Starting phenix.real_space_refine on Wed Apr 10 09:33:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zji_14749/04_2024/7zji_14749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zji_14749/04_2024/7zji_14749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zji_14749/04_2024/7zji_14749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zji_14749/04_2024/7zji_14749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zji_14749/04_2024/7zji_14749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zji_14749/04_2024/7zji_14749.pdb" } resolution = 3.4 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= 0.044 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 112 5.16 5 C 12641 2.51 5 N 3203 2.21 5 O 3275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 173": "OE1" <-> "OE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19231 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4809 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4804 Classifications: {'peptide': 593} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4809 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4809 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 575} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 9.93, per 1000 atoms: 0.52 Number of scatterers: 19231 At special positions: 0 Unit cell: (126.114, 156.584, 153.198, 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 112 16.00 O 3275 8.00 N 3203 7.00 C 12641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.70 Conformation dependent library (CDL) restraints added in 3.4 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4486 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 4 sheets defined 56.6% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 132 through 135 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.661A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.846A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.574A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 324 removed outlier: 4.238A pdb=" N TYR B 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.641A pdb=" N MET B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 470 through 490 removed outlier: 3.793A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 494 through 495 No H-bonds generated for 'chain 'B' and resid 494 through 495' Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.889A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 522 through 543 removed outlier: 3.999A pdb=" N SER B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 559 Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 627 through 650 removed outlier: 4.073A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 674 removed outlier: 4.461A pdb=" N SER B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 119 through 125 removed outlier: 3.794A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.967A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.525A pdb=" N SER A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 320 through 324 removed outlier: 4.022A pdb=" N TYR A 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 389 through 413 removed outlier: 3.640A pdb=" N HIS A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.688A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 516 removed outlier: 4.181A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.928A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 543 removed outlier: 3.542A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 595 through 605 removed outlier: 4.258A pdb=" N LEU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 Processing helix chain 'A' and resid 628 through 647 removed outlier: 3.735A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 674 removed outlier: 4.333A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.614A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.734A pdb=" N LYS C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.831A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.779A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.550A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 324 removed outlier: 4.121A pdb=" N TYR C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 375 through 387 Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 470 through 491 removed outlier: 3.745A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 516 removed outlier: 3.837A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 534 removed outlier: 3.732A pdb=" N SER C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 541 removed outlier: 4.056A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 541 " --> pdb=" O LEU C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 5.001A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C 557 " --> pdb=" O VAL C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.922A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 599 " --> pdb=" O ASP C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 650 removed outlier: 4.662A pdb=" N VAL C 630 " --> pdb=" O LEU C 626 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 674 removed outlier: 4.091A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY C 674 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 107 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.547A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.584A pdb=" N LYS D 174 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.890A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.542A pdb=" N GLU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.591A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.510A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 320 through 324 removed outlier: 4.170A pdb=" N TYR D 323 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.530A pdb=" N MET D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 388 removed outlier: 3.733A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.518A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 516 removed outlier: 4.488A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 528 removed outlier: 3.550A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 Processing helix chain 'D' and resid 539 through 544 removed outlier: 3.705A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 544 " --> pdb=" O PHE D 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 539 through 544' Processing helix chain 'D' and resid 544 through 557 removed outlier: 3.949A pdb=" N GLY D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 551 " --> pdb=" O PHE D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 604 removed outlier: 3.564A pdb=" N SER D 597 " --> pdb=" O ILE D 593 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU D 598 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU D 599 " --> pdb=" O ASP D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 649 removed outlier: 4.151A pdb=" N VAL D 630 " --> pdb=" O LEU D 626 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU D 631 " --> pdb=" O LEU D 627 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU D 644 " --> pdb=" O MET D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 674 removed outlier: 4.066A pdb=" N SER D 658 " --> pdb=" O ASP D 654 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 715 removed outlier: 3.682A pdb=" N TRP D 715 " --> pdb=" O TRP D 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.584A pdb=" N CYS B 704 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 687 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.564A pdb=" N CYS D 704 " --> pdb=" O ARG D 687 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 687 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2496 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: 5.21 Time building geometry restraints manager: 8.10 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: 5944 1.34 - 1.46: 4559 1.46 - 1.58: 9044 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 19719 Sorted by residual: bond pdb=" N ASP A 108 " pdb=" CA ASP A 108 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.70e+00 bond pdb=" N PHE A 601 " pdb=" CA PHE A 601 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.33e-02 5.65e+03 7.25e+00 bond pdb=" N HIS D 651 " pdb=" CA HIS D 651 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.97e+00 bond pdb=" N THR A 604 " pdb=" CA THR A 604 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 6.30e+00 bond pdb=" N VAL D 652 " pdb=" CA VAL D 652 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.14e-02 7.69e+03 5.91e+00 ... (remaining 19714 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.67: 230 104.67 - 112.01: 9729 112.01 - 119.35: 6625 119.35 - 126.69: 9786 126.69 - 134.03: 390 Bond angle restraints: 26760 Sorted by residual: angle pdb=" N ASP D 654 " pdb=" CA ASP D 654 " pdb=" C ASP D 654 " ideal model delta sigma weight residual 114.16 104.78 9.38 1.48e+00 4.57e-01 4.01e+01 angle pdb=" N LEU D 641 " pdb=" CA LEU D 641 " pdb=" C LEU D 641 " ideal model delta sigma weight residual 113.18 105.24 7.94 1.33e+00 5.65e-01 3.57e+01 angle pdb=" N VAL C 621 " pdb=" CA VAL C 621 " pdb=" C VAL C 621 " ideal model delta sigma weight residual 113.43 107.90 5.53 1.09e+00 8.42e-01 2.57e+01 angle pdb=" CA LEU D 641 " pdb=" C LEU D 641 " pdb=" N ILE D 642 " ideal model delta sigma weight residual 118.22 113.58 4.64 1.03e+00 9.43e-01 2.03e+01 angle pdb=" N TYR A 525 " pdb=" CA TYR A 525 " pdb=" C TYR A 525 " ideal model delta sigma weight residual 114.62 109.58 5.04 1.14e+00 7.69e-01 1.95e+01 ... (remaining 26755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10358 17.92 - 35.83: 946 35.83 - 53.74: 183 53.74 - 71.66: 21 71.66 - 89.57: 17 Dihedral angle restraints: 11525 sinusoidal: 4580 harmonic: 6945 Sorted by residual: dihedral pdb=" CA TRP A 464 " pdb=" C TRP A 464 " pdb=" N ILE A 465 " pdb=" CA ILE A 465 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual 180.00 158.49 21.51 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU D 345 " pdb=" C LEU D 345 " pdb=" N SER D 346 " pdb=" CA SER D 346 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2321 0.045 - 0.090: 608 0.090 - 0.135: 89 0.135 - 0.179: 10 0.179 - 0.224: 3 Chirality restraints: 3031 Sorted by residual: chirality pdb=" CB ILE C 158 " pdb=" CA ILE C 158 " pdb=" CG1 ILE C 158 " pdb=" CG2 ILE C 158 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA MET D 137 " pdb=" N MET D 137 " pdb=" C MET D 137 " pdb=" CB MET D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB THR A 604 " pdb=" CA THR A 604 " pdb=" OG1 THR A 604 " pdb=" CG2 THR A 604 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 3028 not shown) Planarity restraints: 3286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 150 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO C 151 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 151 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 151 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 601 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C PHE A 601 " -0.039 2.00e-02 2.50e+03 pdb=" O PHE A 601 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 602 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 601 " 0.017 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE D 601 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 601 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 601 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 601 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 601 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE D 601 " 0.003 2.00e-02 2.50e+03 ... (remaining 3283 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1408 2.74 - 3.28: 19917 3.28 - 3.82: 30145 3.82 - 4.36: 34379 4.36 - 4.90: 58561 Nonbonded interactions: 144410 Sorted by model distance: nonbonded pdb=" O PHE B 601 " pdb=" OG1 THR B 604 " model vdw 2.197 2.440 nonbonded pdb=" OH TYR A 525 " pdb=" NH1 ARG D 535 " model vdw 2.212 2.520 nonbonded pdb=" OH TYR A 412 " pdb=" O SER D 592 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR C 271 " pdb=" OE2 GLU C 288 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR B 271 " pdb=" OE2 GLU B 288 " model vdw 2.239 2.440 ... (remaining 144405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 75 through 559 or resid 589 through 716)) selection = (chain 'C' and (resid 75 through 559 or resid 589 through 716)) selection = (chain 'D' and (resid 75 through 559 or resid 589 through 716)) } 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=1.00 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: 2.810 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: 10.570 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.140 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.090 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 0.037 19719 Z= 0.171 Angle : 0.658 9.376 26760 Z= 0.362 Chirality : 0.040 0.224 3031 Planarity : 0.004 0.088 3286 Dihedral : 14.202 89.574 7039 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.28 % Favored : 91.46 % Rotamer: Outliers : 0.10 % Allowed : 0.10 % Favored : 99.81 % 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: -0.82 (0.18), residues: 2343 helix: 1.18 (0.16), residues: 1209 sheet: -1.61 (0.62), residues: 61 loop : -2.68 (0.17), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 464 HIS 0.003 0.001 HIS B 293 PHE 0.035 0.001 PHE D 601 TYR 0.024 0.001 TYR D 471 ARG 0.006 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 269 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 528 MET cc_start: 0.7766 (mpp) cc_final: 0.7524 (mpp) REVERT: B 645 MET cc_start: 0.8880 (mpp) cc_final: 0.8489 (mpp) REVERT: A 137 MET cc_start: 0.6914 (mmp) cc_final: 0.6472 (tpp) REVERT: A 141 GLN cc_start: 0.7988 (pp30) cc_final: 0.7722 (pp30) REVERT: A 645 MET cc_start: 0.9114 (tmm) cc_final: 0.8763 (tmm) REVERT: C 602 LYS cc_start: 0.9395 (tppt) cc_final: 0.9067 (tppt) REVERT: C 603 PHE cc_start: 0.8123 (m-10) cc_final: 0.7649 (m-80) REVERT: D 81 PHE cc_start: 0.5319 (m-80) cc_final: 0.5105 (m-10) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.2651 time to fit residues: 114.9741 Evaluate side-chains 222 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.2980 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 0.1980 chunk 61 optimal weight: 20.0000 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 30.0000 chunk 137 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19719 Z= 0.238 Angle : 0.620 8.092 26760 Z= 0.306 Chirality : 0.039 0.158 3031 Planarity : 0.004 0.053 3286 Dihedral : 4.257 30.540 2583 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.96 % Favored : 90.78 % Rotamer: Outliers : 1.16 % Allowed : 9.12 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.73 (0.18), residues: 2343 helix: 1.34 (0.16), residues: 1206 sheet: -1.65 (0.63), residues: 63 loop : -2.73 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 351 HIS 0.005 0.001 HIS A 251 PHE 0.032 0.001 PHE D 601 TYR 0.027 0.001 TYR A 544 ARG 0.004 0.000 ARG D 535 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 681 LYS cc_start: 0.7844 (mttp) cc_final: 0.7595 (pttp) REVERT: A 137 MET cc_start: 0.7035 (mmp) cc_final: 0.6479 (tpp) REVERT: A 141 GLN cc_start: 0.8245 (pp30) cc_final: 0.7942 (pp30) REVERT: A 498 LEU cc_start: 0.7139 (tp) cc_final: 0.6890 (tp) REVERT: A 645 MET cc_start: 0.9096 (tmm) cc_final: 0.8784 (tmm) REVERT: C 603 PHE cc_start: 0.8104 (m-10) cc_final: 0.7647 (m-80) REVERT: D 81 PHE cc_start: 0.5417 (m-80) cc_final: 0.5101 (m-10) REVERT: D 468 MET cc_start: 0.7968 (tmm) cc_final: 0.7687 (tmm) REVERT: D 676 TRP cc_start: 0.6994 (p-90) cc_final: 0.6770 (p-90) outliers start: 24 outliers final: 19 residues processed: 251 average time/residue: 0.2733 time to fit residues: 110.6725 Evaluate side-chains 241 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 222 time to evaluate : 2.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 663 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 178 optimal weight: 20.0000 chunk 145 optimal weight: 5.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19719 Z= 0.191 Angle : 0.572 8.396 26760 Z= 0.282 Chirality : 0.038 0.169 3031 Planarity : 0.003 0.045 3286 Dihedral : 4.125 31.895 2583 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.41 % Favored : 91.29 % Rotamer: Outliers : 1.88 % Allowed : 11.87 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.58 (0.18), residues: 2343 helix: 1.47 (0.16), residues: 1209 sheet: -1.72 (0.62), residues: 63 loop : -2.67 (0.17), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 676 HIS 0.004 0.001 HIS A 251 PHE 0.036 0.001 PHE D 601 TYR 0.022 0.001 TYR B 471 ARG 0.002 0.000 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 228 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 MET cc_start: 0.8948 (mmp) cc_final: 0.8652 (mmt) REVERT: B 681 LYS cc_start: 0.7841 (mttp) cc_final: 0.7606 (pttp) REVERT: A 137 MET cc_start: 0.7042 (mmp) cc_final: 0.6470 (tpp) REVERT: A 141 GLN cc_start: 0.8295 (pp30) cc_final: 0.8019 (pp30) REVERT: A 239 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8996 (tt) REVERT: A 498 LEU cc_start: 0.7034 (tp) cc_final: 0.6714 (tp) REVERT: A 645 MET cc_start: 0.9080 (tmm) cc_final: 0.8795 (tmm) REVERT: C 603 PHE cc_start: 0.8090 (m-10) cc_final: 0.7634 (m-80) REVERT: D 81 PHE cc_start: 0.5442 (m-80) cc_final: 0.5106 (m-10) REVERT: D 163 GLN cc_start: 0.5682 (tp-100) cc_final: 0.5222 (tt0) REVERT: D 450 LEU cc_start: 0.8802 (tp) cc_final: 0.7895 (tp) REVERT: D 468 MET cc_start: 0.7948 (tmm) cc_final: 0.7726 (tmm) REVERT: D 676 TRP cc_start: 0.7002 (p-90) cc_final: 0.6720 (p-90) outliers start: 39 outliers final: 24 residues processed: 246 average time/residue: 0.2674 time to fit residues: 106.6688 Evaluate side-chains 244 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 228 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19719 Z= 0.328 Angle : 0.652 9.965 26760 Z= 0.324 Chirality : 0.041 0.185 3031 Planarity : 0.004 0.046 3286 Dihedral : 4.479 33.191 2583 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.07 % Favored : 89.63 % Rotamer: Outliers : 2.80 % Allowed : 15.35 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.86 (0.18), residues: 2343 helix: 1.16 (0.15), residues: 1228 sheet: -2.01 (0.59), residues: 63 loop : -2.75 (0.17), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 703 HIS 0.008 0.001 HIS B 363 PHE 0.035 0.002 PHE D 601 TYR 0.022 0.002 TYR B 471 ARG 0.006 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 645 MET cc_start: 0.9011 (mmp) cc_final: 0.8692 (mmt) REVERT: A 137 MET cc_start: 0.7310 (mmp) cc_final: 0.6667 (tpp) REVERT: A 141 GLN cc_start: 0.8346 (pp30) cc_final: 0.8133 (pp30) REVERT: A 239 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9020 (tt) REVERT: A 339 ARG cc_start: 0.6290 (mtp85) cc_final: 0.5962 (mtp85) REVERT: A 498 LEU cc_start: 0.7174 (tp) cc_final: 0.6819 (tp) REVERT: A 618 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7239 (t80) REVERT: C 162 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2523 (m-10) REVERT: C 224 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7714 (p0) REVERT: C 517 ARG cc_start: 0.6874 (tpp-160) cc_final: 0.6553 (tpp-160) REVERT: C 528 MET cc_start: 0.8886 (mmm) cc_final: 0.8567 (mtt) REVERT: C 603 PHE cc_start: 0.8190 (m-10) cc_final: 0.7720 (m-80) REVERT: D 81 PHE cc_start: 0.5560 (m-80) cc_final: 0.5208 (m-10) REVERT: D 163 GLN cc_start: 0.5711 (tp-100) cc_final: 0.5144 (tt0) REVERT: D 270 MET cc_start: 0.8511 (mmm) cc_final: 0.8125 (tpt) REVERT: D 450 LEU cc_start: 0.8801 (tp) cc_final: 0.7800 (tp) REVERT: D 517 ARG cc_start: 0.7908 (tpt-90) cc_final: 0.7528 (tpt-90) REVERT: D 640 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6598 (ppp) REVERT: D 676 TRP cc_start: 0.7046 (p-90) cc_final: 0.6612 (p-90) outliers start: 58 outliers final: 33 residues processed: 278 average time/residue: 0.2221 time to fit residues: 97.8921 Evaluate side-chains 259 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 221 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 663 GLN Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 0.4980 chunk 204 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.004 0.040 19719 Z= 0.233 Angle : 0.623 12.582 26760 Z= 0.301 Chirality : 0.039 0.224 3031 Planarity : 0.003 0.046 3286 Dihedral : 4.300 33.333 2583 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.88 % Favored : 90.78 % Rotamer: Outliers : 2.94 % Allowed : 17.47 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.18), residues: 2343 helix: 1.24 (0.15), residues: 1232 sheet: -2.08 (0.59), residues: 63 loop : -2.70 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 333 HIS 0.005 0.001 HIS B 363 PHE 0.034 0.001 PHE D 601 TYR 0.022 0.001 TYR B 471 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 230 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9081 (tt) REVERT: B 645 MET cc_start: 0.9020 (mmp) cc_final: 0.8684 (mmt) REVERT: A 137 MET cc_start: 0.7298 (mmp) cc_final: 0.6656 (tpp) REVERT: A 141 GLN cc_start: 0.8388 (pp30) cc_final: 0.8180 (pp30) REVERT: A 239 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9009 (tt) REVERT: A 498 LEU cc_start: 0.7225 (tp) cc_final: 0.6883 (tp) REVERT: A 544 TYR cc_start: 0.8811 (m-80) cc_final: 0.8547 (m-80) REVERT: A 618 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 645 MET cc_start: 0.8998 (tmm) cc_final: 0.8737 (tmm) REVERT: C 162 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2692 (m-10) REVERT: C 286 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7721 (mt0) REVERT: C 517 ARG cc_start: 0.6788 (tpp-160) cc_final: 0.6454 (tpp-160) REVERT: C 603 PHE cc_start: 0.8113 (m-10) cc_final: 0.7643 (m-80) REVERT: D 81 PHE cc_start: 0.5469 (m-80) cc_final: 0.5053 (m-80) REVERT: D 163 GLN cc_start: 0.5784 (tp-100) cc_final: 0.5162 (tt0) REVERT: D 270 MET cc_start: 0.8521 (mmm) cc_final: 0.8160 (tpt) REVERT: D 473 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: D 517 ARG cc_start: 0.7884 (tpt-90) cc_final: 0.7179 (tpt-90) REVERT: D 637 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7632 (pp) REVERT: D 640 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6483 (ppp) outliers start: 61 outliers final: 37 residues processed: 268 average time/residue: 0.2801 time to fit residues: 119.1018 Evaluate side-chains 262 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 618 PHE Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 473 GLU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 2.9990 chunk 205 optimal weight: 0.0470 chunk 45 optimal weight: 20.0000 chunk 133 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 189 optimal weight: 0.0270 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 0.0470 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19719 Z= 0.127 Angle : 0.584 14.427 26760 Z= 0.276 Chirality : 0.037 0.210 3031 Planarity : 0.003 0.045 3286 Dihedral : 3.922 31.998 2583 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.47 % Favored : 92.19 % Rotamer: Outliers : 2.17 % Allowed : 18.82 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2343 helix: 1.61 (0.16), residues: 1219 sheet: -1.97 (0.60), residues: 67 loop : -2.62 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 657 HIS 0.002 0.000 HIS A 521 PHE 0.034 0.001 PHE D 601 TYR 0.023 0.001 TYR A 471 ARG 0.007 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 240 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 MET cc_start: 0.9019 (mmp) cc_final: 0.8673 (mmt) REVERT: A 137 MET cc_start: 0.7276 (mmp) cc_final: 0.6639 (tpp) REVERT: A 498 LEU cc_start: 0.7124 (tp) cc_final: 0.6702 (tp) REVERT: A 645 MET cc_start: 0.8975 (tmm) cc_final: 0.8691 (tmm) REVERT: C 286 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7691 (mt0) REVERT: C 517 ARG cc_start: 0.6831 (tpp-160) cc_final: 0.6489 (tpp-160) REVERT: C 528 MET cc_start: 0.8856 (mmm) cc_final: 0.8560 (mtt) REVERT: C 529 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8514 (mm) REVERT: C 603 PHE cc_start: 0.8064 (m-10) cc_final: 0.7621 (m-80) REVERT: C 607 MET cc_start: 0.3562 (mmm) cc_final: 0.2801 (mmm) REVERT: D 81 PHE cc_start: 0.5403 (m-80) cc_final: 0.5018 (m-80) REVERT: D 163 GLN cc_start: 0.5730 (tp-100) cc_final: 0.5099 (tt0) REVERT: D 270 MET cc_start: 0.8604 (mmm) cc_final: 0.8385 (tpt) REVERT: D 517 ARG cc_start: 0.7887 (tpt-90) cc_final: 0.7536 (ttt-90) REVERT: D 637 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7423 (pp) REVERT: D 640 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6062 (ppp) outliers start: 45 outliers final: 28 residues processed: 270 average time/residue: 0.2809 time to fit residues: 120.6523 Evaluate side-chains 257 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 226 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 333 TRP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.0270 chunk 25 optimal weight: 0.0970 chunk 130 optimal weight: 0.4980 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19719 Z= 0.130 Angle : 0.601 13.994 26760 Z= 0.283 Chirality : 0.037 0.198 3031 Planarity : 0.003 0.046 3286 Dihedral : 3.857 31.732 2583 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.47 % Favored : 92.23 % Rotamer: Outliers : 1.88 % Allowed : 19.98 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.35 (0.18), residues: 2343 helix: 1.68 (0.16), residues: 1219 sheet: -1.74 (0.62), residues: 67 loop : -2.62 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D 676 HIS 0.003 0.000 HIS A 313 PHE 0.034 0.001 PHE D 601 TYR 0.020 0.001 TYR B 471 ARG 0.014 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 235 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 MET cc_start: 0.9033 (mmp) cc_final: 0.8674 (mmt) REVERT: A 137 MET cc_start: 0.7247 (mmp) cc_final: 0.6797 (tpp) REVERT: A 468 MET cc_start: 0.7655 (mpp) cc_final: 0.7446 (tpt) REVERT: A 498 LEU cc_start: 0.7170 (tp) cc_final: 0.6748 (tp) REVERT: A 645 MET cc_start: 0.8980 (tmm) cc_final: 0.8706 (tmm) REVERT: C 286 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7697 (mt0) REVERT: C 517 ARG cc_start: 0.6798 (tpp-160) cc_final: 0.6464 (tpp-160) REVERT: C 524 ILE cc_start: 0.7835 (mp) cc_final: 0.7153 (mm) REVERT: C 528 MET cc_start: 0.8858 (mmm) cc_final: 0.8531 (mtt) REVERT: C 529 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (mm) REVERT: C 603 PHE cc_start: 0.8011 (m-10) cc_final: 0.7565 (m-80) REVERT: C 607 MET cc_start: 0.3472 (mmm) cc_final: 0.2840 (mmm) REVERT: D 81 PHE cc_start: 0.5452 (m-80) cc_final: 0.5058 (m-80) REVERT: D 163 GLN cc_start: 0.5626 (tp-100) cc_final: 0.5124 (tt0) REVERT: D 517 ARG cc_start: 0.7880 (tpt-90) cc_final: 0.7396 (tpt-90) REVERT: D 637 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7416 (pp) REVERT: D 640 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.5851 (ppp) outliers start: 39 outliers final: 29 residues processed: 259 average time/residue: 0.2889 time to fit residues: 119.4220 Evaluate side-chains 256 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 333 TRP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN D 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19719 Z= 0.275 Angle : 0.663 12.579 26760 Z= 0.319 Chirality : 0.040 0.220 3031 Planarity : 0.004 0.050 3286 Dihedral : 4.200 32.099 2583 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.35 % Favored : 90.31 % Rotamer: Outliers : 2.41 % Allowed : 20.03 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.64 (0.18), residues: 2343 helix: 1.36 (0.16), residues: 1219 sheet: -1.57 (0.63), residues: 63 loop : -2.66 (0.18), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 676 HIS 0.006 0.001 HIS B 363 PHE 0.034 0.002 PHE D 601 TYR 0.020 0.002 TYR B 471 ARG 0.011 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 231 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 645 MET cc_start: 0.9062 (mmp) cc_final: 0.8716 (mmt) REVERT: A 137 MET cc_start: 0.7460 (mmp) cc_final: 0.7249 (tpp) REVERT: A 468 MET cc_start: 0.7748 (mpp) cc_final: 0.7355 (tpp) REVERT: A 498 LEU cc_start: 0.7436 (tp) cc_final: 0.7111 (tp) REVERT: C 162 TYR cc_start: 0.3718 (OUTLIER) cc_final: 0.2728 (m-10) REVERT: C 517 ARG cc_start: 0.6849 (tpp-160) cc_final: 0.6470 (tpp-160) REVERT: C 524 ILE cc_start: 0.7867 (mp) cc_final: 0.7658 (mm) REVERT: C 529 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8557 (mm) REVERT: C 603 PHE cc_start: 0.8012 (m-10) cc_final: 0.7569 (m-80) REVERT: C 607 MET cc_start: 0.3539 (mmm) cc_final: 0.2843 (mmm) REVERT: D 81 PHE cc_start: 0.5431 (m-80) cc_final: 0.5033 (m-80) REVERT: D 163 GLN cc_start: 0.5704 (tp-100) cc_final: 0.5189 (tt0) REVERT: D 517 ARG cc_start: 0.7920 (tpt-90) cc_final: 0.7412 (tpt-90) REVERT: D 637 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7608 (pp) REVERT: D 640 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.5921 (ppp) REVERT: D 676 TRP cc_start: 0.7285 (p-90) cc_final: 0.7058 (p-90) outliers start: 50 outliers final: 37 residues processed: 261 average time/residue: 0.2834 time to fit residues: 118.2438 Evaluate side-chains 263 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 222 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 351 TRP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 19719 Z= 0.300 Angle : 0.690 13.229 26760 Z= 0.333 Chirality : 0.040 0.214 3031 Planarity : 0.004 0.049 3286 Dihedral : 4.393 33.211 2583 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.22 % Favored : 90.44 % Rotamer: Outliers : 2.90 % Allowed : 20.61 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.90 (0.18), residues: 2343 helix: 1.10 (0.15), residues: 1232 sheet: -1.64 (0.63), residues: 63 loop : -2.77 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 676 HIS 0.007 0.001 HIS B 363 PHE 0.034 0.002 PHE D 601 TYR 0.018 0.002 TYR A 471 ARG 0.015 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 227 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8241 (mtt) cc_final: 0.7875 (mtm) REVERT: B 645 MET cc_start: 0.9044 (mmp) cc_final: 0.8724 (mmt) REVERT: A 468 MET cc_start: 0.7754 (mpp) cc_final: 0.7484 (tpt) REVERT: A 498 LEU cc_start: 0.7503 (tp) cc_final: 0.7171 (tp) REVERT: A 548 LEU cc_start: 0.8346 (tt) cc_final: 0.7985 (tp) REVERT: A 645 MET cc_start: 0.8986 (tmm) cc_final: 0.8707 (tmm) REVERT: C 162 TYR cc_start: 0.3752 (OUTLIER) cc_final: 0.2792 (m-10) REVERT: C 517 ARG cc_start: 0.6850 (tpp-160) cc_final: 0.6442 (tpp-160) REVERT: C 524 ILE cc_start: 0.7853 (mp) cc_final: 0.7142 (mm) REVERT: C 528 MET cc_start: 0.8833 (mmm) cc_final: 0.8527 (mtt) REVERT: C 603 PHE cc_start: 0.8088 (m-10) cc_final: 0.7629 (m-80) REVERT: C 607 MET cc_start: 0.3605 (mmm) cc_final: 0.2868 (mmm) REVERT: D 81 PHE cc_start: 0.5393 (m-80) cc_final: 0.5000 (m-80) REVERT: D 163 GLN cc_start: 0.5786 (tp-100) cc_final: 0.5162 (tt0) REVERT: D 517 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7546 (ttt-90) REVERT: D 637 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7730 (pp) REVERT: D 640 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5943 (ppp) outliers start: 60 outliers final: 46 residues processed: 268 average time/residue: 0.2886 time to fit residues: 123.8521 Evaluate side-chains 274 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 225 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 349 ASP Chi-restraints excluded: chain C residue 351 TRP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 663 GLN Chi-restraints excluded: chain D residue 671 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 0.0170 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 216 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 199 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN ** B 521 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19719 Z= 0.153 Angle : 0.636 13.675 26760 Z= 0.300 Chirality : 0.038 0.210 3031 Planarity : 0.003 0.055 3286 Dihedral : 4.046 32.773 2583 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.85 % Favored : 91.81 % Rotamer: Outliers : 1.83 % Allowed : 21.77 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.59 (0.18), residues: 2343 helix: 1.40 (0.16), residues: 1224 sheet: -1.55 (0.64), residues: 65 loop : -2.67 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 676 HIS 0.002 0.001 HIS A 521 PHE 0.034 0.001 PHE D 601 TYR 0.018 0.001 TYR B 471 ARG 0.014 0.000 ARG A 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 277 MET cc_start: 0.8195 (mtt) cc_final: 0.7846 (mtm) REVERT: B 528 MET cc_start: 0.7996 (mpp) cc_final: 0.7686 (mpp) REVERT: B 645 MET cc_start: 0.9048 (mmp) cc_final: 0.8711 (mmt) REVERT: A 277 MET cc_start: 0.8224 (mtp) cc_final: 0.8021 (mtp) REVERT: A 468 MET cc_start: 0.7915 (mpp) cc_final: 0.7404 (tpt) REVERT: A 498 LEU cc_start: 0.7361 (tp) cc_final: 0.7068 (tp) REVERT: A 548 LEU cc_start: 0.8409 (tt) cc_final: 0.8126 (tt) REVERT: A 645 MET cc_start: 0.8977 (tmm) cc_final: 0.8722 (tmm) REVERT: C 517 ARG cc_start: 0.6838 (tpp-160) cc_final: 0.6449 (tpp-160) REVERT: C 603 PHE cc_start: 0.8006 (m-10) cc_final: 0.7562 (m-80) REVERT: C 607 MET cc_start: 0.3431 (mmm) cc_final: 0.2839 (mmm) REVERT: D 81 PHE cc_start: 0.5371 (m-80) cc_final: 0.4978 (m-80) REVERT: D 163 GLN cc_start: 0.5772 (tp-100) cc_final: 0.5174 (tt0) REVERT: D 509 TRP cc_start: 0.6503 (m100) cc_final: 0.6021 (m100) REVERT: D 517 ARG cc_start: 0.7920 (tpt-90) cc_final: 0.7484 (ttt-90) REVERT: D 637 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7518 (pp) REVERT: D 640 MET cc_start: 0.6627 (OUTLIER) cc_final: 0.5732 (ppp) outliers start: 38 outliers final: 31 residues processed: 253 average time/residue: 0.2782 time to fit residues: 112.5189 Evaluate side-chains 255 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 365 LYS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 234 HIS Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.178532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125784 restraints weight = 35805.864| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 4.13 r_work: 0.3411 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19719 Z= 0.268 Angle : 0.681 12.800 26760 Z= 0.327 Chirality : 0.040 0.208 3031 Planarity : 0.004 0.056 3286 Dihedral : 4.252 32.845 2583 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.56 % Favored : 90.14 % Rotamer: Outliers : 2.17 % Allowed : 21.96 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.78 (0.18), residues: 2343 helix: 1.22 (0.15), residues: 1230 sheet: -1.67 (0.63), residues: 65 loop : -2.73 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 676 HIS 0.008 0.001 HIS B 521 PHE 0.033 0.001 PHE D 601 TYR 0.019 0.001 TYR B 471 ARG 0.014 0.000 ARG A 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4332.59 seconds wall clock time: 83 minutes 28.33 seconds (5008.33 seconds total)