Starting phenix.real_space_refine on Mon Apr 8 19:07:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2024/7dge_30672_neut_updated.pdb" } resolution = 3.65 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9110 2.51 5 N 2403 2.21 5 O 2628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14249 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6183 Classifications: {'peptide': 784} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 751} Chain breaks: 1 Chain: "B" Number of atoms: 6183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6183 Classifications: {'peptide': 784} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 751} Chain breaks: 1 Chain: "C" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 931 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 939 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 119} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'QUS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.78, per 1000 atoms: 0.55 Number of scatterers: 14249 At special positions: 0 Unit cell: (169.52, 144.56, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2628 8.00 N 2403 7.00 C 9110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.01 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 543 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 394 " distance=2.00 Simple disulfide: pdb=" SG CYS A 432 " - pdb=" SG CYS A 439 " distance=1.99 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 544 " distance=2.02 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 547 " distance=2.02 Simple disulfide: pdb=" SG CYS A 550 " - pdb=" SG CYS A 562 " distance=2.04 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 578 " distance=2.00 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.01 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 543 " distance=2.01 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 439 " distance=2.04 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 544 " distance=2.02 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 547 " distance=2.02 Simple disulfide: pdb=" SG CYS B 550 " - pdb=" SG CYS B 562 " distance=2.02 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 578 " distance=2.04 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 98 " 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: 6.10 Conformation dependent library (CDL) restraints added in 2.9 seconds 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3368 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 14 sheets defined 38.0% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.574A pdb=" N GLN A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 removed outlier: 4.861A pdb=" N LEU A 177 " --> pdb=" O ASN A 173 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.606A pdb=" N GLN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.553A pdb=" N LEU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 366 through 375 removed outlier: 4.277A pdb=" N GLN A 369 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 370 " --> pdb=" O TRP A 367 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 373 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 431 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 591 through 614 removed outlier: 5.247A pdb=" N ALA A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 648 Proline residue: A 645 - end of helix Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 703 through 727 removed outlier: 4.759A pdb=" N GLN A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 776 removed outlier: 3.560A pdb=" N VAL A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA A 755 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Proline residue: A 756 - end of helix removed outlier: 3.594A pdb=" N ASN A 760 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 762 " --> pdb=" O TYR A 759 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 763 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 768 " --> pdb=" O MET A 765 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 772 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 773 " --> pdb=" O TYR A 770 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 774 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG A 775 " --> pdb=" O PHE A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 805 Proline residue: A 803 - end of helix Processing helix chain 'A' and resid 812 through 830 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.109A pdb=" N ASP B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 removed outlier: 4.350A pdb=" N GLN B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU B 174 " --> pdb=" O GLN B 170 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 193 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 235 through 251 Processing helix chain 'B' and resid 267 through 280 Processing helix chain 'B' and resid 293 through 306 Processing helix chain 'B' and resid 318 through 320 No H-bonds generated for 'chain 'B' and resid 318 through 320' Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 369 through 375 Processing helix chain 'B' and resid 410 through 431 Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 591 through 617 removed outlier: 4.250A pdb=" N ALA B 596 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B 617 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 643 Processing helix chain 'B' and resid 657 through 688 removed outlier: 3.506A pdb=" N LEU B 663 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY B 665 " --> pdb=" O ARG B 661 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 667 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER B 668 " --> pdb=" O VAL B 664 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU B 675 " --> pdb=" O CYS B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 726 removed outlier: 4.361A pdb=" N ALA B 710 " --> pdb=" O GLN B 706 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 773 removed outlier: 5.162A pdb=" N ALA B 755 " --> pdb=" O GLY B 752 " (cutoff:3.500A) Proline residue: B 756 - end of helix removed outlier: 3.636A pdb=" N LEU B 762 " --> pdb=" O TYR B 759 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER B 766 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 768 " --> pdb=" O MET B 765 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 772 " --> pdb=" O TYR B 769 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS B 773 " --> pdb=" O TYR B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 806 removed outlier: 4.095A pdb=" N ILE B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) Proline residue: B 803 - end of helix Processing helix chain 'B' and resid 812 through 830 Processing helix chain 'B' and resid 832 through 837 removed outlier: 4.087A pdb=" N TYR B 836 " --> pdb=" O THR B 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing sheet with id= A, first strand: chain 'A' and resid 39 through 41 removed outlier: 7.125A pdb=" N GLY A 48 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 159 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU A 50 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 182 through 184 Processing sheet with id= C, first strand: chain 'A' and resid 229 through 232 Processing sheet with id= D, first strand: chain 'A' and resid 338 through 342 removed outlier: 4.115A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASN A 483 " --> pdb=" O HIS A 496 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN A 485 " --> pdb=" O TYR A 494 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N TYR A 494 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 569 through 571 Processing sheet with id= F, first strand: chain 'A' and resid 554 through 558 removed outlier: 3.796A pdb=" N GLN A 557 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.472A pdb=" N VAL B 45 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLU B 104 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 47 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG B 106 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA B 49 " --> pdb=" O ARG B 106 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY B 48 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL B 159 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 50 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLY B 161 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLY B 161 " --> pdb=" O PRO B 181 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 183 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 258 through 261 removed outlier: 7.225A pdb=" N ALA B 229 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 261 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS B 231 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER B 313 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS B 289 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE B 315 " --> pdb=" O CYS B 289 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 337 through 342 removed outlier: 4.356A pdb=" N GLY B 337 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 484 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 481 " --> pdb=" O GLY B 498 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 498 " --> pdb=" O ILE B 481 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASN B 483 " --> pdb=" O HIS B 496 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N HIS B 496 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 533 through 535 Processing sheet with id= K, first strand: chain 'C' and resid 5 through 7 removed outlier: 3.652A pdb=" N GLN C 5 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.769A pdb=" N TRP C 38 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA C 52 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET C 36 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 114 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 6 through 9 Processing sheet with id= N, first strand: chain 'D' and resid 95 through 101 removed outlier: 6.318A pdb=" N ARG D 40 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER D 49 " --> pdb=" O ARG D 40 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1497 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: 4.54 Time building geometry restraints manager: 6.63 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: 2332 1.32 - 1.45: 4135 1.45 - 1.57: 7948 1.57 - 1.70: 0 1.70 - 1.83: 154 Bond restraints: 14569 Sorted by residual: bond pdb=" CD GLU A 370 " pdb=" OE1 GLU A 370 " ideal model delta sigma weight residual 1.249 1.357 -0.108 1.90e-02 2.77e+03 3.24e+01 bond pdb=" CG ASP A 208 " pdb=" OD2 ASP A 208 " ideal model delta sigma weight residual 1.249 1.357 -0.108 1.90e-02 2.77e+03 3.24e+01 bond pdb=" CD GLU A 386 " pdb=" OE1 GLU A 386 " ideal model delta sigma weight residual 1.249 1.355 -0.106 1.90e-02 2.77e+03 3.09e+01 bond pdb=" CD GLU B 238 " pdb=" OE2 GLU B 238 " ideal model delta sigma weight residual 1.249 1.353 -0.104 1.90e-02 2.77e+03 3.01e+01 bond pdb=" CA PRO A 57 " pdb=" C PRO A 57 " ideal model delta sigma weight residual 1.514 1.544 -0.030 5.50e-03 3.31e+04 2.93e+01 ... (remaining 14564 not shown) Histogram of bond angle deviations from ideal: 96.63 - 104.32: 212 104.32 - 112.01: 5248 112.01 - 119.70: 7900 119.70 - 127.39: 6188 127.39 - 135.08: 205 Bond angle restraints: 19753 Sorted by residual: angle pdb=" C PHE B 368 " pdb=" N GLN B 369 " pdb=" CA GLN B 369 " ideal model delta sigma weight residual 120.54 130.51 -9.97 1.35e+00 5.49e-01 5.46e+01 angle pdb=" C ALA B 636 " pdb=" N GLY B 637 " pdb=" CA GLY B 637 " ideal model delta sigma weight residual 119.99 127.82 -7.83 1.13e+00 7.83e-01 4.80e+01 angle pdb=" CA CYS B 657 " pdb=" CB CYS B 657 " pdb=" SG CYS B 657 " ideal model delta sigma weight residual 114.40 100.28 14.12 2.30e+00 1.89e-01 3.77e+01 angle pdb=" C ASP D 64 " pdb=" N SER D 65 " pdb=" CA SER D 65 " ideal model delta sigma weight residual 120.38 129.03 -8.65 1.46e+00 4.69e-01 3.51e+01 angle pdb=" C LEU A 757 " pdb=" N GLY A 758 " pdb=" CA GLY A 758 " ideal model delta sigma weight residual 120.00 126.46 -6.46 1.10e+00 8.26e-01 3.45e+01 ... (remaining 19748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 7687 17.88 - 35.76: 868 35.76 - 53.64: 139 53.64 - 71.53: 20 71.53 - 89.41: 7 Dihedral angle restraints: 8721 sinusoidal: 3461 harmonic: 5260 Sorted by residual: dihedral pdb=" CB CYS A 657 " pdb=" SG CYS A 657 " pdb=" SG CYS A 746 " pdb=" CB CYS A 746 " ideal model delta sinusoidal sigma weight residual -86.00 -164.55 78.55 1 1.00e+01 1.00e-02 7.69e+01 dihedral pdb=" CB CYS B 565 " pdb=" SG CYS B 565 " pdb=" SG CYS B 578 " pdb=" CB CYS B 578 " ideal model delta sinusoidal sigma weight residual 93.00 157.88 -64.88 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CA HIS B 496 " pdb=" C HIS B 496 " pdb=" N VAL B 497 " pdb=" CA VAL B 497 " ideal model delta harmonic sigma weight residual 180.00 143.24 36.76 0 5.00e+00 4.00e-02 5.41e+01 ... (remaining 8718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1613 0.131 - 0.262: 522 0.262 - 0.392: 64 0.392 - 0.523: 9 0.523 - 0.654: 1 Chirality restraints: 2209 Sorted by residual: chirality pdb=" CB THR B 679 " pdb=" CA THR B 679 " pdb=" OG1 THR B 679 " pdb=" CG2 THR B 679 " both_signs ideal model delta sigma weight residual False 2.55 1.90 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB THR A 793 " pdb=" CA THR A 793 " pdb=" OG1 THR A 793 " pdb=" CG2 THR A 793 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CB VAL B 610 " pdb=" CA VAL B 610 " pdb=" CG1 VAL B 610 " pdb=" CG2 VAL B 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 2206 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 330 " -0.179 2.00e-02 2.50e+03 1.04e-01 2.18e+02 pdb=" CG TYR B 330 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 330 " 0.104 2.00e-02 2.50e+03 pdb=" CD2 TYR B 330 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR B 330 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR B 330 " 0.088 2.00e-02 2.50e+03 pdb=" CZ TYR B 330 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 330 " -0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 672 " -0.181 2.00e-02 2.50e+03 9.52e-02 1.81e+02 pdb=" CG TYR A 672 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 672 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR A 672 " 0.108 2.00e-02 2.50e+03 pdb=" CE1 TYR A 672 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR A 672 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 672 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 672 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 672 " -0.173 2.00e-02 2.50e+03 9.10e-02 1.66e+02 pdb=" CG TYR B 672 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B 672 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TYR B 672 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR B 672 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 672 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR B 672 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 672 " -0.127 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 6601 2.98 - 3.46: 16043 3.46 - 3.94: 24176 3.94 - 4.42: 27984 4.42 - 4.90: 43523 Nonbonded interactions: 118327 Sorted by model distance: nonbonded pdb=" OE2 GLU B 386 " pdb=" O SER D 59 " model vdw 2.503 3.040 nonbonded pdb=" O PHE A 801 " pdb=" N TYR A 805 " model vdw 2.511 2.520 nonbonded pdb=" OG1 THR D 93 " pdb=" O VAL D 121 " model vdw 2.512 2.440 nonbonded pdb=" N HIS B 501 " pdb=" O HIS B 501 " model vdw 2.531 2.496 nonbonded pdb=" N THR B 653 " pdb=" O THR B 653 " model vdw 2.542 2.496 ... (remaining 118322 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 35 through 839) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 3 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 116 or (resid 117 and (name N or na \ me CA or name C or name O or name CB )) or resid 118 through 125)) } 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: 1.370 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: 5.720 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 41.750 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.013 0.108 14569 Z= 0.837 Angle : 1.986 14.124 19753 Z= 1.326 Chirality : 0.122 0.654 2209 Planarity : 0.015 0.160 2501 Dihedral : 14.945 89.407 5296 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.15 % Favored : 87.01 % Rotamer: Outliers : 2.25 % Allowed : 10.28 % Favored : 87.47 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.12 % 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: -4.67 (0.16), residues: 1802 helix: -2.83 (0.14), residues: 689 sheet: -3.15 (0.30), residues: 218 loop : -3.31 (0.17), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.131 0.024 TRP B 798 HIS 0.024 0.006 HIS B 428 PHE 0.105 0.022 PHE D 39 TYR 0.181 0.024 TYR A 672 ARG 0.020 0.001 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASN cc_start: 0.5332 (OUTLIER) cc_final: 0.5129 (p0) REVERT: A 427 MET cc_start: 0.7640 (ttp) cc_final: 0.7390 (ttm) REVERT: A 658 TYR cc_start: 0.2901 (t80) cc_final: 0.2697 (t80) REVERT: A 731 MET cc_start: 0.7010 (ppp) cc_final: 0.6413 (ppp) REVERT: B 231 HIS cc_start: 0.6932 (p-80) cc_final: 0.6695 (p-80) REVERT: B 270 PHE cc_start: 0.7576 (m-80) cc_final: 0.7311 (m-80) REVERT: B 303 MET cc_start: 0.7569 (mtp) cc_final: 0.7295 (mtm) REVERT: B 647 THR cc_start: 0.5902 (t) cc_final: 0.5239 (m) REVERT: B 745 ILE cc_start: 0.0922 (OUTLIER) cc_final: 0.0360 (mt) REVERT: B 759 TYR cc_start: 0.6294 (m-80) cc_final: 0.6020 (m-80) REVERT: B 786 TYR cc_start: 0.5327 (m-10) cc_final: 0.4977 (m-10) REVERT: B 835 MET cc_start: 0.0768 (ttp) cc_final: 0.0405 (ttp) REVERT: D 88 LEU cc_start: 0.6430 (tp) cc_final: 0.5755 (tp) outliers start: 35 outliers final: 15 residues processed: 298 average time/residue: 0.2947 time to fit residues: 124.9683 Evaluate side-chains 208 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 620 THR Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 79 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 0.0870 chunk 72 optimal weight: 0.0870 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 250 GLN A 377 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 776 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN B 387 ASN B 389 ASN B 426 ASN B 429 HIS B 515 ASN B 660 GLN B 809 ASN C 84 GLN D 3 GLN D 79 ASN D 84 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14569 Z= 0.242 Angle : 0.766 9.647 19753 Z= 0.402 Chirality : 0.047 0.186 2209 Planarity : 0.005 0.059 2501 Dihedral : 7.463 55.935 2017 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.21 % Favored : 92.73 % Rotamer: Outliers : 3.28 % Allowed : 14.97 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.18), residues: 1802 helix: -1.31 (0.18), residues: 684 sheet: -2.54 (0.30), residues: 232 loop : -2.64 (0.18), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 468 HIS 0.010 0.001 HIS B 429 PHE 0.031 0.002 PHE A 368 TYR 0.031 0.002 TYR A 672 ARG 0.005 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 211 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7552 (ttp) cc_final: 0.7339 (ttm) REVERT: A 630 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4553 (pp) REVERT: A 670 MET cc_start: 0.4617 (mpp) cc_final: 0.4298 (mpp) REVERT: A 692 LYS cc_start: 0.0764 (tptm) cc_final: -0.0587 (tttm) REVERT: A 731 MET cc_start: 0.7009 (ppp) cc_final: 0.6349 (ppp) REVERT: B 116 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7695 (tt) REVERT: B 303 MET cc_start: 0.7463 (mtp) cc_final: 0.7262 (mtm) REVERT: B 410 MET cc_start: 0.7854 (tpp) cc_final: 0.7592 (mmm) REVERT: B 427 MET cc_start: 0.6842 (ttm) cc_final: 0.6605 (ttm) REVERT: B 647 THR cc_start: 0.5666 (t) cc_final: 0.4969 (m) REVERT: B 786 TYR cc_start: 0.5319 (m-10) cc_final: 0.4867 (m-10) REVERT: B 836 TYR cc_start: 0.0574 (OUTLIER) cc_final: -0.1006 (m-80) outliers start: 51 outliers final: 27 residues processed: 256 average time/residue: 0.2077 time to fit residues: 77.7437 Evaluate side-chains 219 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 121 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS C 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14569 Z= 0.404 Angle : 0.793 10.592 19753 Z= 0.413 Chirality : 0.048 0.220 2209 Planarity : 0.006 0.055 2501 Dihedral : 7.256 52.618 2005 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 4.76 % Allowed : 18.44 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.88 (0.18), residues: 1802 helix: -0.96 (0.19), residues: 675 sheet: -2.27 (0.31), residues: 236 loop : -2.60 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 107 HIS 0.010 0.002 HIS D 61 PHE 0.017 0.002 PHE A 801 TYR 0.022 0.002 TYR B 672 ARG 0.004 0.001 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 200 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 630 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4439 (pp) REVERT: A 670 MET cc_start: 0.4716 (mpp) cc_final: 0.4436 (mpp) REVERT: A 692 LYS cc_start: 0.0598 (tptm) cc_final: -0.0293 (tttm) REVERT: A 830 MET cc_start: 0.3982 (mmt) cc_final: 0.3410 (tpt) REVERT: A 835 MET cc_start: 0.3090 (mtt) cc_final: 0.2779 (mtt) REVERT: B 116 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7707 (tt) REVERT: B 410 MET cc_start: 0.7970 (tpp) cc_final: 0.7681 (mmm) REVERT: B 420 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7760 (tpp) REVERT: B 427 MET cc_start: 0.6942 (ttm) cc_final: 0.6657 (ttm) REVERT: B 653 THR cc_start: 0.2872 (p) cc_final: 0.2569 (m) REVERT: B 786 TYR cc_start: 0.5227 (m-10) cc_final: 0.4871 (m-10) REVERT: B 836 TYR cc_start: 0.0932 (OUTLIER) cc_final: -0.0923 (m-80) outliers start: 74 outliers final: 46 residues processed: 257 average time/residue: 0.2733 time to fit residues: 104.1038 Evaluate side-chains 229 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 553 ASN Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 815 THR Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 0.0370 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 513 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14569 Z= 0.196 Angle : 0.663 7.974 19753 Z= 0.346 Chirality : 0.043 0.178 2209 Planarity : 0.004 0.055 2501 Dihedral : 6.465 51.155 2005 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.53 % Allowed : 20.57 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.19 (0.19), residues: 1802 helix: -0.38 (0.19), residues: 681 sheet: -1.98 (0.33), residues: 222 loop : -2.18 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 468 HIS 0.008 0.001 HIS B 429 PHE 0.015 0.002 PHE A 801 TYR 0.025 0.002 TYR A 672 ARG 0.007 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 215 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.6998 (m) REVERT: A 208 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6482 (m-30) REVERT: A 630 LEU cc_start: 0.4639 (OUTLIER) cc_final: 0.4350 (pp) REVERT: A 692 LYS cc_start: 0.0555 (tptm) cc_final: -0.0601 (tttt) REVERT: A 724 LEU cc_start: 0.3709 (tt) cc_final: 0.2878 (mt) REVERT: A 830 MET cc_start: 0.4276 (mmt) cc_final: 0.3754 (tpt) REVERT: B 116 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7792 (tt) REVERT: B 278 ARG cc_start: 0.6500 (mmm160) cc_final: 0.6241 (mmm-85) REVERT: B 410 MET cc_start: 0.7780 (tpp) cc_final: 0.7478 (mmm) REVERT: B 427 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6397 (ttm) REVERT: B 442 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5739 (ptm) REVERT: B 496 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6238 (m-70) REVERT: B 514 MET cc_start: 0.3380 (mmp) cc_final: 0.2975 (mpp) REVERT: B 530 LYS cc_start: 0.1810 (OUTLIER) cc_final: 0.1481 (ttpt) REVERT: B 653 THR cc_start: 0.3200 (p) cc_final: 0.2872 (m) REVERT: B 727 MET cc_start: 0.5638 (mtt) cc_final: 0.3740 (ttm) REVERT: B 765 MET cc_start: 0.3654 (tpt) cc_final: 0.3331 (tpt) REVERT: B 786 TYR cc_start: 0.5171 (m-10) cc_final: 0.4833 (m-10) REVERT: C 39 PHE cc_start: 0.7048 (m-10) cc_final: 0.6775 (m-10) REVERT: D 38 TRP cc_start: 0.6292 (m100) cc_final: 0.5992 (m100) outliers start: 55 outliers final: 29 residues processed: 256 average time/residue: 0.2731 time to fit residues: 101.4919 Evaluate side-chains 227 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 0.0170 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 429 HIS D 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14569 Z= 0.382 Angle : 0.751 12.003 19753 Z= 0.390 Chirality : 0.046 0.202 2209 Planarity : 0.005 0.057 2501 Dihedral : 6.609 54.015 2002 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 5.27 % Allowed : 21.14 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.31 (0.19), residues: 1802 helix: -0.47 (0.19), residues: 672 sheet: -1.83 (0.32), residues: 242 loop : -2.31 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 545 HIS 0.006 0.001 HIS A 55 PHE 0.018 0.002 PHE A 801 TYR 0.020 0.002 TYR C 112 ARG 0.006 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 186 time to evaluate : 1.654 Fit side-chains revert: symmetry clash REVERT: A 208 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: A 370 GLU cc_start: 0.7494 (mp0) cc_final: 0.7209 (mp0) REVERT: A 692 LYS cc_start: 0.0642 (tptm) cc_final: -0.0489 (tttt) REVERT: A 830 MET cc_start: 0.4086 (mmt) cc_final: 0.3336 (tpt) REVERT: A 835 MET cc_start: 0.3034 (mtt) cc_final: 0.2825 (mtt) REVERT: B 116 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7747 (tt) REVERT: B 231 HIS cc_start: 0.6960 (p-80) cc_final: 0.6720 (p-80) REVERT: B 278 ARG cc_start: 0.6674 (mmm160) cc_final: 0.6417 (mmm-85) REVERT: B 410 MET cc_start: 0.7900 (tpp) cc_final: 0.7625 (mmm) REVERT: B 496 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6279 (m-70) REVERT: B 530 LYS cc_start: 0.1614 (OUTLIER) cc_final: 0.1236 (ttpt) REVERT: B 653 THR cc_start: 0.2924 (p) cc_final: 0.2593 (m) REVERT: B 765 MET cc_start: 0.3638 (tpt) cc_final: 0.3305 (tpt) REVERT: B 786 TYR cc_start: 0.5205 (m-10) cc_final: 0.4838 (m-10) REVERT: B 836 TYR cc_start: 0.0877 (OUTLIER) cc_final: -0.0928 (m-80) outliers start: 82 outliers final: 53 residues processed: 252 average time/residue: 0.2599 time to fit residues: 97.6877 Evaluate side-chains 238 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 180 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14569 Z= 0.279 Angle : 0.696 10.292 19753 Z= 0.359 Chirality : 0.045 0.183 2209 Planarity : 0.005 0.056 2501 Dihedral : 6.361 55.697 2000 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.27 % Allowed : 21.72 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -2.15 (0.19), residues: 1802 helix: -0.32 (0.19), residues: 672 sheet: -1.75 (0.33), residues: 236 loop : -2.23 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 107 HIS 0.006 0.001 HIS A 429 PHE 0.024 0.002 PHE A 806 TYR 0.019 0.002 TYR A 672 ARG 0.005 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 199 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.6962 (m) REVERT: A 208 ASP cc_start: 0.7034 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: A 268 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6346 (tptt) REVERT: A 290 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 670 MET cc_start: 0.4686 (mpp) cc_final: 0.4461 (mpp) REVERT: A 692 LYS cc_start: 0.0838 (tptm) cc_final: -0.0359 (tttt) REVERT: A 830 MET cc_start: 0.4215 (OUTLIER) cc_final: 0.3613 (tpt) REVERT: B 116 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7740 (tt) REVERT: B 278 ARG cc_start: 0.6638 (mmm160) cc_final: 0.6401 (mmm-85) REVERT: B 410 MET cc_start: 0.7850 (tpp) cc_final: 0.7574 (mmm) REVERT: B 427 MET cc_start: 0.6350 (ttm) cc_final: 0.6140 (ttm) REVERT: B 496 HIS cc_start: 0.6880 (OUTLIER) cc_final: 0.6201 (m-70) REVERT: B 530 LYS cc_start: 0.1563 (OUTLIER) cc_final: 0.1178 (ttpt) REVERT: B 653 THR cc_start: 0.2963 (p) cc_final: 0.2601 (m) REVERT: B 727 MET cc_start: 0.5917 (mtt) cc_final: 0.3940 (ttm) REVERT: B 765 MET cc_start: 0.3760 (tpt) cc_final: 0.3435 (tpt) REVERT: B 836 TYR cc_start: 0.0881 (OUTLIER) cc_final: -0.0989 (m-80) REVERT: D 97 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6131 (m-10) outliers start: 82 outliers final: 53 residues processed: 263 average time/residue: 0.2788 time to fit residues: 109.6369 Evaluate side-chains 248 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 185 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 97 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 105 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14569 Z= 0.232 Angle : 0.671 11.133 19753 Z= 0.346 Chirality : 0.044 0.192 2209 Planarity : 0.004 0.053 2501 Dihedral : 6.137 57.274 2000 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.46 % Allowed : 21.59 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.95 (0.19), residues: 1802 helix: -0.18 (0.19), residues: 681 sheet: -1.61 (0.33), residues: 222 loop : -2.12 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 107 HIS 0.004 0.001 HIS B 429 PHE 0.034 0.002 PHE B 789 TYR 0.019 0.002 TYR A 672 ARG 0.006 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 200 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.6811 (m) REVERT: A 208 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.6347 (m-30) REVERT: A 290 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.6688 (t80) REVERT: A 514 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.3819 (ptp) REVERT: A 670 MET cc_start: 0.4510 (mpp) cc_final: 0.4185 (mpp) REVERT: A 692 LYS cc_start: 0.1010 (tptm) cc_final: -0.0329 (tttt) REVERT: A 724 LEU cc_start: 0.3765 (tt) cc_final: 0.2926 (mt) REVERT: A 830 MET cc_start: 0.4225 (mmt) cc_final: 0.3606 (tpt) REVERT: B 116 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7731 (tt) REVERT: B 231 HIS cc_start: 0.6954 (p-80) cc_final: 0.6746 (p-80) REVERT: B 278 ARG cc_start: 0.6646 (mmm160) cc_final: 0.6399 (mmm-85) REVERT: B 330 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.5192 (t80) REVERT: B 410 MET cc_start: 0.7789 (tpp) cc_final: 0.7511 (mmm) REVERT: B 496 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6154 (m-70) REVERT: B 530 LYS cc_start: 0.1532 (OUTLIER) cc_final: 0.1198 (ttpt) REVERT: B 727 MET cc_start: 0.5860 (mtt) cc_final: 0.4007 (ttm) REVERT: B 765 MET cc_start: 0.3802 (tpt) cc_final: 0.3434 (tpt) REVERT: B 836 TYR cc_start: 0.0794 (OUTLIER) cc_final: -0.1090 (m-80) REVERT: D 97 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6142 (m-10) outliers start: 85 outliers final: 55 residues processed: 265 average time/residue: 0.2541 time to fit residues: 100.8885 Evaluate side-chains 257 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 192 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 0.0040 chunk 85 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14569 Z= 0.210 Angle : 0.647 9.122 19753 Z= 0.333 Chirality : 0.043 0.200 2209 Planarity : 0.004 0.050 2501 Dihedral : 5.928 59.754 2000 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.24 % Allowed : 22.49 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.79 (0.19), residues: 1802 helix: -0.02 (0.20), residues: 684 sheet: -1.57 (0.32), residues: 236 loop : -2.05 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 107 HIS 0.004 0.001 HIS B 429 PHE 0.028 0.001 PHE B 789 TYR 0.018 0.002 TYR A 617 ARG 0.007 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 207 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.6656 (m) REVERT: A 208 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6250 (m-30) REVERT: A 268 LYS cc_start: 0.6427 (OUTLIER) cc_final: 0.6178 (tptt) REVERT: A 290 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7089 (t80) REVERT: A 514 MET cc_start: 0.5981 (mmm) cc_final: 0.3801 (ptp) REVERT: A 670 MET cc_start: 0.4628 (mpp) cc_final: 0.4351 (mpp) REVERT: A 692 LYS cc_start: 0.1083 (tptm) cc_final: -0.0269 (tttt) REVERT: A 724 LEU cc_start: 0.3856 (tt) cc_final: 0.3126 (mt) REVERT: A 830 MET cc_start: 0.4250 (mmt) cc_final: 0.3673 (tpt) REVERT: B 116 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7608 (tt) REVERT: B 231 HIS cc_start: 0.6810 (p-80) cc_final: 0.6540 (p-80) REVERT: B 278 ARG cc_start: 0.6448 (mmm160) cc_final: 0.6239 (mmm-85) REVERT: B 330 TYR cc_start: 0.5796 (OUTLIER) cc_final: 0.5407 (t80) REVERT: B 410 MET cc_start: 0.7748 (tpp) cc_final: 0.7463 (mmm) REVERT: B 420 MET cc_start: 0.7537 (tpp) cc_final: 0.7312 (tpp) REVERT: B 496 HIS cc_start: 0.6605 (OUTLIER) cc_final: 0.5948 (m-70) REVERT: B 530 LYS cc_start: 0.1546 (OUTLIER) cc_final: 0.1285 (tmmt) REVERT: B 727 MET cc_start: 0.5772 (mtt) cc_final: 0.4019 (ttm) REVERT: B 740 LYS cc_start: 0.5446 (mptt) cc_final: 0.5209 (pttp) REVERT: B 765 MET cc_start: 0.3752 (tpt) cc_final: 0.3310 (tpt) REVERT: D 78 LYS cc_start: 0.5713 (pttm) cc_final: 0.5454 (tppt) outliers start: 66 outliers final: 50 residues processed: 259 average time/residue: 0.2651 time to fit residues: 101.6816 Evaluate side-chains 255 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 197 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 10.0000 chunk 166 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 152 optimal weight: 0.0980 chunk 106 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14569 Z= 0.251 Angle : 0.663 8.990 19753 Z= 0.342 Chirality : 0.044 0.197 2209 Planarity : 0.004 0.049 2501 Dihedral : 5.932 57.733 2000 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.56 % Allowed : 22.43 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.79 (0.19), residues: 1802 helix: 0.00 (0.20), residues: 685 sheet: -1.57 (0.32), residues: 238 loop : -2.07 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 588 HIS 0.004 0.001 HIS A 429 PHE 0.042 0.002 PHE B 789 TYR 0.020 0.002 TYR A 617 ARG 0.004 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 199 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.7608 (OUTLIER) cc_final: 0.6856 (m) REVERT: A 208 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6412 (m-30) REVERT: A 268 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.6231 (tptt) REVERT: A 514 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.3786 (ptp) REVERT: A 670 MET cc_start: 0.4610 (mpp) cc_final: 0.4328 (mpp) REVERT: A 692 LYS cc_start: 0.0977 (tptm) cc_final: -0.0286 (tttt) REVERT: A 724 LEU cc_start: 0.3717 (tt) cc_final: 0.2942 (mt) REVERT: A 830 MET cc_start: 0.4116 (OUTLIER) cc_final: 0.3482 (tpt) REVERT: B 116 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7634 (tt) REVERT: B 231 HIS cc_start: 0.6849 (p-80) cc_final: 0.6585 (p-80) REVERT: B 278 ARG cc_start: 0.6443 (mmm160) cc_final: 0.6201 (mmm-85) REVERT: B 330 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.5488 (t80) REVERT: B 410 MET cc_start: 0.7773 (tpp) cc_final: 0.7475 (mmm) REVERT: B 420 MET cc_start: 0.7580 (tpp) cc_final: 0.7008 (mpp) REVERT: B 496 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.6035 (m-70) REVERT: B 530 LYS cc_start: 0.1472 (OUTLIER) cc_final: 0.1162 (tmmt) REVERT: B 727 MET cc_start: 0.5769 (mtt) cc_final: 0.4034 (ttm) REVERT: B 740 LYS cc_start: 0.5470 (mptt) cc_final: 0.5225 (pttp) REVERT: B 765 MET cc_start: 0.3792 (tpt) cc_final: 0.3348 (tpt) REVERT: D 78 LYS cc_start: 0.5821 (pttm) cc_final: 0.5587 (tppt) outliers start: 71 outliers final: 55 residues processed: 253 average time/residue: 0.2620 time to fit residues: 99.1199 Evaluate side-chains 252 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 188 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 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 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14569 Z= 0.273 Angle : 0.679 8.994 19753 Z= 0.350 Chirality : 0.044 0.194 2209 Planarity : 0.005 0.146 2501 Dihedral : 5.965 56.239 2000 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.76 % Allowed : 22.24 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.82 (0.19), residues: 1802 helix: -0.03 (0.20), residues: 685 sheet: -1.57 (0.32), residues: 238 loop : -2.07 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 545 HIS 0.005 0.001 HIS B 428 PHE 0.031 0.002 PHE B 789 TYR 0.022 0.002 TYR A 617 ARG 0.017 0.001 ARG C 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 195 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.6880 (m) REVERT: A 208 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: A 268 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6248 (tptt) REVERT: A 290 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7249 (t80) REVERT: A 514 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.3799 (ptp) REVERT: A 670 MET cc_start: 0.4740 (mpp) cc_final: 0.4421 (mpp) REVERT: A 692 LYS cc_start: 0.1035 (tptm) cc_final: -0.0287 (tttt) REVERT: A 724 LEU cc_start: 0.3763 (tt) cc_final: 0.2937 (mt) REVERT: A 798 TRP cc_start: 0.4694 (m-10) cc_final: 0.3468 (m-10) REVERT: A 830 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.3582 (tpt) REVERT: B 116 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7731 (tt) REVERT: B 231 HIS cc_start: 0.6991 (p-80) cc_final: 0.6788 (p-80) REVERT: B 330 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.5566 (t80) REVERT: B 410 MET cc_start: 0.7772 (tpp) cc_final: 0.7509 (mmm) REVERT: B 420 MET cc_start: 0.7681 (tpp) cc_final: 0.7012 (mpp) REVERT: B 496 HIS cc_start: 0.6683 (OUTLIER) cc_final: 0.6022 (m-70) REVERT: B 530 LYS cc_start: 0.1279 (OUTLIER) cc_final: 0.0974 (tmmt) REVERT: B 727 MET cc_start: 0.5792 (mtt) cc_final: 0.4184 (ttm) REVERT: B 765 MET cc_start: 0.3806 (tpt) cc_final: 0.3361 (tpt) REVERT: D 78 LYS cc_start: 0.5884 (pttm) cc_final: 0.5603 (tppt) REVERT: D 97 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.6030 (m-10) REVERT: D 109 ASP cc_start: 0.4314 (m-30) cc_final: 0.4099 (m-30) outliers start: 74 outliers final: 57 residues processed: 252 average time/residue: 0.2528 time to fit residues: 95.3040 Evaluate side-chains 257 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 189 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 528 CYS Chi-restraints excluded: chain A residue 547 CYS Chi-restraints excluded: chain A residue 578 CYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 620 THR Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 832 THR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 496 HIS Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 562 CYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 657 CYS Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 813 ILE Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 36 MET Chi-restraints excluded: chain D residue 70 PHE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 97 TYR Chi-restraints excluded: chain D residue 102 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0020 chunk 43 optimal weight: 0.0060 chunk 131 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 496 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.153531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.126869 restraints weight = 31331.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.122145 restraints weight = 36164.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.121367 restraints weight = 33454.036| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14569 Z= 0.182 Angle : 0.642 8.354 19753 Z= 0.330 Chirality : 0.043 0.215 2209 Planarity : 0.005 0.125 2501 Dihedral : 5.629 54.571 2000 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.21 % Allowed : 23.91 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.67 (0.19), residues: 1802 helix: 0.15 (0.20), residues: 686 sheet: -1.70 (0.32), residues: 221 loop : -1.99 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 107 HIS 0.005 0.001 HIS D 61 PHE 0.041 0.001 PHE B 789 TYR 0.022 0.001 TYR A 617 ARG 0.015 0.000 ARG C 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.01 seconds wall clock time: 65 minutes 40.93 seconds (3940.93 seconds total)