Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 23:49:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/07_2023/8jcu_36165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/07_2023/8jcu_36165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/07_2023/8jcu_36165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/07_2023/8jcu_36165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/07_2023/8jcu_36165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/07_2023/8jcu_36165_updated.pdb" } resolution = 2.8 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6814 2.51 5 N 1915 2.21 5 O 2041 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 440": "OE1" <-> "OE2" Residue "2 TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 257": "OD1" <-> "OD2" Residue "3 PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10830 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 762, 5371 Classifications: {'peptide': 762} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 37, 'TRANS': 724} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 591 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 11, 'GLU:plan': 10, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 331 Chain: "3" Number of atoms: 5379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5379 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 718 Unresolved non-hydrogen angles: 923 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 9, 'TYR:plan': 11, 'ASN:plan1': 8, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 16, 'GLU:plan': 9, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 383 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.90, per 1000 atoms: 0.54 Number of scatterers: 10830 At special positions: 0 Unit cell: (91.035, 121.023, 184.212, 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 60 16.00 O 2041 8.00 N 1915 7.00 C 6814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " 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 Links applied NAG-ASN " NAG 21102 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 4.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2866 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 43.0% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain '2' and resid 59 through 73 Processing helix chain '2' and resid 95 through 102 Processing helix chain '2' and resid 105 through 109 Processing helix chain '2' and resid 145 through 156 Processing helix chain '2' and resid 170 through 172 No H-bonds generated for 'chain '2' and resid 170 through 172' Processing helix chain '2' and resid 190 through 201 Processing helix chain '2' and resid 219 through 231 removed outlier: 3.578A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 259 Processing helix chain '2' and resid 272 through 285 Processing helix chain '2' and resid 325 through 332 Processing helix chain '2' and resid 345 through 352 Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 415 through 422 Processing helix chain '2' and resid 486 through 488 No H-bonds generated for 'chain '2' and resid 486 through 488' Processing helix chain '2' and resid 568 through 588 Processing helix chain '2' and resid 596 through 600 Processing helix chain '2' and resid 603 through 624 removed outlier: 3.657A pdb=" N ILE 2 608 " --> pdb=" O GLU 2 604 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR 2 617 " --> pdb=" O VAL 2 613 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR 2 620 " --> pdb=" O CYS 2 616 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) Processing helix chain '2' and resid 631 through 658 removed outlier: 3.556A pdb=" N LEU 2 639 " --> pdb=" O ARG 2 635 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER 2 644 " --> pdb=" O GLY 2 640 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS 2 646 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 698 removed outlier: 3.630A pdb=" N ILE 2 693 " --> pdb=" O GLY 2 689 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL 2 694 " --> pdb=" O GLN 2 690 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA 2 696 " --> pdb=" O LEU 2 692 " (cutoff:3.500A) Processing helix chain '2' and resid 726 through 748 removed outlier: 3.565A pdb=" N ASN 2 735 " --> pdb=" O SER 2 731 " (cutoff:3.500A) Processing helix chain '2' and resid 756 through 783 removed outlier: 3.747A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix removed outlier: 3.747A pdb=" N TYR 2 781 " --> pdb=" O LEU 2 777 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 806 Processing helix chain '2' and resid 809 through 818 removed outlier: 3.778A pdb=" N LYS 2 813 " --> pdb=" O LEU 2 809 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 81 Processing helix chain '3' and resid 102 through 116 removed outlier: 3.553A pdb=" N GLU 3 107 " --> pdb=" O THR 3 103 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN 3 108 " --> pdb=" O TYR 3 104 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER 3 116 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 164 removed outlier: 4.078A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 179 Processing helix chain '3' and resid 194 through 207 Processing helix chain '3' and resid 222 through 236 removed outlier: 3.745A pdb=" N GLU 3 231 " --> pdb=" O ILE 3 227 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU 3 233 " --> pdb=" O ALA 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 264 Processing helix chain '3' and resid 278 through 291 removed outlier: 3.512A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 331 through 338 removed outlier: 4.009A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR 3 336 " --> pdb=" O GLN 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 351 through 359 Processing helix chain '3' and resid 390 through 411 Processing helix chain '3' and resid 421 through 424 No H-bonds generated for 'chain '3' and resid 421 through 424' Processing helix chain '3' and resid 427 through 432 Processing helix chain '3' and resid 435 through 437 No H-bonds generated for 'chain '3' and resid 435 through 437' Processing helix chain '3' and resid 575 through 602 removed outlier: 3.853A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix Processing helix chain '3' and resid 611 through 632 removed outlier: 3.997A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE 3 631 " --> pdb=" O CYS 3 627 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 664 removed outlier: 3.804A pdb=" N LEU 3 646 " --> pdb=" O ALA 3 642 " (cutoff:3.500A) Processing helix chain '3' and resid 683 through 700 Processing helix chain '3' and resid 703 through 706 No H-bonds generated for 'chain '3' and resid 703 through 706' Processing helix chain '3' and resid 734 through 757 removed outlier: 3.632A pdb=" N VAL 3 745 " --> pdb=" O LEU 3 741 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU 3 747 " --> pdb=" O TYR 3 743 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL 3 748 " --> pdb=" O ASP 3 744 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR 3 754 " --> pdb=" O LEU 3 750 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA 3 755 " --> pdb=" O CYS 3 751 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 791 removed outlier: 3.824A pdb=" N TYR 3 776 " --> pdb=" O GLY 3 772 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR 3 777 " --> pdb=" O PHE 3 773 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU 3 786 " --> pdb=" O TRP 3 782 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.853A pdb=" N VAL 3 791 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 4.488A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id= A, first strand: chain '2' and resid 26 through 28 removed outlier: 3.730A pdb=" N ALA 2 86 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLY 2 35 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL 2 139 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU 2 37 " --> pdb=" O VAL 2 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY 2 141 " --> pdb=" O LEU 2 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 162 through 164 Processing sheet with id= C, first strand: chain '2' and resid 208 through 210 removed outlier: 6.032A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 315 through 319 removed outlier: 3.789A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 91 through 97 removed outlier: 6.519A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY 3 147 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLY 3 147 " --> pdb=" O PRO 3 167 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE 3 169 " --> pdb=" O GLY 3 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 296 through 299 removed outlier: 7.411A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N CYS 3 240 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N THR 3 215 " --> pdb=" O CYS 3 240 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA 3 242 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N ALA 3 217 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N ALA 3 244 " --> pdb=" O ALA 3 217 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 321 through 325 removed outlier: 6.252A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1326 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: 3.54 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3680 1.35 - 1.47: 2635 1.47 - 1.59: 4659 1.59 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 11050 Sorted by residual: bond pdb=" CAT Z99 21101 " pdb=" OAP Z99 21101 " ideal model delta sigma weight residual 1.364 1.456 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" CAT Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.364 1.452 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CAS Z99 21101 " pdb=" OAP Z99 21101 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CAS Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.369 1.450 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" CAO Z99 32002 " pdb=" CAZ Z99 32002 " ideal model delta sigma weight residual 1.488 1.530 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 11045 not shown) Histogram of bond angle deviations from ideal: 59.82 - 74.67: 6 74.67 - 89.53: 0 89.53 - 104.38: 162 104.38 - 119.23: 8913 119.23 - 134.09: 6017 Bond angle restraints: 15098 Sorted by residual: angle pdb=" N VAL 3 639 " pdb=" CA VAL 3 639 " pdb=" C VAL 3 639 " ideal model delta sigma weight residual 113.20 108.69 4.51 9.60e-01 1.09e+00 2.21e+01 angle pdb=" CA GLY 2 570 " pdb=" C GLY 2 570 " pdb=" N PRO 2 571 " ideal model delta sigma weight residual 119.27 116.63 2.64 8.50e-01 1.38e+00 9.63e+00 angle pdb=" CAX Z99 21101 " pdb=" CAZ Z99 21101 " pdb=" CAY Z99 21101 " ideal model delta sigma weight residual 120.67 112.19 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" N PHE 3 275 " pdb=" CA PHE 3 275 " pdb=" C PHE 3 275 " ideal model delta sigma weight residual 110.44 107.09 3.35 1.20e+00 6.94e-01 7.81e+00 angle pdb=" CA GLY 2 570 " pdb=" C GLY 2 570 " pdb=" O GLY 2 570 " ideal model delta sigma weight residual 119.65 121.51 -1.86 6.70e-01 2.23e+00 7.72e+00 ... (remaining 15093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6131 17.76 - 35.53: 363 35.53 - 53.29: 66 53.29 - 71.05: 14 71.05 - 88.81: 7 Dihedral angle restraints: 6581 sinusoidal: 2152 harmonic: 4429 Sorted by residual: dihedral pdb=" CB CYS 2 50 " pdb=" SG CYS 2 50 " pdb=" SG CYS 2 92 " pdb=" CB CYS 2 92 " ideal model delta sinusoidal sigma weight residual 93.00 9.12 83.88 1 1.00e+01 1.00e-02 8.58e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 12.74 80.26 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS 3 412 " pdb=" SG CYS 3 412 " pdb=" SG CYS 3 419 " pdb=" CB CYS 3 419 " ideal model delta sinusoidal sigma weight residual 93.00 171.91 -78.91 1 1.00e+01 1.00e-02 7.75e+01 ... (remaining 6578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.054: 1749 1.054 - 2.108: 0 2.108 - 3.162: 0 3.162 - 4.216: 0 4.216 - 5.270: 2 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAU Z99 32002 " pdb=" CAV Z99 32002 " both_signs ideal model delta sigma weight residual False 2.61 -2.66 5.27 2.00e-01 2.50e+01 6.94e+02 chirality pdb=" CAW Z99 21101 " pdb=" CAN Z99 21101 " pdb=" CAU Z99 21101 " pdb=" CAV Z99 21101 " both_signs ideal model delta sigma weight residual False 2.61 -2.55 5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" CAZ Z99 32002 " pdb=" CAO Z99 32002 " pdb=" CAX Z99 32002 " pdb=" CAY Z99 32002 " both_signs ideal model delta sigma weight residual True 2.39 -2.75 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 1748 not shown) Planarity restraints: 1993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 3 504 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO 3 505 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO 3 505 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 3 505 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 2 433 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO 2 434 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO 2 434 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO 2 434 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 3 261 " 0.125 9.50e-02 1.11e+02 5.64e-02 2.51e+00 pdb=" NE ARG 3 261 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG 3 261 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG 3 261 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG 3 261 " 0.000 2.00e-02 2.50e+03 ... (remaining 1990 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2668 2.79 - 3.32: 10392 3.32 - 3.85: 17533 3.85 - 4.37: 19974 4.37 - 4.90: 34311 Nonbonded interactions: 84878 Sorted by model distance: nonbonded pdb=" O ASP 3 97 " pdb=" NE2 GLN 3 108 " model vdw 2.268 2.520 nonbonded pdb=" OD1 ASP 2 49 " pdb=" NZ LYS 2 94 " model vdw 2.301 2.520 nonbonded pdb=" OG SER 3 218 " pdb=" OD2 ASP 3 280 " model vdw 2.312 2.440 nonbonded pdb=" OG SER 2 148 " pdb=" OG SER 2 167 " model vdw 2.318 2.440 nonbonded pdb=" O SER 2 784 " pdb=" OG SER 2 784 " model vdw 2.335 2.440 ... (remaining 84873 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 10.650 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.580 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 : 0.003 0.092 11050 Z= 0.188 Angle : 0.545 8.483 15098 Z= 0.268 Chirality : 0.181 5.270 1751 Planarity : 0.003 0.056 1991 Dihedral : 11.820 88.814 3661 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1515 helix: 1.83 (0.20), residues: 668 sheet: -0.52 (0.45), residues: 141 loop : -1.51 (0.21), residues: 706 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.182 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.9581 time to fit residues: 151.1493 Evaluate side-chains 110 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.314 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.7229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 41 HIS 2 42 GLN 2 439 ASN 3 67 GLN 3 357 GLN 3 445 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 11050 Z= 0.406 Angle : 0.639 12.731 15098 Z= 0.320 Chirality : 0.044 0.192 1751 Planarity : 0.005 0.038 1991 Dihedral : 4.178 24.549 1641 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1515 helix: 1.74 (0.20), residues: 684 sheet: -1.06 (0.39), residues: 159 loop : -1.72 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 1.252 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 122 average time/residue: 0.9468 time to fit residues: 128.3511 Evaluate side-chains 107 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.2016 time to fit residues: 2.5727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 137 optimal weight: 30.0000 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN 3 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 11050 Z= 0.286 Angle : 0.549 9.645 15098 Z= 0.276 Chirality : 0.042 0.144 1751 Planarity : 0.004 0.039 1991 Dihedral : 4.084 19.927 1641 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1515 helix: 1.80 (0.21), residues: 683 sheet: -1.18 (0.39), residues: 159 loop : -1.68 (0.22), residues: 673 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.155 Fit side-chains outliers start: 31 outliers final: 15 residues processed: 123 average time/residue: 0.8888 time to fit residues: 123.1108 Evaluate side-chains 109 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.2372 time to fit residues: 2.8287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 101 GLN 3 67 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.087 11050 Z= 0.626 Angle : 0.705 8.637 15098 Z= 0.363 Chirality : 0.049 0.245 1751 Planarity : 0.005 0.040 1991 Dihedral : 4.843 28.209 1641 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 5.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1515 helix: 1.53 (0.21), residues: 680 sheet: -1.73 (0.36), residues: 162 loop : -1.92 (0.22), residues: 673 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 99 time to evaluate : 1.217 Fit side-chains outliers start: 50 outliers final: 25 residues processed: 133 average time/residue: 0.8937 time to fit residues: 133.0060 Evaluate side-chains 117 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 92 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 0.3380 time to fit residues: 4.2366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11050 Z= 0.210 Angle : 0.524 10.582 15098 Z= 0.267 Chirality : 0.041 0.144 1751 Planarity : 0.004 0.038 1991 Dihedral : 4.377 29.350 1641 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 3.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.22), residues: 1515 helix: 1.74 (0.21), residues: 687 sheet: -1.44 (0.39), residues: 156 loop : -1.88 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.224 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 123 average time/residue: 0.9596 time to fit residues: 131.2425 Evaluate side-chains 115 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.5382 time to fit residues: 3.5505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 473 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 11050 Z= 0.501 Angle : 0.637 8.401 15098 Z= 0.325 Chirality : 0.046 0.201 1751 Planarity : 0.005 0.039 1991 Dihedral : 4.660 31.386 1641 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.22), residues: 1515 helix: 1.55 (0.21), residues: 689 sheet: -1.69 (0.37), residues: 162 loop : -2.03 (0.21), residues: 664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 1.206 Fit side-chains outliers start: 37 outliers final: 26 residues processed: 123 average time/residue: 0.9054 time to fit residues: 124.4065 Evaluate side-chains 117 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.272 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.7725 time to fit residues: 6.0257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11050 Z= 0.252 Angle : 0.536 8.277 15098 Z= 0.273 Chirality : 0.042 0.143 1751 Planarity : 0.004 0.038 1991 Dihedral : 4.420 33.253 1641 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1515 helix: 1.75 (0.21), residues: 681 sheet: -1.51 (0.39), residues: 156 loop : -1.97 (0.21), residues: 678 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.161 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 117 average time/residue: 0.9022 time to fit residues: 117.9050 Evaluate side-chains 115 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.188 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 1.0706 time to fit residues: 2.8392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 0.0970 chunk 28 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 30.0000 chunk 140 optimal weight: 9.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN 3 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11050 Z= 0.187 Angle : 0.502 7.964 15098 Z= 0.255 Chirality : 0.040 0.141 1751 Planarity : 0.003 0.038 1991 Dihedral : 4.197 33.109 1641 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1515 helix: 1.91 (0.21), residues: 680 sheet: -1.32 (0.42), residues: 146 loop : -1.87 (0.21), residues: 689 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 1.248 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 118 average time/residue: 0.9066 time to fit residues: 120.1656 Evaluate side-chains 114 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.6238 time to fit residues: 3.9651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 11050 Z= 0.269 Angle : 0.539 7.854 15098 Z= 0.272 Chirality : 0.042 0.141 1751 Planarity : 0.004 0.039 1991 Dihedral : 4.285 30.423 1641 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.22), residues: 1515 helix: 1.80 (0.21), residues: 687 sheet: -1.34 (0.40), residues: 156 loop : -1.90 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.178 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 121 average time/residue: 0.9729 time to fit residues: 130.7696 Evaluate side-chains 114 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.1007 time to fit residues: 1.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 40.0000 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.093 11050 Z= 0.649 Angle : 0.723 9.388 15098 Z= 0.369 Chirality : 0.050 0.221 1751 Planarity : 0.005 0.043 1991 Dihedral : 4.894 28.412 1641 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.22), residues: 1515 helix: 1.48 (0.21), residues: 689 sheet: -1.90 (0.37), residues: 163 loop : -2.14 (0.21), residues: 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3030 Ramachandran restraints generated. 1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 97 time to evaluate : 1.125 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 118 average time/residue: 0.9134 time to fit residues: 120.5951 Evaluate side-chains 118 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.8057 time to fit residues: 3.5720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.0770 chunk 111 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.212894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135867 restraints weight = 13014.905| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.26 r_work: 0.3356 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11050 Z= 0.211 Angle : 0.539 8.585 15098 Z= 0.274 Chirality : 0.041 0.181 1751 Planarity : 0.004 0.037 1991 Dihedral : 4.413 31.713 1641 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1515 helix: 1.81 (0.21), residues: 682 sheet: -1.50 (0.42), residues: 144 loop : -2.00 (0.21), residues: 689 =============================================================================== Job complete usr+sys time: 3512.74 seconds wall clock time: 63 minutes 20.73 seconds (3800.73 seconds total)