 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.32e+01 bond pdb=" C5 ATP A 800 " pdb=" C6 ATP A 800 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.32e+01 bond pdb=" C5 ATP B 800 " pdb=" N7 ATP B 800 " ideal model delta sigma weight residual 1.387 1.334 0.053 1.00e-02 1.00e+04 2.80e+01 ... (remaining 11369 not shown) Histogram of bond angle deviations from ideal: 96.74 - 104.71: 205 104.71 - 112.68: 6107 112.68 - 120.66: 5600 120.66 - 128.63: 3465 128.63 - 136.60: 107 Bond angle restraints: 15484 Sorted by residual: angle pdb=" PB ATP B 800 " pdb=" O3B ATP B 800 " pdb=" PG ATP B 800 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB ATP A 800 " pdb=" O3B ATP A 800 " pdb=" PG ATP A 800 " ideal model delta sigma weight residual 139.87 120.40 19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP B 800 " pdb=" O3A ATP B 800 " pdb=" PB ATP B 800 " ideal model delta sigma weight residual 136.83 120.48 16.35 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PA ATP A 800 " pdb=" O3A ATP A 800 " pdb=" PB ATP A 800 " ideal model delta sigma weight residual 136.83 120.50 16.33 1.00e+00 1.00e+00 2.67e+02 angle pdb=" C5 ATP B 800 " pdb=" C4 ATP B 800 " pdb=" N3 ATP B 800 " ideal model delta sigma weight residual 126.80 117.52 9.28 1.00e+00 1.00e+00 8.61e+01 ... (remaining 15479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 5847 16.44 - 32.87: 690 32.87 - 49.31: 111 49.31 - 65.75: 33 65.75 - 82.19: 15 Dihedral angle restraints: 6696 sinusoidal: 2676 harmonic: 4020 Sorted by residual: dihedral pdb=" CB CYS A 397 " pdb=" SG CYS A 397 " pdb=" SG CYS A 405 " pdb=" CB CYS A 405 " ideal model delta sinusoidal sigma weight residual 93.00 170.30 -77.30 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CB CYS B 397 " pdb=" SG CYS B 397 " pdb=" SG CYS B 405 " pdb=" CB CYS B 405 " ideal model delta sinusoidal sigma weight residual 93.00 170.29 -77.29 1 1.00e+01 1.00e-02 7.49e+01 dihedral pdb=" CA THR B 554 " pdb=" C THR B 554 " pdb=" N VAL B 555 " pdb=" CA VAL B 555 " ideal model delta harmonic sigma weight residual 180.00 155.78 24.22 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 6693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1462 0.070 - 0.141: 299 0.141 - 0.211: 46 0.211 - 0.282: 1 0.282 - 0.352: 2 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CB VAL B 319 " pdb=" CA VAL B 319 " pdb=" CG1 VAL B 319 " pdb=" CG2 VAL B 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL A 319 " pdb=" CA VAL A 319 " pdb=" CG1 VAL A 319 " pdb=" CG2 VAL A 319 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C2C PIO A 804 " pdb=" C1C PIO A 804 " pdb=" C3C PIO A 804 " pdb=" O2C PIO A 804 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1807 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 402 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" CG ASP B 402 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASP B 402 " 0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP B 402 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 402 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" CG ASP A 402 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASP A 402 " -0.022 2.00e-02 2.50e+03 pdb=" OD2 ASP A 402 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 402 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C ASP B 402 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP B 402 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B 403 " -0.018 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 82 2.55 - 3.14: 8425 3.14 - 3.72: 17103 3.72 - 4.31: 24433 4.31 - 4.90: 41258 Nonbonded interactions: 91301 Sorted by model distance: nonbonded pdb=" O1B ATP A 800 " pdb="MG MG A 801 " model vdw 1.961 2.170 nonbonded pdb=" O1B ATP B 800 " pdb="MG MG B 801 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 55 " pdb="MG MG B 801 " model vdw 2.123 2.170 nonbonded pdb=" OE1 GLU A 55 " pdb="MG MG A 801 " model vdw 2.171 2.170 nonbonded pdb=" O VAL B 614 " pdb=" OG1 THR B 618 " model vdw 2.274 2.440 ... (remaining 91296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.900 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 33.370 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.009 0.093 11374 Z= 0.614 Angle : 1.059 19.505 15484 Z= 0.626 Chirality : 0.058 0.352 1810 Planarity : 0.007 0.058 1918 Dihedral : 14.819 82.186 4102 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.38 % Favored : 93.48 % Rotamer: Outliers : 0.25 % Allowed : 10.32 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -4.34 (0.16), residues: 1396 helix: -2.86 (0.12), residues: 832 sheet: None (None), residues: 0 loop : -2.71 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 274 HIS 0.003 0.001 HIS A 353 PHE 0.027 0.003 PHE B 417 TYR 0.013 0.002 TYR A 463 ARG 0.005 0.001 ARG A 325 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.223 Fit side-chains REVERT: A 184 MET cc_start: 0.7628 (mmt) cc_final: 0.7315 (mmm) REVERT: A 200 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 493 MET cc_start: 0.7527 (mtp) cc_final: 0.7319 (mtp) REVERT: A 658 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7346 (mm-30) REVERT: B 184 MET cc_start: 0.7613 (mmt) cc_final: 0.7301 (mmm) REVERT: B 200 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8315 (pp) REVERT: B 658 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7423 (mm-30) outliers start: 3 outliers final: 0 residues processed: 164 average time/residue: 0.2972 time to fit residues: 65.1477 Evaluate side-chains 116 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 327 HIS A 503 ASN A 569 HIS A 586 ASN A 593 ASN A 730 HIS A 758 ASN A 761 GLN B 125 GLN B 327 HIS B 503 ASN B 569 HIS B 586 ASN B 593 ASN B 730 HIS B 758 ASN B 761 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11374 Z= 0.183 Angle : 0.535 6.796 15484 Z= 0.275 Chirality : 0.040 0.182 1810 Planarity : 0.004 0.040 1918 Dihedral : 8.936 88.194 1632 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.76 % Allowed : 15.27 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.35 (0.20), residues: 1396 helix: -1.11 (0.17), residues: 836 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 457 HIS 0.010 0.001 HIS B 569 PHE 0.015 0.001 PHE A 723 TYR 0.013 0.001 TYR A 121 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.237 Fit side-chains REVERT: A 121 TYR cc_start: 0.8226 (t80) cc_final: 0.8006 (t80) REVERT: A 164 GLU cc_start: 0.6131 (mt-10) cc_final: 0.5735 (mt-10) REVERT: A 203 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: A 550 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6563 (mm) REVERT: A 658 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 121 TYR cc_start: 0.8255 (t80) cc_final: 0.8029 (t80) REVERT: B 164 GLU cc_start: 0.6323 (mt-10) cc_final: 0.5962 (mt-10) REVERT: B 203 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: B 493 MET cc_start: 0.7044 (mtp) cc_final: 0.6720 (mtp) REVERT: B 550 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6591 (mm) REVERT: B 658 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7325 (mm-30) outliers start: 21 outliers final: 9 residues processed: 142 average time/residue: 0.2669 time to fit residues: 52.6429 Evaluate side-chains 131 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS A 408 ASN A 503 ASN A 569 HIS A 620 HIS A 752 GLN B 408 ASN B 569 HIS B 620 HIS B 752 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11374 Z= 0.339 Angle : 0.597 9.529 15484 Z= 0.300 Chirality : 0.043 0.177 1810 Planarity : 0.004 0.037 1918 Dihedral : 8.657 80.717 1628 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.52 % Allowed : 17.53 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.83 (0.21), residues: 1396 helix: -0.70 (0.17), residues: 828 sheet: None (None), residues: 0 loop : -1.89 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 274 HIS 0.012 0.001 HIS B 569 PHE 0.016 0.002 PHE B 417 TYR 0.010 0.001 TYR B 121 ARG 0.004 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.235 Fit side-chains REVERT: A 164 GLU cc_start: 0.6254 (mt-10) cc_final: 0.5948 (mt-10) REVERT: A 284 PHE cc_start: 0.6254 (t80) cc_final: 0.5830 (t80) REVERT: A 453 MET cc_start: 0.7634 (mmm) cc_final: 0.7360 (tpp) REVERT: A 550 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6692 (mm) REVERT: A 658 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 164 GLU cc_start: 0.6298 (mt-10) cc_final: 0.6038 (mt-10) REVERT: B 453 MET cc_start: 0.7679 (mmm) cc_final: 0.7098 (tpt) REVERT: B 542 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7700 (tp) REVERT: B 550 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6814 (mm) REVERT: B 658 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7481 (mm-30) outliers start: 30 outliers final: 21 residues processed: 138 average time/residue: 0.2663 time to fit residues: 51.4824 Evaluate side-chains 134 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 752 GLN B 569 HIS B 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11374 Z= 0.204 Angle : 0.511 6.604 15484 Z= 0.259 Chirality : 0.040 0.151 1810 Planarity : 0.003 0.039 1918 Dihedral : 8.202 74.547 1628 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.10 % Allowed : 17.11 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.06 (0.22), residues: 1396 helix: -0.16 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -1.40 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 457 HIS 0.010 0.001 HIS B 569 PHE 0.013 0.001 PHE A 723 TYR 0.009 0.001 TYR B 463 ARG 0.004 0.000 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 127 time to evaluate : 1.283 Fit side-chains REVERT: A 164 GLU cc_start: 0.6310 (mt-10) cc_final: 0.6047 (mt-10) REVERT: A 203 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: A 453 MET cc_start: 0.7611 (mmm) cc_final: 0.7350 (tpp) REVERT: A 550 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6672 (mm) REVERT: A 658 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7300 (mm-30) REVERT: B 203 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7334 (mm-30) REVERT: B 453 MET cc_start: 0.7649 (mmm) cc_final: 0.7101 (tpt) REVERT: B 550 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6767 (mm) REVERT: B 658 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7375 (mm-30) outliers start: 37 outliers final: 24 residues processed: 148 average time/residue: 0.2354 time to fit residues: 50.2404 Evaluate side-chains 143 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 115 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 93 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 0.0270 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 752 GLN B 569 HIS B 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11374 Z= 0.291 Angle : 0.549 7.812 15484 Z= 0.276 Chirality : 0.042 0.167 1810 Planarity : 0.004 0.040 1918 Dihedral : 8.121 71.012 1628 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.02 % Allowed : 18.96 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.22), residues: 1396 helix: -0.13 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 457 HIS 0.008 0.001 HIS A 569 PHE 0.014 0.001 PHE B 723 TYR 0.009 0.001 TYR B 463 ARG 0.004 0.000 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 1.229 Fit side-chains REVERT: A 164 GLU cc_start: 0.6314 (mt-10) cc_final: 0.5954 (mt-10) REVERT: A 177 MET cc_start: 0.8704 (tpp) cc_final: 0.8502 (tpt) REVERT: A 453 MET cc_start: 0.7629 (mmm) cc_final: 0.7080 (tpt) REVERT: A 550 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6706 (mm) REVERT: A 658 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 164 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6369 (mt-10) REVERT: B 453 MET cc_start: 0.7685 (mmm) cc_final: 0.7118 (tpt) REVERT: B 550 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6743 (mm) REVERT: B 658 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7458 (mm-30) outliers start: 36 outliers final: 29 residues processed: 139 average time/residue: 0.2345 time to fit residues: 46.6029 Evaluate side-chains 147 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 635 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 130 optimal weight: 0.0170 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 752 GLN B 569 HIS B 752 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11374 Z= 0.165 Angle : 0.482 6.557 15484 Z= 0.246 Chirality : 0.039 0.141 1810 Planarity : 0.003 0.040 1918 Dihedral : 7.688 65.431 1628 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.10 % Allowed : 19.38 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.47 (0.22), residues: 1396 helix: 0.25 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 457 HIS 0.008 0.001 HIS A 569 PHE 0.013 0.001 PHE A 723 TYR 0.009 0.001 TYR B 463 ARG 0.004 0.000 ARG B 653 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.125 Fit side-chains REVERT: A 164 GLU cc_start: 0.6257 (mt-10) cc_final: 0.6056 (mt-10) REVERT: A 203 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: A 453 MET cc_start: 0.7584 (mmm) cc_final: 0.7353 (tpp) REVERT: A 550 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6689 (mm) REVERT: B 203 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7321 (mm-30) REVERT: B 453 MET cc_start: 0.7651 (mmm) cc_final: 0.7115 (tpt) outliers start: 37 outliers final: 32 residues processed: 147 average time/residue: 0.2393 time to fit residues: 49.7067 Evaluate side-chains 151 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS A 752 GLN B 569 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11374 Z= 0.234 Angle : 0.520 8.702 15484 Z= 0.260 Chirality : 0.040 0.155 1810 Planarity : 0.003 0.039 1918 Dihedral : 7.650 64.068 1628 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.86 % Allowed : 19.13 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.44 (0.22), residues: 1396 helix: 0.26 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 457 HIS 0.008 0.001 HIS A 569 PHE 0.014 0.001 PHE A 723 TYR 0.021 0.001 TYR B 121 ARG 0.006 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 120 time to evaluate : 1.247 Fit side-chains REVERT: A 105 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7000 (m-40) REVERT: A 164 GLU cc_start: 0.6226 (mt-10) cc_final: 0.5809 (mt-10) REVERT: A 177 MET cc_start: 0.8643 (tpp) cc_final: 0.8245 (tpt) REVERT: A 203 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: A 403 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: A 453 MET cc_start: 0.7611 (mmm) cc_final: 0.7078 (tpt) REVERT: A 550 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6750 (mm) REVERT: B 105 ASN cc_start: 0.7393 (OUTLIER) cc_final: 0.7010 (m-40) REVERT: B 203 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7336 (mm-30) REVERT: B 403 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: B 453 MET cc_start: 0.7639 (mmm) cc_final: 0.7089 (tpt) REVERT: B 550 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6771 (mm) outliers start: 46 outliers final: 35 residues processed: 152 average time/residue: 0.2399 time to fit residues: 52.2070 Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 112 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.0370 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 85 optimal weight: 0.3980 chunk 91 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 0.3980 chunk 129 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11374 Z= 0.138 Angle : 0.478 7.651 15484 Z= 0.242 Chirality : 0.038 0.124 1810 Planarity : 0.003 0.040 1918 Dihedral : 7.196 59.207 1628 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.61 % Allowed : 19.63 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.02 (0.23), residues: 1396 helix: 0.63 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -0.79 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 457 HIS 0.010 0.001 HIS B 569 PHE 0.013 0.001 PHE A 723 TYR 0.007 0.001 TYR B 463 ARG 0.008 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 1.318 Fit side-chains REVERT: A 105 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.7006 (m110) REVERT: A 164 GLU cc_start: 0.6255 (mt-10) cc_final: 0.5907 (mt-10) REVERT: A 177 MET cc_start: 0.8671 (tpp) cc_final: 0.8358 (tpt) REVERT: A 403 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: A 453 MET cc_start: 0.7601 (mmm) cc_final: 0.7387 (tpp) REVERT: A 550 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6795 (mm) REVERT: A 605 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8112 (t) REVERT: B 105 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7019 (m110) REVERT: B 403 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: B 550 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6772 (mm) REVERT: B 605 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8102 (t) outliers start: 43 outliers final: 29 residues processed: 155 average time/residue: 0.2283 time to fit residues: 51.7738 Evaluate side-chains 153 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 116 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11374 Z= 0.177 Angle : 0.492 7.364 15484 Z= 0.246 Chirality : 0.039 0.141 1810 Planarity : 0.003 0.039 1918 Dihedral : 7.049 58.209 1628 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.19 % Allowed : 19.63 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.15 (0.23), residues: 1396 helix: 0.75 (0.19), residues: 806 sheet: None (None), residues: 0 loop : -0.74 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 457 HIS 0.009 0.001 HIS A 569 PHE 0.013 0.001 PHE A 723 TYR 0.019 0.001 TYR A 121 ARG 0.005 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 1.272 Fit side-chains REVERT: A 105 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: A 121 TYR cc_start: 0.7895 (t80) cc_final: 0.7648 (t80) REVERT: A 164 GLU cc_start: 0.6124 (mt-10) cc_final: 0.5759 (mt-10) REVERT: A 403 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: A 453 MET cc_start: 0.7633 (mmm) cc_final: 0.7108 (tpt) REVERT: A 493 MET cc_start: 0.7040 (mtp) cc_final: 0.6776 (mtp) REVERT: A 550 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6795 (mm) REVERT: B 105 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7066 (m-40) REVERT: B 121 TYR cc_start: 0.7887 (t80) cc_final: 0.7638 (t80) REVERT: B 403 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: B 453 MET cc_start: 0.7674 (mmm) cc_final: 0.7149 (tpt) REVERT: B 493 MET cc_start: 0.7015 (mtp) cc_final: 0.6748 (mtp) REVERT: B 550 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6803 (mm) outliers start: 38 outliers final: 31 residues processed: 145 average time/residue: 0.2320 time to fit residues: 48.9713 Evaluate side-chains 152 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 115 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11374 Z= 0.189 Angle : 0.495 7.303 15484 Z= 0.248 Chirality : 0.039 0.135 1810 Planarity : 0.003 0.039 1918 Dihedral : 6.915 57.446 1628 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.27 % Allowed : 19.71 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.03 (0.23), residues: 1396 helix: 0.67 (0.19), residues: 834 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 457 HIS 0.010 0.001 HIS B 569 PHE 0.013 0.001 PHE B 723 TYR 0.017 0.001 TYR A 121 ARG 0.005 0.000 ARG A 258 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2792 Ramachandran restraints generated. 1396 Oldfield, 0 Emsley, 1396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 116 time to evaluate : 1.249 Fit side-chains REVERT: A 105 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7057 (m-40) REVERT: A 121 TYR cc_start: 0.7904 (t80) cc_final: 0.7660 (t80) REVERT: A 164 GLU cc_start: 0.6445 (mt-10) cc_final: 0.6064 (mt-10) REVERT: A 177 MET cc_start: 0.8740 (tpt) cc_final: 0.8219 (tpt) REVERT: A 403 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: A 453 MET cc_start: 0.7655 (mmm) cc_final: 0.7432 (tpp) REVERT: A 493 MET cc_start: 0.7061 (mtp) cc_final: 0.6740 (mtp) REVERT: A 550 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6806 (mm) REVERT: B 105 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7061 (m-40) REVERT: B 121 TYR cc_start: 0.7897 (t80) cc_final: 0.7653 (t80) REVERT: B 403 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: B 453 MET cc_start: 0.7674 (mmm) cc_final: 0.7147 (tpt) REVERT: B 493 MET cc_start: 0.7057 (mtp) cc_final: 0.6772 (mtp) REVERT: B 550 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6812 (mm) outliers start: 39 outliers final: 31 residues processed: 142 average time/residue: 0.2349 time to fit residues: 47.6921 Evaluate side-chains 150 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 403 GLU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 529 CYS Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 403 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 418 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 550 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 0.0000 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 0.0070 chunk 6 optimal weight: 4.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 HIS B 569 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106552 restraints weight = 12472.899| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.55 r_work: 0.3080 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11374 Z= 0.128 Angle : 0.469 8.042 15484 Z= 0.236 Chirality : 0.038 0.127 1810 Planarity : 0.003 0.040 1918 Dihedral : 6.511 57.915 1628 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.19 % Allowed : 19.97 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.45 (0.23), residues: 1396 helix: 0.97 (0.19), residues: 824 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 457 HIS 0.010 0.001 HIS B 569 PHE 0.013 0.001 PHE B 723 TYR 0.018 0.001 TYR A 121 ARG 0.005 0.000 ARG A 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2207.83 seconds wall clock time: 40 minutes 49.41 seconds (2449.41 seconds total)