Starting phenix.real_space_refine on Sun Apr 7 15:14:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/04_2024/8jcu_36165_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/04_2024/8jcu_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_36165/04_2024/8jcu_36165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/04_2024/8jcu_36165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/04_2024/8jcu_36165_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcu_36165/04_2024/8jcu_36165_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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-dev-5288/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.21, per 1000 atoms: 0.57 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: 4.49 Conformation dependent library (CDL) restraints added in 2.4 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: 2.49 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: 3.27 Time building geometry restraints manager: 4.85 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 - 35.94: 6554 35.94 - 71.89: 92 71.89 - 107.83: 13 107.83 - 143.78: 4 143.78 - 179.72: 2 Dihedral angle restraints: 6665 sinusoidal: 2236 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 6662 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: 3.390 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: 10.420 Check model and map are aligned: 0.160 Set scattering table: 0.080 Process input model: 32.170 Find NCS groups from input model: 0.390 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:18.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.100 ------------------------------------------------------------------------------- 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 : 14.086 179.723 3745 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 % Allowed : 0.21 % Favored : 99.79 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 487 HIS 0.003 0.000 HIS 3 498 PHE 0.021 0.001 PHE 3 195 TYR 0.009 0.001 TYR 3 104 ARG 0.013 0.000 ARG 3 261 *********************** 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 : 1.172 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 142 average time/residue: 0.9351 time to fit residues: 147.1213 Evaluate side-chains 110 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 439 ASN 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: 2.9990 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: 0.5980 chunk 138 optimal weight: 0.5980 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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 3 470 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1916 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= 0.455 Angle : 0.663 10.489 15098 Z= 0.334 Chirality : 0.046 0.196 1751 Planarity : 0.005 0.040 1991 Dihedral : 5.270 40.192 1727 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.52 % Allowed : 9.78 % Favored : 87.70 % 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: -0.13 (0.21), residues: 1515 helix: 1.64 (0.20), residues: 684 sheet: -1.15 (0.39), residues: 158 loop : -1.71 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 3 297 HIS 0.010 0.002 HIS 2 390 PHE 0.026 0.002 PHE 3 195 TYR 0.019 0.002 TYR 2 468 ARG 0.007 0.001 ARG 3 235 *********************** 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 142 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.7633 (mt) cc_final: 0.7386 (mt) REVERT: 2 286 ASN cc_start: 0.7863 (t0) cc_final: 0.7661 (t0) REVERT: 2 413 VAL cc_start: 0.4612 (t) cc_final: 0.4258 (p) REVERT: 2 524 PRO cc_start: 0.6274 (Cg_exo) cc_final: 0.6004 (Cg_endo) REVERT: 3 228 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6749 (tm-30) REVERT: 3 235 ARG cc_start: 0.7133 (mtm110) cc_final: 0.6831 (mtm-85) outliers start: 24 outliers final: 10 residues processed: 130 average time/residue: 0.9558 time to fit residues: 138.5940 Evaluate side-chains 113 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 213 GLU Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 817 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 0.5980 chunk 137 optimal weight: 30.0000 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7305 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11050 Z= 0.221 Angle : 0.525 7.157 15098 Z= 0.263 Chirality : 0.041 0.174 1751 Planarity : 0.004 0.039 1991 Dihedral : 4.740 35.453 1725 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.05 % Allowed : 10.94 % Favored : 86.01 % 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: 0.00 (0.22), residues: 1515 helix: 1.83 (0.21), residues: 684 sheet: -1.21 (0.40), residues: 151 loop : -1.70 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 520 HIS 0.006 0.001 HIS 3 498 PHE 0.021 0.001 PHE 3 195 TYR 0.014 0.001 TYR 2 178 ARG 0.005 0.000 ARG 2 416 *********************** 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 133 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 104 time to evaluate : 1.176 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7672 (mt) cc_final: 0.7393 (mt) REVERT: 2 286 ASN cc_start: 0.7863 (t0) cc_final: 0.7480 (t0) REVERT: 2 524 PRO cc_start: 0.6374 (Cg_exo) cc_final: 0.6124 (Cg_endo) REVERT: 3 228 GLU cc_start: 0.7455 (tm-30) cc_final: 0.6917 (tm-30) REVERT: 3 235 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6857 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6848 (mm) REVERT: 3 275 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7680 (m-80) outliers start: 29 outliers final: 15 residues processed: 124 average time/residue: 0.8771 time to fit residues: 121.2557 Evaluate side-chains 115 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER 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: 0.5980 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 72 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 11050 Z= 0.702 Angle : 0.769 9.480 15098 Z= 0.392 Chirality : 0.051 0.261 1751 Planarity : 0.006 0.047 1991 Dihedral : 6.988 66.097 1725 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.57 % Allowed : 10.73 % Favored : 83.70 % 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: -0.61 (0.21), residues: 1515 helix: 1.41 (0.20), residues: 682 sheet: -1.79 (0.36), residues: 162 loop : -2.04 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 3 303 HIS 0.010 0.002 HIS 3 498 PHE 0.021 0.003 PHE 3 74 TYR 0.022 0.003 TYR 2 178 ARG 0.005 0.001 ARG 3 347 *********************** 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 151 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 98 time to evaluate : 1.136 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7637 (mt) cc_final: 0.7398 (mt) REVERT: 2 286 ASN cc_start: 0.7698 (t0) cc_final: 0.7362 (t0) REVERT: 2 332 GLN cc_start: 0.7795 (mt0) cc_final: 0.7455 (mt0) REVERT: 2 520 TRP cc_start: 0.5274 (OUTLIER) cc_final: 0.4977 (t-100) REVERT: 2 524 PRO cc_start: 0.6504 (Cg_exo) cc_final: 0.6296 (Cg_endo) REVERT: 3 203 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: 3 228 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6892 (tm-30) REVERT: 3 252 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6803 (mm) REVERT: 3 257 ASP cc_start: 0.7432 (t0) cc_final: 0.7153 (t70) REVERT: 3 275 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7663 (m-80) outliers start: 53 outliers final: 29 residues processed: 135 average time/residue: 0.9497 time to fit residues: 141.9671 Evaluate side-chains 126 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 213 GLU Chi-restraints excluded: chain 2 residue 279 LEU Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 520 TRP Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 113 VAL Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 203 GLU Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 260 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 310 ILE Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 438 ILE Chi-restraints excluded: chain 3 residue 817 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7364 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11050 Z= 0.243 Angle : 0.545 9.604 15098 Z= 0.276 Chirality : 0.042 0.162 1751 Planarity : 0.004 0.038 1991 Dihedral : 6.062 59.593 1725 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.26 % Allowed : 14.72 % Favored : 82.02 % 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: -0.29 (0.22), residues: 1515 helix: 1.68 (0.21), residues: 687 sheet: -1.62 (0.38), residues: 162 loop : -1.92 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 520 HIS 0.009 0.001 HIS 3 498 PHE 0.017 0.002 PHE 3 195 TYR 0.016 0.001 TYR 3 256 ARG 0.004 0.000 ARG 2 352 *********************** 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 127 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 96 time to evaluate : 1.041 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7540 (mt) cc_final: 0.7270 (mt) REVERT: 2 286 ASN cc_start: 0.7848 (t0) cc_final: 0.7507 (t0) REVERT: 2 332 GLN cc_start: 0.7717 (mt0) cc_final: 0.7443 (mt0) REVERT: 3 228 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7006 (tm-30) REVERT: 3 252 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6761 (mm) outliers start: 31 outliers final: 14 residues processed: 117 average time/residue: 0.9430 time to fit residues: 122.5938 Evaluate side-chains 109 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11050 Z= 0.201 Angle : 0.514 8.837 15098 Z= 0.259 Chirality : 0.041 0.142 1751 Planarity : 0.004 0.038 1991 Dihedral : 5.610 54.441 1725 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.26 % Allowed : 15.25 % Favored : 81.49 % 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: -0.14 (0.22), residues: 1515 helix: 1.84 (0.21), residues: 687 sheet: -1.38 (0.39), residues: 156 loop : -1.92 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 487 HIS 0.011 0.001 HIS 3 498 PHE 0.016 0.001 PHE 3 195 TYR 0.017 0.001 TYR 3 256 ARG 0.004 0.000 ARG 2 411 *********************** 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 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 1.202 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7547 (mt) cc_final: 0.7257 (mt) REVERT: 2 286 ASN cc_start: 0.7878 (t0) cc_final: 0.7592 (t0) REVERT: 2 332 GLN cc_start: 0.7673 (mt0) cc_final: 0.7390 (mt0) REVERT: 2 379 MET cc_start: 0.8031 (ttt) cc_final: 0.7784 (ttt) REVERT: 3 228 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6943 (tm-30) REVERT: 3 235 ARG cc_start: 0.7170 (mtm110) cc_final: 0.6908 (mtm-85) REVERT: 3 252 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6783 (mm) REVERT: 3 262 GLU cc_start: 0.7477 (tp30) cc_final: 0.6995 (tp30) outliers start: 31 outliers final: 21 residues processed: 121 average time/residue: 0.9514 time to fit residues: 127.4499 Evaluate side-chains 117 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 509 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 146 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11050 Z= 0.292 Angle : 0.546 8.606 15098 Z= 0.277 Chirality : 0.042 0.193 1751 Planarity : 0.004 0.038 1991 Dihedral : 5.768 56.244 1725 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.58 % Allowed : 14.51 % Favored : 81.91 % 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: -0.17 (0.22), residues: 1515 helix: 1.81 (0.21), residues: 687 sheet: -1.43 (0.39), residues: 156 loop : -1.93 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 487 HIS 0.010 0.001 HIS 3 498 PHE 0.015 0.002 PHE 3 195 TYR 0.017 0.002 TYR 3 256 ARG 0.003 0.000 ARG 2 416 *********************** 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 129 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 1.151 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7578 (mt) cc_final: 0.7290 (mt) REVERT: 2 286 ASN cc_start: 0.7855 (t0) cc_final: 0.7577 (t0) REVERT: 2 332 GLN cc_start: 0.7683 (mt0) cc_final: 0.7389 (mt0) REVERT: 3 228 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7022 (tm-30) REVERT: 3 252 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6790 (mm) REVERT: 3 262 GLU cc_start: 0.7542 (tp30) cc_final: 0.7062 (tp30) REVERT: 3 275 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7640 (m-80) outliers start: 34 outliers final: 27 residues processed: 121 average time/residue: 0.9040 time to fit residues: 122.0018 Evaluate side-chains 123 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 59 ARG Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 113 VAL Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 473 ASN Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 532 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 115 optimal weight: 0.8980 chunk 133 optimal weight: 30.0000 chunk 140 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11050 Z= 0.203 Angle : 0.519 8.374 15098 Z= 0.262 Chirality : 0.041 0.156 1751 Planarity : 0.004 0.038 1991 Dihedral : 5.538 53.291 1725 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.05 % Allowed : 15.35 % Favored : 81.60 % 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: -0.09 (0.22), residues: 1515 helix: 1.89 (0.21), residues: 687 sheet: -1.38 (0.41), residues: 146 loop : -1.91 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 520 HIS 0.010 0.001 HIS 3 498 PHE 0.015 0.001 PHE 3 195 TYR 0.023 0.001 TYR 3 256 ARG 0.003 0.000 ARG 2 352 *********************** 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 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.218 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7601 (mt) cc_final: 0.7313 (mt) REVERT: 2 286 ASN cc_start: 0.7856 (t0) cc_final: 0.7571 (t0) REVERT: 2 332 GLN cc_start: 0.7677 (mt0) cc_final: 0.7400 (mt0) REVERT: 3 228 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7002 (tm-30) REVERT: 3 252 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6766 (mm) REVERT: 3 262 GLU cc_start: 0.7560 (tp30) cc_final: 0.7119 (tp30) outliers start: 29 outliers final: 23 residues processed: 120 average time/residue: 0.8512 time to fit residues: 114.2853 Evaluate side-chains 121 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 113 VAL Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 509 CYS 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: 0.0670 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 50.0000 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11050 Z= 0.352 Angle : 0.583 8.207 15098 Z= 0.293 Chirality : 0.043 0.157 1751 Planarity : 0.004 0.039 1991 Dihedral : 6.005 59.227 1725 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.47 % Allowed : 15.14 % Favored : 81.39 % 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: -0.23 (0.22), residues: 1515 helix: 1.77 (0.21), residues: 689 sheet: -1.59 (0.38), residues: 162 loop : -1.95 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 2 520 HIS 0.012 0.001 HIS 3 498 PHE 0.015 0.002 PHE 3 74 TYR 0.023 0.002 TYR 3 256 ARG 0.003 0.000 ARG 3 277 *********************** 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 128 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 1.151 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7602 (mt) cc_final: 0.7319 (mt) REVERT: 2 286 ASN cc_start: 0.7876 (t0) cc_final: 0.7596 (t0) REVERT: 2 332 GLN cc_start: 0.7704 (mt0) cc_final: 0.7402 (mt0) REVERT: 3 228 GLU cc_start: 0.7508 (tm-30) cc_final: 0.6928 (tm-30) REVERT: 3 252 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6787 (mm) REVERT: 3 262 GLU cc_start: 0.7551 (tp30) cc_final: 0.7118 (tp30) outliers start: 33 outliers final: 27 residues processed: 120 average time/residue: 0.8766 time to fit residues: 117.4008 Evaluate side-chains 121 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 110 LEU Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 113 VAL Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 509 CYS Chi-restraints excluded: chain 3 residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 40.0000 chunk 139 optimal weight: 40.0000 chunk 120 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 30.0000 overall best weight: 1.6962 ------------------------------------------------------------------------------- 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: 0.7412 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11050 Z= 0.437 Angle : 0.632 8.315 15098 Z= 0.319 Chirality : 0.045 0.173 1751 Planarity : 0.004 0.039 1991 Dihedral : 6.624 70.999 1725 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.94 % Allowed : 15.77 % Favored : 81.28 % 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: -0.42 (0.22), residues: 1515 helix: 1.67 (0.21), residues: 685 sheet: -1.78 (0.37), residues: 162 loop : -2.07 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 2 520 HIS 0.013 0.001 HIS 3 498 PHE 0.017 0.002 PHE 2 189 TYR 0.025 0.002 TYR 3 256 ARG 0.004 0.000 ARG 3 189 ********************** 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 126 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.163 Fit side-chains REVERT: 2 258 LEU cc_start: 0.7577 (mt) cc_final: 0.7320 (mt) REVERT: 2 286 ASN cc_start: 0.7889 (t0) cc_final: 0.7575 (t0) REVERT: 2 332 GLN cc_start: 0.7721 (mt0) cc_final: 0.7457 (mt0) REVERT: 3 228 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6815 (tm-30) REVERT: 3 252 ILE cc_start: 0.7029 (OUTLIER) cc_final: 0.6741 (mm) REVERT: 3 262 GLU cc_start: 0.7552 (tp30) cc_final: 0.7127 (tp30) outliers start: 28 outliers final: 25 residues processed: 120 average time/residue: 0.9063 time to fit residues: 121.2310 Evaluate side-chains 122 residues out of total 1296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 110 LEU Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 307 SER Chi-restraints excluded: chain 2 residue 438 HIS Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 616 CYS Chi-restraints excluded: chain 2 residue 795 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 113 VAL Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 278 SER Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 509 CYS Chi-restraints excluded: chain 3 residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.2980 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 0.0060 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 67 GLN ** 3 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.213261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137328 restraints weight = 13010.190| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.14 r_work: 0.3366 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11050 Z= 0.182 Angle : 0.522 8.550 15098 Z= 0.262 Chirality : 0.041 0.142 1751 Planarity : 0.004 0.038 1991 Dihedral : 5.861 61.272 1725 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.21 % Allowed : 17.03 % Favored : 80.76 % 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: -0.12 (0.22), residues: 1515 helix: 1.93 (0.21), residues: 680 sheet: -1.49 (0.41), residues: 146 loop : -1.93 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 520 HIS 0.010 0.001 HIS 3 498 PHE 0.016 0.001 PHE 3 195 TYR 0.022 0.001 TYR 3 256 ARG 0.003 0.000 ARG 2 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3607.94 seconds wall clock time: 65 minutes 9.49 seconds (3909.49 seconds total)