Starting phenix.real_space_refine on Mon Mar 18 01:08:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjg_14747/03_2024/7zjg_14747.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjg_14747/03_2024/7zjg_14747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjg_14747/03_2024/7zjg_14747.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjg_14747/03_2024/7zjg_14747.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjg_14747/03_2024/7zjg_14747.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjg_14747/03_2024/7zjg_14747.pdb" } resolution = 3.49 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= -0.001 sd= 0.043 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 12808 2.51 5 N 3256 2.21 5 O 3356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 358": "OE1" <-> "OE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 647": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 647": "OE1" <-> "OE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 647": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19532 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4883 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 579} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 10.13, per 1000 atoms: 0.52 Number of scatterers: 19532 At special positions: 0 Unit cell: (132.02, 132.02, 113.16, 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 3356 8.00 N 3256 7.00 C 12808 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: 7.68 Conformation dependent library (CDL) restraints added in 3.2 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 4 sheets defined 68.7% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 76 through 81 removed outlier: 4.010A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.826A pdb=" N GLU A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 removed outlier: 3.590A pdb=" N THR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.525A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 4.108A pdb=" N VAL A 180 " --> pdb=" O SER A 176 " (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 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.723A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.891A pdb=" N VAL A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 374 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 414 removed outlier: 5.054A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.955A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.170A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.616A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 604 removed outlier: 3.853A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL A 652 " --> pdb=" O VAL A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 3.709A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 679 removed outlier: 6.126A pdb=" N TRP A 677 " --> pdb=" O GLY A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.567A pdb=" N GLU A 716 " --> pdb=" O TRP A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 87 through 103 removed outlier: 3.827A pdb=" N GLU B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.590A pdb=" N THR B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.526A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 removed outlier: 4.109A pdb=" N VAL B 180 " --> pdb=" O SER B 176 " (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 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.723A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.891A pdb=" N VAL B 373 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 374 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 414 removed outlier: 5.055A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 459 through 466 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.955A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.171A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.616A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 522 No H-bonds generated for 'chain 'B' and resid 520 through 522' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 604 removed outlier: 3.852A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL B 652 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 3.707A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 6.125A pdb=" N TRP B 677 " --> pdb=" O GLY B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.567A pdb=" N GLU B 716 " --> pdb=" O TRP B 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.825A pdb=" N GLU C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.590A pdb=" N THR C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.525A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 removed outlier: 4.109A pdb=" N VAL C 180 " --> pdb=" O SER C 176 " (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 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.723A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 286 through 290' Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.891A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 374 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 414 removed outlier: 5.054A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 459 through 466 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.955A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.169A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.616A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 522 No H-bonds generated for 'chain 'C' and resid 520 through 522' Processing helix chain 'C' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.853A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL C 652 " --> pdb=" O VAL C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 673 removed outlier: 3.708A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 679 removed outlier: 6.125A pdb=" N TRP C 677 " --> pdb=" O GLY C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.566A pdb=" N GLU C 716 " --> pdb=" O TRP C 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 87 through 103 removed outlier: 3.825A pdb=" N GLU D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.591A pdb=" N THR D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.525A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 146 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.594A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 removed outlier: 4.108A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.724A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 286 through 290' Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.890A pdb=" N VAL D 373 " --> pdb=" O HIS D 370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 374 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 414 removed outlier: 5.054A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 459 through 466 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.954A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.170A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.613A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 522 No H-bonds generated for 'chain 'D' and resid 520 through 522' Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.174A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 528 through 561 removed outlier: 4.007A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 604 removed outlier: 3.853A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 647 removed outlier: 3.999A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 removed outlier: 4.246A pdb=" N VAL D 652 " --> pdb=" O VAL D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 673 removed outlier: 3.708A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 679 removed outlier: 6.125A pdb=" N TRP D 677 " --> pdb=" O GLY D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.566A pdb=" N GLU D 716 " --> pdb=" O TRP D 712 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 334 removed outlier: 6.005A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 702 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 691 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 331 through 334 removed outlier: 6.005A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 702 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 691 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.005A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 702 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 691 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 331 through 334 removed outlier: 6.006A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 702 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 691 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3048 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: 5.79 Time building geometry restraints manager: 8.19 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: 6017 1.34 - 1.46: 3747 1.46 - 1.58: 10088 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 20024 Sorted by residual: bond pdb=" CA SER D 504 " pdb=" CB SER D 504 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.55e-02 4.16e+03 1.03e+01 bond pdb=" CA SER A 504 " pdb=" CB SER A 504 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.55e-02 4.16e+03 1.02e+01 bond pdb=" CA SER C 504 " pdb=" CB SER C 504 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 1.01e+01 bond pdb=" CA SER B 504 " pdb=" CB SER B 504 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.55e-02 4.16e+03 9.91e+00 bond pdb=" N ARG B 517 " pdb=" CA ARG B 517 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.33e-02 5.65e+03 6.89e+00 ... (remaining 20019 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.74: 309 105.74 - 112.83: 10750 112.83 - 119.91: 6773 119.91 - 126.99: 9045 126.99 - 134.08: 275 Bond angle restraints: 27152 Sorted by residual: angle pdb=" N SER D 504 " pdb=" CA SER D 504 " pdb=" C SER D 504 " ideal model delta sigma weight residual 111.07 107.15 3.92 1.07e+00 8.73e-01 1.34e+01 angle pdb=" N SER A 504 " pdb=" CA SER A 504 " pdb=" C SER A 504 " ideal model delta sigma weight residual 111.07 107.16 3.91 1.07e+00 8.73e-01 1.34e+01 angle pdb=" N SER C 504 " pdb=" CA SER C 504 " pdb=" C SER C 504 " ideal model delta sigma weight residual 111.07 107.19 3.88 1.07e+00 8.73e-01 1.31e+01 angle pdb=" N SER B 504 " pdb=" CA SER B 504 " pdb=" C SER B 504 " ideal model delta sigma weight residual 111.07 107.19 3.88 1.07e+00 8.73e-01 1.31e+01 angle pdb=" CA LEU D 99 " pdb=" C LEU D 99 " pdb=" O LEU D 99 " ideal model delta sigma weight residual 121.84 117.77 4.07 1.16e+00 7.43e-01 1.23e+01 ... (remaining 27147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 10357 14.68 - 29.36: 978 29.36 - 44.04: 350 44.04 - 58.72: 51 58.72 - 73.40: 12 Dihedral angle restraints: 11748 sinusoidal: 4740 harmonic: 7008 Sorted by residual: dihedral pdb=" CA GLY B 608 " pdb=" C GLY B 608 " pdb=" N GLU B 609 " pdb=" CA GLU B 609 " ideal model delta harmonic sigma weight residual -180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY D 608 " pdb=" C GLY D 608 " pdb=" N GLU D 609 " pdb=" CA GLU D 609 " ideal model delta harmonic sigma weight residual -180.00 -162.62 -17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY A 608 " pdb=" C GLY A 608 " pdb=" N GLU A 609 " pdb=" CA GLU A 609 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2658 0.057 - 0.114: 388 0.114 - 0.171: 10 0.171 - 0.228: 0 0.228 - 0.285: 4 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ARG C 517 " pdb=" N ARG C 517 " pdb=" C ARG C 517 " pdb=" CB ARG C 517 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ARG B 517 " pdb=" N ARG B 517 " pdb=" C ARG B 517 " pdb=" CB ARG B 517 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA ARG D 517 " pdb=" N ARG D 517 " pdb=" C ARG D 517 " pdb=" CB ARG D 517 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3057 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 149 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 148 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 148 " 0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO B 149 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " 0.024 5.00e-02 4.00e+02 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3790 2.77 - 3.30: 20256 3.30 - 3.84: 31896 3.84 - 4.37: 35728 4.37 - 4.90: 61065 Nonbonded interactions: 152735 Sorted by model distance: nonbonded pdb=" O VAL D 153 " pdb=" OG SER D 166 " model vdw 2.241 2.440 nonbonded pdb=" O VAL C 153 " pdb=" OG SER C 166 " model vdw 2.242 2.440 nonbonded pdb=" O VAL B 153 " pdb=" OG SER B 166 " model vdw 2.242 2.440 nonbonded pdb=" O VAL A 153 " pdb=" OG SER A 166 " model vdw 2.243 2.440 nonbonded pdb=" O THR B 483 " pdb=" OG SER B 486 " model vdw 2.251 2.440 ... (remaining 152730 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' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 10.400 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 49.850 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 0.050 20024 Z= 0.169 Angle : 0.641 6.906 27152 Z= 0.332 Chirality : 0.039 0.285 3060 Planarity : 0.004 0.044 3340 Dihedral : 13.033 73.404 7220 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.33 % Favored : 91.33 % Rotamer: Outliers : 0.52 % Allowed : 0.05 % Favored : 99.44 % 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: -0.33 (0.18), residues: 2364 helix: 1.13 (0.14), residues: 1456 sheet: -0.40 (0.68), residues: 56 loop : -2.73 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 715 HIS 0.003 0.001 HIS D 313 PHE 0.010 0.001 PHE B 407 TYR 0.023 0.001 TYR B 471 ARG 0.008 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 308 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.6170 (p90) cc_final: 0.5878 (p90) REVERT: D 623 LEU cc_start: 0.8682 (tt) cc_final: 0.8472 (mt) outliers start: 11 outliers final: 4 residues processed: 319 average time/residue: 0.3063 time to fit residues: 150.9653 Evaluate side-chains 259 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 2.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 137 optimal weight: 0.6980 chunk 214 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 HIS ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 HIS ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 HIS ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20024 Z= 0.163 Angle : 0.595 8.086 27152 Z= 0.286 Chirality : 0.037 0.130 3060 Planarity : 0.004 0.037 3340 Dihedral : 4.246 57.613 2622 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.16 % Favored : 91.50 % Rotamer: Outliers : 1.37 % Allowed : 11.25 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.18), residues: 2364 helix: 1.51 (0.14), residues: 1472 sheet: -0.51 (0.67), residues: 56 loop : -2.76 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 715 HIS 0.004 0.001 HIS D 313 PHE 0.014 0.001 PHE D 540 TYR 0.034 0.001 TYR D 98 ARG 0.005 0.000 ARG D 687 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 264 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 591 ARG cc_start: 0.6581 (mmp80) cc_final: 0.6172 (mmp80) REVERT: B 591 ARG cc_start: 0.6614 (mmp80) cc_final: 0.6222 (mmp80) REVERT: C 277 MET cc_start: 0.8518 (mtt) cc_final: 0.8295 (mtt) REVERT: C 591 ARG cc_start: 0.6613 (mmp80) cc_final: 0.6203 (mmp80) outliers start: 29 outliers final: 20 residues processed: 283 average time/residue: 0.2900 time to fit residues: 128.2062 Evaluate side-chains 263 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 243 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 413 HIS Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 413 HIS Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 559 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 178 optimal weight: 6.9990 chunk 145 optimal weight: 0.0670 chunk 59 optimal weight: 30.0000 chunk 214 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20024 Z= 0.171 Angle : 0.590 9.235 27152 Z= 0.280 Chirality : 0.036 0.116 3060 Planarity : 0.004 0.041 3340 Dihedral : 4.134 50.718 2622 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.66 % Favored : 92.01 % Rotamer: Outliers : 1.84 % Allowed : 13.84 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.18), residues: 2364 helix: 1.72 (0.14), residues: 1448 sheet: -0.57 (0.68), residues: 56 loop : -2.69 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 715 HIS 0.014 0.001 HIS A 413 PHE 0.018 0.001 PHE D 540 TYR 0.007 0.001 TYR C 228 ARG 0.005 0.000 ARG D 687 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 258 time to evaluate : 2.181 Fit side-chains revert: symmetry clash REVERT: A 591 ARG cc_start: 0.6697 (mmp80) cc_final: 0.6374 (mmp80) REVERT: B 591 ARG cc_start: 0.6726 (mmp80) cc_final: 0.6258 (mmp80) REVERT: C 591 ARG cc_start: 0.6757 (mmp80) cc_final: 0.6278 (mmp80) outliers start: 39 outliers final: 29 residues processed: 277 average time/residue: 0.2914 time to fit residues: 126.4603 Evaluate side-chains 277 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 413 HIS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 413 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 559 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.0070 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.3980 chunk 228 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 663 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN C 169 HIS ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 663 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20024 Z= 0.155 Angle : 0.576 9.975 27152 Z= 0.273 Chirality : 0.036 0.115 3060 Planarity : 0.004 0.041 3340 Dihedral : 3.732 42.081 2612 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.95 % Favored : 91.71 % Rotamer: Outliers : 1.98 % Allowed : 16.29 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2364 helix: 1.81 (0.14), residues: 1448 sheet: -0.71 (0.68), residues: 56 loop : -2.38 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 386 HIS 0.004 0.001 HIS C 313 PHE 0.008 0.001 PHE B 547 TYR 0.025 0.001 TYR A 98 ARG 0.005 0.000 ARG D 687 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 278 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 491 PHE cc_start: 0.7505 (m-80) cc_final: 0.7133 (m-80) REVERT: A 591 ARG cc_start: 0.6815 (mmp80) cc_final: 0.6319 (mmp80) REVERT: B 491 PHE cc_start: 0.7510 (m-80) cc_final: 0.7139 (m-80) REVERT: B 591 ARG cc_start: 0.6828 (mmp80) cc_final: 0.6340 (mmp80) REVERT: C 491 PHE cc_start: 0.7511 (m-80) cc_final: 0.7141 (m-80) REVERT: C 591 ARG cc_start: 0.6864 (mmp80) cc_final: 0.6364 (mmp80) REVERT: D 491 PHE cc_start: 0.7457 (m-80) cc_final: 0.6974 (m-80) outliers start: 42 outliers final: 36 residues processed: 299 average time/residue: 0.2919 time to fit residues: 136.1887 Evaluate side-chains 292 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 256 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 413 HIS Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 413 HIS B 156 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 269 HIS C 156 GLN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 269 HIS D 156 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 269 HIS D 413 HIS D 487 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20024 Z= 0.408 Angle : 0.756 9.982 27152 Z= 0.367 Chirality : 0.041 0.132 3060 Planarity : 0.005 0.051 3340 Dihedral : 4.435 21.673 2608 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.93 % Favored : 90.74 % Rotamer: Outliers : 3.63 % Allowed : 18.74 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2364 helix: 1.23 (0.14), residues: 1424 sheet: -0.76 (0.80), residues: 56 loop : -2.60 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 715 HIS 0.007 0.002 HIS C 313 PHE 0.017 0.002 PHE C 603 TYR 0.023 0.002 TYR C 98 ARG 0.007 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 257 time to evaluate : 2.327 Fit side-chains REVERT: A 137 MET cc_start: 0.3917 (OUTLIER) cc_final: 0.3607 (pmm) REVERT: A 517 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7223 (ptp-110) REVERT: B 137 MET cc_start: 0.4048 (OUTLIER) cc_final: 0.3737 (pmm) REVERT: C 137 MET cc_start: 0.3985 (OUTLIER) cc_final: 0.3656 (pmm) REVERT: C 640 MET cc_start: 0.8223 (mmp) cc_final: 0.7717 (tpp) REVERT: D 491 PHE cc_start: 0.7942 (m-80) cc_final: 0.7662 (m-80) REVERT: D 517 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7113 (ptp-110) outliers start: 77 outliers final: 50 residues processed: 300 average time/residue: 0.3042 time to fit residues: 140.7324 Evaluate side-chains 300 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 245 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 637 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 517 ARG Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 644 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 119 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 169 HIS ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 156 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20024 Z= 0.168 Angle : 0.616 10.954 27152 Z= 0.297 Chirality : 0.037 0.157 3060 Planarity : 0.004 0.044 3340 Dihedral : 4.019 19.413 2608 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.25 % Favored : 91.58 % Rotamer: Outliers : 2.45 % Allowed : 20.24 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2364 helix: 1.53 (0.14), residues: 1416 sheet: -0.73 (0.79), residues: 56 loop : -2.59 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 715 HIS 0.003 0.001 HIS C 313 PHE 0.022 0.001 PHE C 547 TYR 0.027 0.001 TYR D 98 ARG 0.005 0.000 ARG C 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 272 time to evaluate : 2.186 Fit side-chains REVERT: A 126 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7369 (tt) REVERT: A 137 MET cc_start: 0.3322 (OUTLIER) cc_final: 0.2926 (pmm) REVERT: A 637 LEU cc_start: 0.9357 (tp) cc_final: 0.9141 (tp) REVERT: B 137 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.3284 (pmm) REVERT: B 517 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7182 (ptp-110) REVERT: B 605 ILE cc_start: 0.1941 (OUTLIER) cc_final: 0.1250 (pt) REVERT: B 669 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8323 (mm) REVERT: C 137 MET cc_start: 0.3496 (OUTLIER) cc_final: 0.3114 (pmm) REVERT: C 517 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.6455 (ptp-110) REVERT: C 591 ARG cc_start: 0.6813 (mmp80) cc_final: 0.6605 (mmp80) REVERT: C 637 LEU cc_start: 0.9337 (tp) cc_final: 0.9109 (tp) REVERT: C 669 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8312 (mm) REVERT: D 122 MET cc_start: 0.7535 (mtm) cc_final: 0.7046 (mtt) REVERT: D 126 LEU cc_start: 0.7792 (pp) cc_final: 0.7451 (tt) REVERT: D 491 PHE cc_start: 0.7872 (m-80) cc_final: 0.7641 (m-80) REVERT: D 517 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7144 (ptp-110) REVERT: D 669 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8327 (mm) outliers start: 52 outliers final: 23 residues processed: 306 average time/residue: 0.2992 time to fit residues: 140.6533 Evaluate side-chains 284 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 517 ARG Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN D 169 HIS ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20024 Z= 0.182 Angle : 0.618 10.934 27152 Z= 0.298 Chirality : 0.037 0.157 3060 Planarity : 0.004 0.044 3340 Dihedral : 3.978 19.068 2608 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.80 % Favored : 91.03 % Rotamer: Outliers : 2.17 % Allowed : 22.03 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2364 helix: 1.48 (0.14), residues: 1416 sheet: -0.88 (0.77), residues: 56 loop : -2.49 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 715 HIS 0.003 0.001 HIS D 313 PHE 0.022 0.001 PHE A 547 TYR 0.027 0.001 TYR C 98 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 264 time to evaluate : 2.336 Fit side-chains REVERT: A 137 MET cc_start: 0.3271 (OUTLIER) cc_final: 0.2837 (pmm) REVERT: A 637 LEU cc_start: 0.9357 (tp) cc_final: 0.9127 (tp) REVERT: B 126 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7321 (tt) REVERT: B 137 MET cc_start: 0.3607 (OUTLIER) cc_final: 0.3200 (pmm) REVERT: B 517 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7057 (ptp-110) REVERT: C 137 MET cc_start: 0.3422 (OUTLIER) cc_final: 0.3017 (pmm) REVERT: C 517 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6797 (ptp-110) REVERT: C 591 ARG cc_start: 0.6794 (mmp80) cc_final: 0.6566 (mmp80) REVERT: C 637 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9091 (tp) REVERT: C 669 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8262 (mm) REVERT: D 122 MET cc_start: 0.7540 (mtm) cc_final: 0.7092 (mtt) REVERT: D 126 LEU cc_start: 0.7812 (pp) cc_final: 0.7488 (tt) REVERT: D 137 MET cc_start: 0.3775 (OUTLIER) cc_final: 0.3260 (pmm) REVERT: D 433 MET cc_start: 0.6166 (tmm) cc_final: 0.5847 (tmm) REVERT: D 669 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8241 (mm) outliers start: 46 outliers final: 30 residues processed: 295 average time/residue: 0.2915 time to fit residues: 133.5179 Evaluate side-chains 300 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20024 Z= 0.197 Angle : 0.626 15.353 27152 Z= 0.302 Chirality : 0.037 0.171 3060 Planarity : 0.004 0.045 3340 Dihedral : 3.975 19.230 2608 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.76 % Favored : 91.03 % Rotamer: Outliers : 2.26 % Allowed : 22.46 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2364 helix: 1.46 (0.14), residues: 1416 sheet: -1.10 (0.77), residues: 56 loop : -2.48 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 715 HIS 0.003 0.001 HIS A 313 PHE 0.022 0.001 PHE C 547 TYR 0.029 0.001 TYR A 98 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.326 Fit side-chains REVERT: A 137 MET cc_start: 0.3400 (OUTLIER) cc_final: 0.2881 (pmm) REVERT: A 528 MET cc_start: 0.8935 (ppp) cc_final: 0.8583 (ppp) REVERT: A 637 LEU cc_start: 0.9369 (tp) cc_final: 0.9146 (tp) REVERT: B 122 MET cc_start: 0.8028 (ptm) cc_final: 0.7701 (ppp) REVERT: B 137 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.3216 (pmm) REVERT: B 647 GLU cc_start: 0.8147 (pp20) cc_final: 0.7861 (pp20) REVERT: C 122 MET cc_start: 0.7708 (tmm) cc_final: 0.7503 (tmm) REVERT: C 137 MET cc_start: 0.3651 (OUTLIER) cc_final: 0.3179 (pmm) REVERT: C 591 ARG cc_start: 0.6812 (mmp80) cc_final: 0.6569 (mmp80) REVERT: C 637 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9109 (tp) REVERT: D 122 MET cc_start: 0.7528 (mtm) cc_final: 0.7107 (mtt) REVERT: D 126 LEU cc_start: 0.7816 (pp) cc_final: 0.7516 (tt) REVERT: D 137 MET cc_start: 0.3788 (OUTLIER) cc_final: 0.3238 (pmm) REVERT: D 433 MET cc_start: 0.6180 (tmm) cc_final: 0.5887 (tmm) REVERT: D 528 MET cc_start: 0.8932 (ppp) cc_final: 0.8463 (ppp) outliers start: 48 outliers final: 40 residues processed: 297 average time/residue: 0.2872 time to fit residues: 132.6115 Evaluate side-chains 304 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 259 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 644 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 669 LEU 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: 0.8980 chunk 211 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 30.0000 chunk 191 optimal weight: 0.7980 chunk 200 optimal weight: 0.3980 chunk 139 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20024 Z= 0.234 Angle : 0.647 10.639 27152 Z= 0.315 Chirality : 0.038 0.160 3060 Planarity : 0.004 0.047 3340 Dihedral : 4.072 19.870 2608 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.18 % Favored : 90.61 % Rotamer: Outliers : 2.45 % Allowed : 22.60 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2364 helix: 1.38 (0.14), residues: 1420 sheet: -1.29 (0.77), residues: 56 loop : -2.50 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 715 HIS 0.004 0.001 HIS A 313 PHE 0.030 0.002 PHE A 547 TYR 0.030 0.001 TYR C 98 ARG 0.005 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 262 time to evaluate : 2.262 Fit side-chains REVERT: A 137 MET cc_start: 0.3626 (OUTLIER) cc_final: 0.3108 (pmm) REVERT: A 528 MET cc_start: 0.8936 (ppp) cc_final: 0.8612 (ppp) REVERT: B 122 MET cc_start: 0.7968 (ptm) cc_final: 0.7688 (ppp) REVERT: B 137 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.3271 (pmm) REVERT: B 528 MET cc_start: 0.8929 (ppp) cc_final: 0.8312 (ppp) REVERT: B 647 GLU cc_start: 0.8207 (pp20) cc_final: 0.7861 (pp20) REVERT: B 669 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8298 (mm) REVERT: C 137 MET cc_start: 0.3746 (OUTLIER) cc_final: 0.3258 (pmm) REVERT: C 517 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7335 (ptp-110) REVERT: C 528 MET cc_start: 0.8877 (ppp) cc_final: 0.8273 (ppp) REVERT: C 591 ARG cc_start: 0.6792 (mmp80) cc_final: 0.6533 (mmp80) REVERT: C 637 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9108 (tp) REVERT: D 122 MET cc_start: 0.7579 (mtm) cc_final: 0.7187 (mtt) REVERT: D 126 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7551 (tt) REVERT: D 137 MET cc_start: 0.3908 (OUTLIER) cc_final: 0.3317 (pmm) REVERT: D 433 MET cc_start: 0.6239 (tmm) cc_final: 0.5977 (tmm) outliers start: 52 outliers final: 42 residues processed: 293 average time/residue: 0.2776 time to fit residues: 129.6035 Evaluate side-chains 304 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 254 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 644 LEU Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 235 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 187 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 199 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20024 Z= 0.168 Angle : 0.629 10.982 27152 Z= 0.301 Chirality : 0.037 0.162 3060 Planarity : 0.004 0.042 3340 Dihedral : 3.967 18.686 2608 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.46 % Favored : 91.33 % Rotamer: Outliers : 2.17 % Allowed : 23.59 % Favored : 74.25 % 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: 0.08 (0.18), residues: 2364 helix: 1.51 (0.14), residues: 1416 sheet: -1.42 (0.75), residues: 56 loop : -2.38 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 223 HIS 0.002 0.001 HIS A 313 PHE 0.021 0.001 PHE D 547 TYR 0.031 0.001 TYR B 98 ARG 0.005 0.000 ARG B 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 268 time to evaluate : 2.353 Fit side-chains REVERT: A 137 MET cc_start: 0.3652 (OUTLIER) cc_final: 0.3112 (pmm) REVERT: A 517 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7223 (ptp-110) REVERT: A 528 MET cc_start: 0.8877 (ppp) cc_final: 0.8621 (ppp) REVERT: B 122 MET cc_start: 0.7964 (ptm) cc_final: 0.7623 (ppp) REVERT: B 123 LYS cc_start: 0.8414 (tmmt) cc_final: 0.8174 (ptmt) REVERT: B 137 MET cc_start: 0.3726 (OUTLIER) cc_final: 0.3241 (pmm) REVERT: B 528 MET cc_start: 0.8887 (ppp) cc_final: 0.8320 (ppp) REVERT: B 647 GLU cc_start: 0.8099 (pp20) cc_final: 0.7728 (pp20) REVERT: B 669 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8177 (mm) REVERT: C 122 MET cc_start: 0.7850 (tmm) cc_final: 0.7566 (tmm) REVERT: C 137 MET cc_start: 0.3739 (OUTLIER) cc_final: 0.3225 (pmm) REVERT: C 528 MET cc_start: 0.8836 (ppp) cc_final: 0.8197 (ppp) REVERT: C 591 ARG cc_start: 0.6820 (mmp80) cc_final: 0.6579 (mmp80) REVERT: C 637 LEU cc_start: 0.9323 (tp) cc_final: 0.9099 (tp) REVERT: C 647 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7467 (pp20) REVERT: D 122 MET cc_start: 0.7511 (mtm) cc_final: 0.7146 (mtt) REVERT: D 126 LEU cc_start: 0.7867 (pp) cc_final: 0.7604 (tt) REVERT: D 137 MET cc_start: 0.3769 (OUTLIER) cc_final: 0.3142 (pmm) REVERT: D 433 MET cc_start: 0.6150 (tmm) cc_final: 0.5828 (tmm) REVERT: D 528 MET cc_start: 0.8854 (ppp) cc_final: 0.8266 (ppp) outliers start: 46 outliers final: 34 residues processed: 297 average time/residue: 0.2720 time to fit residues: 130.3534 Evaluate side-chains 297 residues out of total 2136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 605 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 605 ILE Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.154034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111927 restraints weight = 38198.804| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.77 r_work: 0.3416 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20024 Z= 0.250 Angle : 0.665 10.847 27152 Z= 0.323 Chirality : 0.038 0.171 3060 Planarity : 0.004 0.048 3340 Dihedral : 4.108 19.735 2608 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.50 % Favored : 91.24 % Rotamer: Outliers : 2.31 % Allowed : 23.68 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2364 helix: 1.38 (0.14), residues: 1416 sheet: -1.55 (0.77), residues: 56 loop : -2.42 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 223 HIS 0.004 0.001 HIS C 313 PHE 0.021 0.002 PHE C 547 TYR 0.030 0.001 TYR C 98 ARG 0.005 0.000 ARG C 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3944.15 seconds wall clock time: 73 minutes 33.68 seconds (4413.68 seconds total)