Starting phenix.real_space_refine on Sat Dec 9 11:12:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/12_2023/8jcy_36169_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/12_2023/8jcy_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_36169/12_2023/8jcy_36169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/12_2023/8jcy_36169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/12_2023/8jcy_36169_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcy_36169/12_2023/8jcy_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-1.21rc1-5172/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: 8.65, per 1000 atoms: 0.80 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: 4.19 Conformation dependent library (CDL) restraints added in 3.2 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: 2.81 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: 3.57 Time building geometry restraints manager: 4.52 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: 1.930 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: 10.460 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 36.400 Find NCS groups from input model: 0.400 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: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.360 ------------------------------------------------------------------------------- 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 : 1.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.9402 time to fit residues: 142.7484 Evaluate side-chains 106 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6446 ------------------------------------------------------------------------------- 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: 0.6956 moved from start: 0.1255 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= 0.252 Angle : 0.557 8.686 15261 Z= 0.277 Chirality : 0.042 0.180 1805 Planarity : 0.004 0.051 1965 Dihedral : 5.050 54.194 2169 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 8.18 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.22), residues: 1516 helix: 2.25 (0.20), residues: 694 sheet: -0.96 (0.44), residues: 158 loop : -1.57 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 297 HIS 0.003 0.001 HIS 2 41 PHE 0.024 0.002 PHE 2 589 TYR 0.022 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 134 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.187 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 125 average time/residue: 0.8856 time to fit residues: 123.3947 Evaluate side-chains 112 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.1181 time to fit residues: 2.6163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 0.0570 chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.0904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11118 Z= 0.322 Angle : 0.566 8.318 15261 Z= 0.287 Chirality : 0.043 0.202 1805 Planarity : 0.004 0.041 1965 Dihedral : 5.328 56.133 2169 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.62 % Allowed : 10.36 % Favored : 87.02 % 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: 0.18 (0.22), residues: 1516 helix: 1.99 (0.20), residues: 697 sheet: -1.12 (0.42), residues: 157 loop : -1.70 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP 3 297 HIS 0.004 0.001 HIS 2 41 PHE 0.015 0.002 PHE 2 589 TYR 0.021 0.002 TYR 3 186 ARG 0.004 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 135 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.119 Fit side-chains outliers start: 24 outliers final: 13 residues processed: 121 average time/residue: 0.9420 time to fit residues: 126.5073 Evaluate side-chains 119 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.179 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.2892 time to fit residues: 3.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.0010 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 30.0000 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.1590 ------------------------------------------------------------------------------- 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 3 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11118 Z= 0.338 Angle : 0.575 8.287 15261 Z= 0.291 Chirality : 0.043 0.190 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.807 57.532 2169 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.84 % Allowed : 12.21 % Favored : 84.95 % 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: 0.02 (0.22), residues: 1516 helix: 1.84 (0.20), residues: 703 sheet: -1.18 (0.42), residues: 157 loop : -1.79 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 3 297 HIS 0.005 0.001 HIS 3 315 PHE 0.014 0.002 PHE 3 333 TYR 0.022 0.002 TYR 3 186 ARG 0.005 0.001 ARG 2 445 *********************** 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 130 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 1.207 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.9606 time to fit residues: 126.5156 Evaluate side-chains 116 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.2110 time to fit residues: 3.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 2 optimal weight: 0.4980 chunk 109 optimal weight: 0.4980 chunk 60 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 chunk 37 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** 3 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 315 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11118 Z= 0.209 Angle : 0.519 8.432 15261 Z= 0.260 Chirality : 0.040 0.164 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.579 56.845 2169 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.29 % Allowed : 14.29 % Favored : 83.42 % 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: 0.16 (0.22), residues: 1516 helix: 2.00 (0.20), residues: 697 sheet: -1.03 (0.44), residues: 148 loop : -1.77 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 520 HIS 0.003 0.001 HIS 3 315 PHE 0.018 0.001 PHE 3 195 TYR 0.014 0.001 TYR 3 186 ARG 0.003 0.000 ARG 2 445 *********************** 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 123 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 1.181 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 114 average time/residue: 0.9220 time to fit residues: 117.2851 Evaluate side-chains 110 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.241 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.1763 time to fit residues: 2.7213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 147 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11118 Z= 0.305 Angle : 0.569 8.657 15261 Z= 0.285 Chirality : 0.042 0.189 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.962 58.078 2169 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.73 % Allowed : 14.61 % Favored : 82.66 % 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: 703 sheet: -1.18 (0.43), residues: 146 loop : -1.83 (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 2 390 PHE 0.014 0.002 PHE 3 333 TYR 0.020 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: 25 poor density : 101 time to evaluate : 1.204 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 118 average time/residue: 0.9466 time to fit residues: 124.1892 Evaluate side-chains 111 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 97 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1949 time to fit residues: 2.4948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.2980 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.0030 chunk 82 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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: 0.6994 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11118 Z= 0.166 Angle : 0.503 9.115 15261 Z= 0.253 Chirality : 0.040 0.169 1805 Planarity : 0.004 0.054 1965 Dihedral : 5.473 56.780 2169 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.07 % Allowed : 15.38 % 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: 0.25 (0.22), residues: 1516 helix: 2.05 (0.20), residues: 698 sheet: -0.93 (0.43), residues: 152 loop : -1.71 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 355 HIS 0.002 0.000 HIS 2 390 PHE 0.021 0.001 PHE 3 195 TYR 0.013 0.001 TYR 3 104 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 116 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.195 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.9214 time to fit residues: 116.1002 Evaluate side-chains 103 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.1900 time to fit residues: 2.2542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 44 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 0.4980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11118 Z= 0.185 Angle : 0.510 9.498 15261 Z= 0.256 Chirality : 0.040 0.168 1805 Planarity : 0.004 0.038 1965 Dihedral : 5.420 56.852 2169 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.64 % Allowed : 16.25 % Favored : 82.12 % 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: 0.32 (0.22), residues: 1516 helix: 2.15 (0.20), residues: 694 sheet: -0.98 (0.44), residues: 148 loop : -1.68 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 529 HIS 0.002 0.000 HIS 2 390 PHE 0.011 0.001 PHE 2 189 TYR 0.012 0.001 TYR 3 186 ARG 0.002 0.000 ARG 2 445 *********************** 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 112 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 1.280 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 109 average time/residue: 0.9489 time to fit residues: 116.9579 Evaluate side-chains 107 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 1.289 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 3 average time/residue: 0.2413 time to fit residues: 2.7192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.1980 chunk 136 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 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: 0.7048 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11118 Z= 0.328 Angle : 0.578 10.934 15261 Z= 0.291 Chirality : 0.042 0.191 1805 Planarity : 0.004 0.051 1965 Dihedral : 5.935 57.382 2169 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.85 % Allowed : 15.92 % Favored : 82.22 % 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: 0.10 (0.22), residues: 1516 helix: 1.92 (0.20), residues: 703 sheet: -1.10 (0.43), residues: 148 loop : -1.79 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 3 297 HIS 0.003 0.001 HIS 2 390 PHE 0.022 0.002 PHE 3 195 TYR 0.019 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 113 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.240 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.8331 time to fit residues: 102.5552 Evaluate side-chains 106 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.2399 time to fit residues: 2.0408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.0670 chunk 68 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 30.0000 overall best weight: 1.5524 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 11118 Z= 0.433 Angle : 0.631 9.961 15261 Z= 0.318 Chirality : 0.044 0.212 1805 Planarity : 0.004 0.037 1965 Dihedral : 6.474 71.503 2169 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.85 % Allowed : 16.36 % Favored : 81.79 % 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: -0.12 (0.22), residues: 1516 helix: 1.75 (0.20), residues: 703 sheet: -1.29 (0.42), residues: 148 loop : -1.90 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 3 297 HIS 0.005 0.001 HIS 2 41 PHE 0.016 0.002 PHE 3 333 TYR 0.024 0.002 TYR 3 186 ARG 0.005 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 111 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.232 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.8438 time to fit residues: 105.3537 Evaluate side-chains 103 residues out of total 1294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.6172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.0980 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.230216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188337 restraints weight = 30124.492| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 3.46 r_work: 0.3650 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11118 Z= 0.201 Angle : 0.542 10.326 15261 Z= 0.271 Chirality : 0.041 0.172 1805 Planarity : 0.004 0.057 1965 Dihedral : 6.034 60.917 2169 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.85 % Allowed : 16.36 % Favored : 81.79 % 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: 0.10 (0.22), residues: 1516 helix: 1.97 (0.20), residues: 699 sheet: -1.40 (0.42), residues: 153 loop : -1.74 (0.23), residues: 664 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 0.025 0.001 PHE 3 195 TYR 0.013 0.001 TYR 2 458 ARG 0.002 0.000 ARG 2 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.34 seconds wall clock time: 57 minutes 56.08 seconds (3476.08 seconds total)