Starting phenix.real_space_refine on Fri Jan 19 08:36:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/01_2024/8jcy_36169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/01_2024/8jcy_36169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/01_2024/8jcy_36169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/01_2024/8jcy_36169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/01_2024/8jcy_36169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/01_2024/8jcy_36169_updated.pdb" } resolution = 2.9 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= 0.049 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 6921 2.51 5 N 1880 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 429": "OD1" <-> "OD2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 83": "OD1" <-> "OD2" Residue "3 GLU 111": "OE1" <-> "OE2" Residue "3 PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10874 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5258 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 37, 'TRANS': 722} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 891 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 6, 'PHE:plan': 12, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 406 Chain: "3" Number of atoms: 5340 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 765, 5330 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 15, 'GLU:plan': 15, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 421 Conformer: "B" Number of residues, atoms: 765, 5330 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 763 Unresolved non-hydrogen angles: 969 Unresolved non-hydrogen dihedrals: 643 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 13, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 15, 'GLU:plan': 15, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 421 bond proxies already assigned to first conformer: 5422 Chain: "2" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 124 Unusual residues: {'CLR': 3, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 152 Unusual residues: {'CLR': 4, 'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS 3 485 " occ=0.68 ... (18 atoms not shown) pdb=" NE2BHIS 3 485 " occ=0.32 Time building chain proxies: 8.81, per 1000 atoms: 0.81 Number of scatterers: 10874 At special positions: 0 Unit cell: (89.964, 122.094, 183.141, 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 2013 8.00 N 1880 7.00 C 6921 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=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.04 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.04 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 22001 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 3.5 seconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 43.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain '2' and resid 59 through 73 Processing helix chain '2' and resid 95 through 102 removed outlier: 3.604A pdb=" N GLU 2 100 " --> pdb=" O THR 2 96 " (cutoff:3.500A) Processing helix chain '2' and resid 105 through 109 Processing helix chain '2' and resid 145 through 158 removed outlier: 4.252A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) 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 188 through 201 Processing helix chain '2' and resid 215 through 229 removed outlier: 4.695A pdb=" N THR 2 219 " --> pdb=" O ASP 2 215 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU 2 226 " --> pdb=" O GLU 2 222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU 2 227 " --> pdb=" O ALA 2 223 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 258 Processing helix chain '2' and resid 272 through 284 Processing helix chain '2' and resid 325 through 332 removed outlier: 3.517A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 352 Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 408 through 410 No H-bonds generated for 'chain '2' and resid 408 through 410' Processing helix chain '2' and resid 415 through 421 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 590 removed outlier: 3.869A pdb=" N VAL 2 590 " --> pdb=" O LEU 2 586 " (cutoff:3.500A) Processing helix chain '2' and resid 596 through 600 Processing helix chain '2' and resid 603 through 624 Processing helix chain '2' and resid 629 through 658 Processing helix chain '2' and resid 676 through 700 Processing helix chain '2' and resid 726 through 748 Processing helix chain '2' and resid 756 through 783 Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 787 through 807 Processing helix chain '2' and resid 809 through 818 Processing helix chain '3' and resid 67 through 81 Processing helix chain '3' and resid 102 through 116 removed outlier: 3.685A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER 3 116 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.255A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 179 Processing helix chain '3' and resid 195 through 207 removed outlier: 3.539A pdb=" N LYS 3 199 " --> pdb=" O PHE 3 195 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 236 Processing helix chain '3' and resid 255 through 264 Processing helix chain '3' and resid 278 through 290 Processing helix chain '3' and resid 331 through 338 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: 4.368A 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 Processing helix chain '3' and resid 639 through 664 removed outlier: 3.529A pdb=" N LYS 3 662 " --> pdb=" O LEU 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 683 through 708 removed outlier: 3.895A pdb=" N LEU 3 707 " --> pdb=" O VAL 3 703 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 3 708 " --> pdb=" O SER 3 704 " (cutoff:3.500A) Processing helix chain '3' and resid 734 through 757 removed outlier: 3.757A pdb=" N ASP 3 744 " --> pdb=" O SER 3 740 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL 3 745 " --> pdb=" O LEU 3 741 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR 3 754 " --> pdb=" O LEU 3 750 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA 3 755 " --> pdb=" O CYS 3 751 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 791 removed outlier: 3.528A pdb=" N THR 3 777 " --> pdb=" O PHE 3 773 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU 3 786 " --> pdb=" O TRP 3 782 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.785A pdb=" N VAL 3 791 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 5.197A 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: 6.562A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU 2 37 " --> pdb=" O ILE 2 140 " (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: 6.181A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.113A 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: 3.777A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 33 through 35 removed outlier: 6.234A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY 3 147 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY 3 147 " --> pdb=" O PRO 3 167 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE 3 169 " --> pdb=" O GLY 3 147 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 244 through 247 removed outlier: 7.178A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL 3 247 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA 3 217 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 321 through 325 removed outlier: 6.470A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER 3 491 " --> pdb=" O AHIS 3 485 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1387 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: 3.12 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3627 1.34 - 1.46: 2552 1.46 - 1.58: 4862 1.58 - 1.70: 0 1.70 - 1.82: 77 Bond restraints: 11118 Sorted by residual: bond pdb=" CAT Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" CAT Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.96e+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 1.63e+01 bond pdb=" CAS Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" CAO Z99 22002 " pdb=" CAZ Z99 22002 " ideal model delta sigma weight residual 1.488 1.533 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 11113 not shown) Histogram of bond angle deviations from ideal: 59.60 - 74.47: 6 74.47 - 89.35: 0 89.35 - 104.23: 184 104.23 - 119.10: 8988 119.10 - 133.98: 6083 Bond angle restraints: 15261 Sorted by residual: angle pdb=" C VAL 3 701 " pdb=" N MET 3 702 " pdb=" CA MET 3 702 " ideal model delta sigma weight residual 121.58 115.13 6.45 1.95e+00 2.63e-01 1.09e+01 angle pdb=" CAX Z99 32002 " pdb=" CAZ Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 120.67 111.08 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CAX Z99 22002 " pdb=" CAZ Z99 22002 " pdb=" CAY Z99 22002 " ideal model delta sigma weight residual 120.67 111.17 9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 117.71 108.57 9.14 3.00e+00 1.11e-01 9.28e+00 angle pdb=" CA MET 3 702 " pdb=" CB MET 3 702 " pdb=" CG MET 3 702 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.09e+00 ... (remaining 15256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 6898 35.91 - 71.83: 75 71.83 - 107.74: 16 107.74 - 143.66: 2 143.66 - 179.57: 2 Dihedral angle restraints: 6993 sinusoidal: 2569 harmonic: 4424 Sorted by residual: dihedral pdb=" CB CYS 2 234 " pdb=" SG CYS 2 234 " pdb=" SG CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sinusoidal sigma weight residual -86.00 -170.72 84.72 1 1.00e+01 1.00e-02 8.72e+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 12.17 80.83 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS 2 504 " pdb=" SG CYS 2 504 " pdb=" SG CYS 2 522 " pdb=" CB CYS 2 522 " ideal model delta sinusoidal sigma weight residual 93.00 16.37 76.63 1 1.00e+01 1.00e-02 7.38e+01 ... (remaining 6990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.034: 1803 1.034 - 2.068: 0 2.068 - 3.101: 0 3.101 - 4.135: 0 4.135 - 5.169: 2 Chirality restraints: 1805 Sorted by residual: chirality pdb=" CAW Z99 22002 " pdb=" CAN Z99 22002 " pdb=" CAU Z99 22002 " pdb=" CAV Z99 22002 " both_signs ideal model delta sigma weight residual False 2.61 -2.56 5.17 2.00e-01 2.50e+01 6.68e+02 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 -2.26 4.87 2.00e-01 2.50e+01 5.93e+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 -2.70 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 1802 not shown) Planarity restraints: 1967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG 2 411 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO 2 412 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO 2 412 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO 2 412 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU 3 224 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C GLU 3 224 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU 3 224 " -0.013 2.00e-02 2.50e+03 pdb=" N THR 3 225 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 3 532 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO 3 533 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO 3 533 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO 3 533 " 0.022 5.00e-02 4.00e+02 ... (remaining 1964 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 719 2.74 - 3.28: 10851 3.28 - 3.82: 18275 3.82 - 4.36: 19981 4.36 - 4.90: 35317 Nonbonded interactions: 85143 Sorted by model distance: nonbonded pdb=" OG1 THR 2 205 " pdb=" O SER 2 498 " model vdw 2.200 2.440 nonbonded pdb=" O ASP 3 97 " pdb=" NE2 GLN 3 108 " model vdw 2.200 2.520 nonbonded pdb=" O ALA 2 746 " pdb=" OG1 THR 2 749 " model vdw 2.264 2.440 nonbonded pdb=" OG SER 3 154 " pdb=" OG SER 3 173 " model vdw 2.274 2.440 nonbonded pdb=" OG SER 3 327 " pdb=" O SER 3 388 " model vdw 2.304 2.440 ... (remaining 85138 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=0.02 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: 1.920 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: 0.000 Extract box with map and model: 10.440 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 36.350 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 0.089 11118 Z= 0.205 Angle : 0.533 9.588 15261 Z= 0.250 Chirality : 0.172 5.169 1805 Planarity : 0.004 0.072 1965 Dihedral : 12.993 179.571 4075 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 0.76 (0.23), residues: 1516 helix: 2.60 (0.20), residues: 693 sheet: -0.75 (0.47), residues: 151 loop : -1.55 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 706 HIS 0.001 0.000 HIS 2 438 PHE 0.012 0.001 PHE 3 275 TYR 0.023 0.001 TYR 3 104 ARG 0.003 0.000 ARG 2 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.279 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7669 (m100) cc_final: 0.7389 (m100) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.8999 time to fit residues: 136.9601 Evaluate side-chains 106 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 0.9980 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11118 Z= 0.251 Angle : 0.561 9.398 15261 Z= 0.279 Chirality : 0.042 0.252 1805 Planarity : 0.004 0.050 1965 Dihedral : 5.105 54.796 2169 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.96 % Allowed : 8.29 % Favored : 89.75 % 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: 0.41 (0.22), residues: 1516 helix: 2.17 (0.20), residues: 698 sheet: -0.97 (0.44), residues: 158 loop : -1.59 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 297 HIS 0.004 0.001 HIS 2 41 PHE 0.025 0.002 PHE 2 589 TYR 0.021 0.002 TYR 3 104 ARG 0.004 0.000 ARG 2 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 1.202 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7797 (m100) cc_final: 0.7472 (m100) REVERT: 3 102 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.6914 (m-30) outliers start: 18 outliers final: 10 residues processed: 127 average time/residue: 0.8639 time to fit residues: 122.2781 Evaluate side-chains 114 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11118 Z= 0.274 Angle : 0.540 8.068 15261 Z= 0.273 Chirality : 0.042 0.186 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.149 55.601 2169 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.94 % Allowed : 10.14 % Favored : 86.91 % 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: 0.26 (0.22), residues: 1516 helix: 2.04 (0.20), residues: 698 sheet: -1.09 (0.43), residues: 158 loop : -1.64 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 297 HIS 0.004 0.001 HIS 2 41 PHE 0.014 0.002 PHE 2 589 TYR 0.018 0.002 TYR 3 186 ARG 0.003 0.000 ARG 3 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.202 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7819 (m100) cc_final: 0.7459 (m100) REVERT: 3 102 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: 3 228 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: 3 387 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6228 (tm-30) outliers start: 27 outliers final: 16 residues processed: 119 average time/residue: 0.8603 time to fit residues: 114.0285 Evaluate side-chains 123 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Chi-restraints excluded: chain 3 residue 473 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 332 GLN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11118 Z= 0.329 Angle : 0.573 7.791 15261 Z= 0.290 Chirality : 0.043 0.180 1805 Planarity : 0.004 0.037 1965 Dihedral : 5.637 57.351 2169 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.16 % Allowed : 11.67 % Favored : 85.17 % 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: 1516 helix: 1.90 (0.20), residues: 702 sheet: -1.18 (0.42), residues: 157 loop : -1.75 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 3 297 HIS 0.004 0.001 HIS 2 97 PHE 0.014 0.002 PHE 3 333 TYR 0.021 0.002 TYR 3 186 ARG 0.004 0.000 ARG 3 347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 1.125 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7911 (m100) cc_final: 0.7515 (m100) REVERT: 2 405 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7123 (mmm-85) REVERT: 2 445 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7509 (mpp-170) REVERT: 2 520 TRP cc_start: 0.4431 (m100) cc_final: 0.4074 (m-90) REVERT: 3 102 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: 3 387 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6426 (tm-30) outliers start: 29 outliers final: 15 residues processed: 122 average time/residue: 0.9671 time to fit residues: 130.5296 Evaluate side-chains 115 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 176 SER Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Chi-restraints excluded: chain 3 residue 495 ASN 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: 0.7980 chunk 2 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11118 Z= 0.332 Angle : 0.579 9.862 15261 Z= 0.291 Chirality : 0.042 0.183 1805 Planarity : 0.004 0.038 1965 Dihedral : 6.018 59.951 2169 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.38 % Allowed : 12.98 % Favored : 83.64 % 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: 1516 helix: 1.84 (0.20), residues: 702 sheet: -1.15 (0.43), residues: 147 loop : -1.84 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 3 297 HIS 0.004 0.001 HIS 3 315 PHE 0.020 0.002 PHE 3 195 TYR 0.021 0.002 TYR 3 186 ARG 0.004 0.000 ARG 3 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.217 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7999 (m100) cc_final: 0.7621 (m100) REVERT: 2 375 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: 2 405 ARG cc_start: 0.7464 (mtp85) cc_final: 0.7172 (mmm-85) REVERT: 3 102 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7006 (m-30) REVERT: 3 245 GLU cc_start: 0.7437 (mp0) cc_final: 0.7199 (mm-30) REVERT: 3 387 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: 3 518 MET cc_start: 0.4407 (tpp) cc_final: 0.4173 (mmm) outliers start: 31 outliers final: 18 residues processed: 118 average time/residue: 0.9342 time to fit residues: 122.3057 Evaluate side-chains 115 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 397 ARG Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 264 LEU Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11118 Z= 0.300 Angle : 0.566 8.880 15261 Z= 0.285 Chirality : 0.042 0.180 1805 Planarity : 0.004 0.038 1965 Dihedral : 6.059 59.848 2169 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.05 % Allowed : 13.96 % Favored : 82.99 % 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: 1516 helix: 1.84 (0.20), residues: 702 sheet: -1.11 (0.42), residues: 151 loop : -1.87 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 297 HIS 0.004 0.001 HIS 2 390 PHE 0.014 0.002 PHE 3 333 TYR 0.019 0.002 TYR 3 186 ARG 0.003 0.000 ARG 3 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.155 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8006 (m100) cc_final: 0.7611 (m100) REVERT: 2 375 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.6541 (tm-30) REVERT: 2 405 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7162 (mmm-85) REVERT: 2 520 TRP cc_start: 0.4688 (m100) cc_final: 0.4328 (m-90) REVERT: 3 387 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6250 (tm-30) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.8913 time to fit residues: 116.0541 Evaluate side-chains 113 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 264 LEU Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 381 SER Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 458 THR 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: 0.8980 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.0970 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11118 Z= 0.192 Angle : 0.522 8.435 15261 Z= 0.262 Chirality : 0.040 0.159 1805 Planarity : 0.004 0.058 1965 Dihedral : 5.702 56.978 2169 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.51 % Allowed : 14.94 % Favored : 82.55 % 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: 1516 helix: 2.01 (0.20), residues: 699 sheet: -0.98 (0.43), residues: 151 loop : -1.79 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 355 HIS 0.003 0.001 HIS 2 390 PHE 0.021 0.001 PHE 3 195 TYR 0.012 0.001 TYR 3 186 ARG 0.002 0.000 ARG 2 445 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.195 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7962 (m100) cc_final: 0.7614 (m100) REVERT: 2 375 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: 2 405 ARG cc_start: 0.7348 (mtp85) cc_final: 0.7068 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6113 (tm-30) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.9409 time to fit residues: 118.2305 Evaluate side-chains 108 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 445 ASN Chi-restraints excluded: chain 3 residue 495 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.0770 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11118 Z= 0.195 Angle : 0.539 13.879 15261 Z= 0.267 Chirality : 0.040 0.167 1805 Planarity : 0.004 0.041 1965 Dihedral : 5.625 56.868 2169 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 15.59 % Favored : 81.90 % 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: 1516 helix: 2.00 (0.20), residues: 705 sheet: -0.97 (0.43), residues: 152 loop : -1.76 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 520 HIS 0.002 0.001 HIS 2 390 PHE 0.012 0.001 PHE 2 189 TYR 0.012 0.001 TYR 3 186 ARG 0.001 0.000 ARG 3 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 1.145 Fit side-chains REVERT: 2 337 TRP cc_start: 0.7961 (m100) cc_final: 0.7615 (m100) REVERT: 2 375 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: 2 405 ARG cc_start: 0.7346 (mtp85) cc_final: 0.7065 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6110 (tm-30) outliers start: 23 outliers final: 17 residues processed: 109 average time/residue: 0.8921 time to fit residues: 108.3126 Evaluate side-chains 109 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 445 ASN Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11118 Z= 0.337 Angle : 0.596 13.639 15261 Z= 0.298 Chirality : 0.043 0.191 1805 Planarity : 0.004 0.046 1965 Dihedral : 5.962 57.169 2169 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.84 % Allowed : 15.59 % Favored : 81.57 % 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: 0.04 (0.22), residues: 1516 helix: 1.90 (0.20), residues: 703 sheet: -1.33 (0.41), residues: 159 loop : -1.79 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 2 520 HIS 0.004 0.001 HIS 2 390 PHE 0.023 0.002 PHE 3 195 TYR 0.020 0.002 TYR 3 186 ARG 0.004 0.000 ARG 3 347 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.260 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8032 (m100) cc_final: 0.7651 (m100) REVERT: 2 375 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: 2 405 ARG cc_start: 0.7415 (mtp85) cc_final: 0.7132 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6439 (tm-30) outliers start: 26 outliers final: 18 residues processed: 111 average time/residue: 0.8745 time to fit residues: 108.4271 Evaluate side-chains 113 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 381 SER Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 445 ASN Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 469 GLN ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 11118 Z= 0.502 Angle : 0.685 14.072 15261 Z= 0.343 Chirality : 0.046 0.268 1805 Planarity : 0.005 0.037 1965 Dihedral : 6.590 73.272 2169 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.51 % Allowed : 16.25 % Favored : 81.24 % 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: 1516 helix: 1.68 (0.20), residues: 702 sheet: -1.62 (0.39), residues: 171 loop : -1.96 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 3 297 HIS 0.006 0.002 HIS 2 41 PHE 0.020 0.002 PHE 2 105 TYR 0.026 0.002 TYR 3 186 ARG 0.006 0.001 ARG 3 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 1.176 Fit side-chains REVERT: 2 337 TRP cc_start: 0.8052 (m100) cc_final: 0.7677 (m100) REVERT: 2 375 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.6547 (tm-30) REVERT: 2 405 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7231 (mmm-85) REVERT: 3 387 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.6466 (tm-30) outliers start: 23 outliers final: 19 residues processed: 110 average time/residue: 0.8779 time to fit residues: 107.6934 Evaluate side-chains 113 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 225 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 268 ASN Chi-restraints excluded: chain 3 residue 294 SER Chi-restraints excluded: chain 3 residue 353 ASP Chi-restraints excluded: chain 3 residue 379 ILE Chi-restraints excluded: chain 3 residue 381 SER Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 445 ASN Chi-restraints excluded: chain 3 residue 458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.229813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188287 restraints weight = 30047.315| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 3.48 r_work: 0.3616 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11118 Z= 0.222 Angle : 0.573 16.261 15261 Z= 0.285 Chirality : 0.041 0.176 1805 Planarity : 0.004 0.044 1965 Dihedral : 6.216 64.969 2169 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.07 % Allowed : 16.90 % Favored : 81.03 % 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: -0.06 (0.22), residues: 1516 helix: 1.81 (0.20), residues: 706 sheet: -1.49 (0.40), residues: 169 loop : -1.83 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 520 HIS 0.003 0.001 HIS 2 390 PHE 0.012 0.001 PHE 2 189 TYR 0.014 0.001 TYR 3 186 ARG 0.002 0.000 ARG 3 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.78 seconds wall clock time: 56 minutes 38.19 seconds (3398.19 seconds total)