Starting phenix.real_space_refine (version: dev) on Tue Apr 5 15:17:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_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_2022/7dge_30672_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/04_2022/7dge_30672_neut_updated.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 31, 'TRANS': 751, 'PCIS': 1} 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: {'PTRANS': 31, 'TRANS': 751, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 119, 'PCIS': 1} 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: {'PTRANS': 2, 'TRANS': 119, 'PCIS': 1} 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: 8.16, per 1000 atoms: 0.57 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: 5.84 Conformation dependent library (CDL) restraints added in 2.2 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: 1.73 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: 3.85 Time building geometry restraints manager: 6.32 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: 138 53.64 - 71.53: 19 71.53 - 89.41: 7 Dihedral angle restraints: 8719 sinusoidal: 3459 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 8716 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 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. 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: 1.210 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: 6.420 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.140 Process input model: 38.450 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 14.914 89.407 5294 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 % 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 *********************** 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 : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 298 average time/residue: 0.2777 time to fit residues: 118.0768 Evaluate side-chains 203 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1260 time to fit residues: 5.8515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 72 optimal weight: 0.0870 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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: 0.7038 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 14569 Z= 0.244 Angle : 0.779 10.096 19753 Z= 0.407 Chirality : 0.047 0.198 2209 Planarity : 0.005 0.067 2501 Dihedral : 6.643 38.030 1987 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.71 % Favored : 93.23 % Rotamer Outliers : 2.89 % 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: -3.12 (0.18), residues: 1802 helix: -1.26 (0.18), residues: 684 sheet: -2.38 (0.32), residues: 215 loop : -2.67 (0.18), residues: 903 *********************** 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 260 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 215 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 251 average time/residue: 0.2699 time to fit residues: 99.3313 Evaluate side-chains 207 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 1.773 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1294 time to fit residues: 6.7625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 0.0570 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 overall best weight: 2.5504 ------------------------------------------------------------------------------- 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 111 HIS ** B 172 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: 0.7172 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.070 14569 Z= 0.468 Angle : 0.860 13.459 19753 Z= 0.446 Chirality : 0.049 0.214 2209 Planarity : 0.006 0.089 2501 Dihedral : 6.727 36.047 1987 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer Outliers : 3.28 % 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: -3.02 (0.18), residues: 1802 helix: -1.09 (0.18), residues: 674 sheet: -2.29 (0.31), residues: 236 loop : -2.68 (0.19), residues: 892 *********************** 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 251 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 1.986 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 237 average time/residue: 0.2913 time to fit residues: 102.4398 Evaluate side-chains 208 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 179 time to evaluate : 1.671 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1394 time to fit residues: 9.8741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 0.0070 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 109 optimal weight: 0.0770 chunk 164 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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: 0.7031 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 14569 Z= 0.215 Angle : 0.729 15.022 19753 Z= 0.379 Chirality : 0.044 0.182 2209 Planarity : 0.005 0.058 2501 Dihedral : 5.946 28.390 1987 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 2.70 % 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: -2.33 (0.19), residues: 1802 helix: -0.53 (0.19), residues: 679 sheet: -1.96 (0.33), residues: 229 loop : -2.27 (0.19), residues: 894 *********************** 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 250 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.681 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 16 residues processed: 235 average time/residue: 0.2731 time to fit residues: 94.3720 Evaluate side-chains 203 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.757 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1417 time to fit residues: 6.6303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 2 optimal weight: 0.0050 chunk 129 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 0.4980 chunk 43 optimal weight: 0.0770 overall best weight: 0.4952 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 14569 Z= 0.217 Angle : 0.725 16.892 19753 Z= 0.376 Chirality : 0.044 0.238 2209 Planarity : 0.004 0.056 2501 Dihedral : 5.543 23.017 1987 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer Outliers : 2.70 % 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: -2.05 (0.19), residues: 1802 helix: -0.26 (0.20), residues: 682 sheet: -1.75 (0.33), residues: 218 loop : -2.16 (0.19), residues: 902 *********************** 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 252 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 210 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 14 residues processed: 243 average time/residue: 0.2714 time to fit residues: 97.7930 Evaluate side-chains 203 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 1.819 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1437 time to fit residues: 6.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 90 ASN B 172 GLN B 182 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.166 14569 Z= 0.242 Angle : 0.740 18.016 19753 Z= 0.385 Chirality : 0.043 0.213 2209 Planarity : 0.004 0.052 2501 Dihedral : 5.383 24.581 1987 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 1.93 % 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: -1.90 (0.19), residues: 1802 helix: -0.06 (0.20), residues: 680 sheet: -1.77 (0.33), residues: 211 loop : -2.11 (0.19), residues: 911 *********************** 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 238 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 208 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 10 residues processed: 229 average time/residue: 0.2670 time to fit residues: 90.0590 Evaluate side-chains 195 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1351 time to fit residues: 4.7380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 146 optimal weight: 0.0770 chunk 97 optimal weight: 0.5980 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 0.0970 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** 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: 0.6942 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.317 14569 Z= 0.271 Angle : 0.775 25.604 19753 Z= 0.414 Chirality : 0.043 0.217 2209 Planarity : 0.004 0.048 2501 Dihedral : 5.155 21.523 1987 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.06 % 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: -1.74 (0.19), residues: 1802 helix: 0.10 (0.20), residues: 685 sheet: -1.78 (0.32), residues: 220 loop : -2.02 (0.19), residues: 897 *********************** 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 225 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 217 average time/residue: 0.2701 time to fit residues: 86.2905 Evaluate side-chains 196 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1255 time to fit residues: 3.9774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.5980 chunk 69 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 750 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** 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: 0.6953 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.621 14569 Z= 0.518 Angle : 0.968 73.884 19753 Z= 0.468 Chirality : 0.043 0.190 2209 Planarity : 0.005 0.086 2501 Dihedral : 5.184 23.340 1987 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 0.90 % 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: -1.71 (0.19), residues: 1802 helix: 0.11 (0.20), residues: 684 sheet: -1.73 (0.32), residues: 220 loop : -2.00 (0.19), residues: 898 *********************** 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 204 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 190 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 196 average time/residue: 0.2723 time to fit residues: 79.2568 Evaluate side-chains 192 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.732 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1487 time to fit residues: 3.9846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 0.0980 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** 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: 0.6957 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.993 14569 Z= 0.598 Angle : 1.239 106.095 19753 Z= 0.546 Chirality : 0.044 0.182 2209 Planarity : 0.005 0.086 2501 Dihedral : 5.180 25.187 1987 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.06 % 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: -1.73 (0.19), residues: 1802 helix: 0.11 (0.20), residues: 684 sheet: -1.73 (0.32), residues: 220 loop : -2.03 (0.19), residues: 898 *********************** 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 195 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 191 average time/residue: 0.2698 time to fit residues: 76.8227 Evaluate side-chains 193 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1361 time to fit residues: 3.2624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** 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: 0.6958 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.993 14569 Z= 0.598 Angle : 1.239 106.095 19753 Z= 0.546 Chirality : 0.044 0.182 2209 Planarity : 0.005 0.086 2501 Dihedral : 5.180 25.187 1987 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.06 % 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: -1.73 (0.19), residues: 1802 helix: 0.11 (0.20), residues: 684 sheet: -1.73 (0.32), residues: 220 loop : -2.03 (0.19), residues: 898 ********************** 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 192 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 190 average time/residue: 0.2740 time to fit residues: 77.3387 Evaluate side-chains 190 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 2.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2064 time to fit residues: 2.7166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- 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** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.153887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.131374 restraints weight = 31568.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.132562 restraints weight = 58679.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.133090 restraints weight = 41281.272| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.993 14569 Z= 0.598 Angle : 1.239 106.094 19753 Z= 0.546 Chirality : 0.044 0.182 2209 Planarity : 0.005 0.086 2501 Dihedral : 5.180 25.187 1987 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.06 % 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: -1.73 (0.19), residues: 1802 helix: 0.11 (0.20), residues: 684 sheet: -1.73 (0.32), residues: 220 loop : -2.03 (0.19), residues: 898 =============================================================================== Job complete usr+sys time: 3002.04 seconds wall clock time: 55 minutes 33.90 seconds (3333.90 seconds total)