Starting phenix.real_space_refine (version: dev) on Tue Feb 21 07:58:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_30672_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_30672.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_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_30672/02_2023/7dge_30672_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_30672_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_30672.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_30672.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_30672_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dge_30672/02_2023/7dge_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 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-4877/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: 7.95, per 1000 atoms: 0.56 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: 5.20 Conformation dependent library (CDL) restraints added in 2.1 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: 1.54 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: 3.99 Time building geometry restraints manager: 5.69 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.080 Check model and map are aligned: 0.180 Process input model: 35.320 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.670 ------------------------------------------------------------------------------- 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 : 14.915 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 : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 298 average time/residue: 0.3090 time to fit residues: 131.2604 Evaluate side-chains 203 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.568 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1274 time to fit residues: 5.8843 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.7041 moved from start: 0.2092 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= 0.241 Angle : 0.764 9.755 19753 Z= 0.401 Chirality : 0.047 0.189 2209 Planarity : 0.005 0.063 2501 Dihedral : 6.652 38.303 1987 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.12 % Rotamer Outliers : 2.63 % 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: -3.13 (0.18), residues: 1802 helix: -1.27 (0.18), residues: 684 sheet: -2.39 (0.31), 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 257 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 248 average time/residue: 0.2785 time to fit residues: 100.7725 Evaluate side-chains 209 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1356 time to fit residues: 7.2351 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 163 optimal weight: 0.0000 chunk 176 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ** 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 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 14569 Z= 0.326 Angle : 0.745 9.963 19753 Z= 0.388 Chirality : 0.046 0.198 2209 Planarity : 0.005 0.056 2501 Dihedral : 6.336 32.989 1987 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 2.76 % 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: -2.68 (0.18), residues: 1802 helix: -0.78 (0.19), residues: 677 sheet: -2.16 (0.32), residues: 227 loop : -2.48 (0.19), residues: 898 *********************** 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 248 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 205 time to evaluate : 1.630 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 20 residues processed: 240 average time/residue: 0.2693 time to fit residues: 95.4774 Evaluate side-chains 206 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.663 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1343 time to fit residues: 7.5220 ------------------------------------------------------------------------------- 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: 6.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 173 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 14569 Z= 0.253 Angle : 0.693 8.988 19753 Z= 0.360 Chirality : 0.045 0.192 2209 Planarity : 0.005 0.058 2501 Dihedral : 5.985 28.881 1987 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer Outliers : 3.08 % 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: -0.45 (0.19), residues: 672 sheet: -1.94 (0.32), residues: 229 loop : -2.32 (0.19), residues: 901 *********************** 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: 48 poor density : 202 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 238 average time/residue: 0.2770 time to fit residues: 97.1619 Evaluate side-chains 203 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 1.622 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1637 time to fit residues: 8.4409 ------------------------------------------------------------------------------- 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: 0.0070 chunk 2 optimal weight: 0.2980 chunk 129 optimal weight: 0.5980 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: 2.9990 chunk 156 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 B 172 GLN B 182 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS B 513 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14569 Z= 0.188 Angle : 0.650 11.864 19753 Z= 0.335 Chirality : 0.043 0.194 2209 Planarity : 0.004 0.056 2501 Dihedral : 5.508 24.227 1987 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 2.12 % 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: -2.02 (0.19), residues: 1802 helix: -0.28 (0.19), residues: 692 sheet: -1.66 (0.35), residues: 208 loop : -2.13 (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 244 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 5 residues processed: 234 average time/residue: 0.2675 time to fit residues: 92.6103 Evaluate side-chains 187 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1292 time to fit residues: 3.2991 ------------------------------------------------------------------------------- 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: 0.5980 chunk 156 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 0.0060 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 425 GLN B 172 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14569 Z= 0.205 Angle : 0.651 10.405 19753 Z= 0.336 Chirality : 0.043 0.183 2209 Planarity : 0.004 0.053 2501 Dihedral : 5.343 23.616 1987 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: -1.82 (0.19), residues: 1802 helix: -0.04 (0.20), residues: 684 sheet: -1.65 (0.33), residues: 228 loop : -2.05 (0.20), residues: 890 *********************** 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 248 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 206 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 234 average time/residue: 0.2696 time to fit residues: 93.7421 Evaluate side-chains 206 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.586 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1460 time to fit residues: 7.0626 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 173 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 425 GLN B 172 GLN ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 14569 Z= 0.233 Angle : 0.659 10.295 19753 Z= 0.340 Chirality : 0.044 0.223 2209 Planarity : 0.004 0.049 2501 Dihedral : 5.323 23.384 1987 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 1.61 % 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: 684 sheet: -1.76 (0.32), residues: 232 loop : -2.08 (0.20), residues: 886 *********************** 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 226 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 201 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 217 average time/residue: 0.2856 time to fit residues: 90.6721 Evaluate side-chains 199 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 187 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1346 time to fit residues: 5.3323 ------------------------------------------------------------------------------- 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: 7.9990 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 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: 0.7001 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14569 Z= 0.218 Angle : 0.658 12.005 19753 Z= 0.340 Chirality : 0.043 0.192 2209 Planarity : 0.004 0.050 2501 Dihedral : 5.247 23.372 1987 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 1.22 % 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: 0.10 (0.20), residues: 682 sheet: -1.65 (0.33), residues: 222 loop : -2.01 (0.20), 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 217 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 211 average time/residue: 0.2751 time to fit residues: 85.8281 Evaluate side-chains 199 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1370 time to fit residues: 4.1942 ------------------------------------------------------------------------------- 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: 9.9990 chunk 166 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 152 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 HIS ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7015 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 : 0.003 0.051 14569 Z= 0.231 Angle : 0.664 11.446 19753 Z= 0.341 Chirality : 0.044 0.214 2209 Planarity : 0.004 0.050 2501 Dihedral : 5.225 23.340 1987 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.58 % 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: -1.69 (0.19), residues: 1802 helix: 0.10 (0.20), residues: 687 sheet: -1.88 (0.33), residues: 224 loop : -1.91 (0.20), residues: 891 *********************** 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 204 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 203 average time/residue: 0.2901 time to fit residues: 86.2428 Evaluate side-chains 187 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.745 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1761 time to fit residues: 2.4622 ------------------------------------------------------------------------------- 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: 0.2980 chunk 118 optimal weight: 0.0010 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 HIS D 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4168 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= 0.205 Angle : 0.668 13.479 19753 Z= 0.342 Chirality : 0.043 0.222 2209 Planarity : 0.004 0.050 2501 Dihedral : 5.164 25.380 1987 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.32 % 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: -1.62 (0.19), residues: 1802 helix: 0.15 (0.20), residues: 688 sheet: -1.69 (0.33), residues: 210 loop : -1.91 (0.20), residues: 904 ********************** 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 201 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 200 average time/residue: 0.2879 time to fit residues: 83.9433 Evaluate side-chains 186 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.659 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1316 time to fit residues: 2.5678 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 146 optimal weight: 0.0570 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** 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 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 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 = 0.4370 r_free = 0.4370 target = 0.153291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.126459 restraints weight = 31517.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.121285 restraints weight = 37835.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119711 restraints weight = 29254.676| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 14569 Z= 0.207 Angle : 0.661 13.316 19753 Z= 0.339 Chirality : 0.043 0.212 2209 Planarity : 0.004 0.050 2501 Dihedral : 5.074 22.308 1987 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.51 % 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: -1.54 (0.19), residues: 1802 helix: 0.20 (0.20), residues: 690 sheet: -1.58 (0.33), residues: 217 loop : -1.89 (0.20), residues: 895 =============================================================================== Job complete usr+sys time: 3147.10 seconds wall clock time: 57 minutes 47.26 seconds (3467.26 seconds total)