Starting phenix.real_space_refine on Tue Mar 19 06:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/03_2024/7e8g_31018.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/03_2024/7e8g_31018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/03_2024/7e8g_31018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/03_2024/7e8g_31018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/03_2024/7e8g_31018.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8g_31018/03_2024/7e8g_31018.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 96 5.16 5 C 14972 2.51 5 N 3988 2.21 5 O 4472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 665": "OE1" <-> "OE2" Residue "J PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 73": "OD1" <-> "OD2" Residue "I GLU 265": "OE1" <-> "OE2" Residue "I TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 665": "OE1" <-> "OE2" Residue "L PHE 690": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 701": "OD1" <-> "OD2" Residue "L PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 73": "OD1" <-> "OD2" Residue "K GLU 265": "OE1" <-> "OE2" Residue "K TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 23528 Number of models: 1 Model: "" Number of chains: 4 Chain: "J" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "I" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "L" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Chain: "K" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5882 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 694} Time building chain proxies: 12.46, per 1000 atoms: 0.53 Number of scatterers: 23528 At special positions: 0 Unit cell: (161.431, 215.576, 106.284, 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 96 16.00 O 4472 8.00 N 3988 7.00 C 14972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS J 349 " - pdb=" SG CYS J 356 " distance=2.03 Simple disulfide: pdb=" SG CYS J 465 " - pdb=" SG CYS J 468 " distance=2.03 Simple disulfide: pdb=" SG CYS J 474 " - pdb=" SG CYS J 492 " distance=2.03 Simple disulfide: pdb=" SG CYS J 673 " - pdb=" SG CYS J 784 " distance=2.03 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 356 " distance=2.03 Simple disulfide: pdb=" SG CYS I 465 " - pdb=" SG CYS I 468 " distance=2.03 Simple disulfide: pdb=" SG CYS I 474 " - pdb=" SG CYS I 492 " distance=2.03 Simple disulfide: pdb=" SG CYS I 673 " - pdb=" SG CYS I 784 " distance=2.03 Simple disulfide: pdb=" SG CYS L 349 " - pdb=" SG CYS L 356 " distance=2.03 Simple disulfide: pdb=" SG CYS L 465 " - pdb=" SG CYS L 468 " distance=2.03 Simple disulfide: pdb=" SG CYS L 474 " - pdb=" SG CYS L 492 " distance=2.03 Simple disulfide: pdb=" SG CYS L 673 " - pdb=" SG CYS L 784 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 356 " distance=2.03 Simple disulfide: pdb=" SG CYS K 465 " - pdb=" SG CYS K 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 474 " - pdb=" SG CYS K 492 " distance=2.03 Simple disulfide: pdb=" SG CYS K 673 " - pdb=" SG CYS K 784 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.01 Conformation dependent library (CDL) restraints added in 3.9 seconds 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5488 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 46 sheets defined 17.7% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.46 Creating SS restraints... Processing helix chain 'J' and resid 70 through 75 Processing helix chain 'J' and resid 76 through 80 Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 582 through 591 Processing helix chain 'J' and resid 607 through 614 removed outlier: 4.427A pdb=" N VAL J 614 " --> pdb=" O LEU J 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 621 through 635 Processing helix chain 'J' and resid 649 through 658 Processing helix chain 'J' and resid 682 through 686 Processing helix chain 'J' and resid 687 through 696 removed outlier: 4.351A pdb=" N ARG J 693 " --> pdb=" O ALA J 689 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR J 694 " --> pdb=" O PHE J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 705 through 709 removed outlier: 3.907A pdb=" N LYS J 709 " --> pdb=" O GLU J 706 " (cutoff:3.500A) Processing helix chain 'J' and resid 710 through 715 removed outlier: 3.755A pdb=" N SER J 715 " --> pdb=" O HIS J 712 " (cutoff:3.500A) Processing helix chain 'J' and resid 734 through 749 removed outlier: 4.144A pdb=" N THR J 738 " --> pdb=" O HIS J 734 " (cutoff:3.500A) Processing helix chain 'J' and resid 766 through 784 removed outlier: 3.763A pdb=" N GLU J 783 " --> pdb=" O ASN J 779 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N CYS J 784 " --> pdb=" O PHE J 780 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 75 removed outlier: 3.875A pdb=" N LEU I 74 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE I 75 " --> pdb=" O VAL I 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 75' Processing helix chain 'I' and resid 118 through 123 removed outlier: 3.872A pdb=" N LYS I 121 " --> pdb=" O GLU I 118 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE I 122 " --> pdb=" O GLY I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 517 through 527 removed outlier: 3.731A pdb=" N ARG I 527 " --> pdb=" O ALA I 523 " (cutoff:3.500A) Processing helix chain 'I' and resid 582 through 590 Processing helix chain 'I' and resid 607 through 614 removed outlier: 4.597A pdb=" N VAL I 614 " --> pdb=" O LEU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 635 Processing helix chain 'I' and resid 649 through 658 removed outlier: 3.613A pdb=" N TYR I 654 " --> pdb=" O ASP I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 686 Processing helix chain 'I' and resid 687 through 696 removed outlier: 3.810A pdb=" N ARG I 693 " --> pdb=" O ALA I 689 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 714 removed outlier: 3.566A pdb=" N HIS I 712 " --> pdb=" O LYS I 709 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 748 removed outlier: 4.390A pdb=" N THR I 738 " --> pdb=" O HIS I 734 " (cutoff:3.500A) Processing helix chain 'I' and resid 766 through 786 removed outlier: 3.573A pdb=" N CYS I 784 " --> pdb=" O PHE I 780 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 75 Processing helix chain 'L' and resid 76 through 80 Processing helix chain 'L' and resid 228 through 234 Processing helix chain 'L' and resid 517 through 527 Processing helix chain 'L' and resid 582 through 592 Processing helix chain 'L' and resid 607 through 614 removed outlier: 4.435A pdb=" N VAL L 614 " --> pdb=" O LEU L 610 " (cutoff:3.500A) Processing helix chain 'L' and resid 621 through 635 Processing helix chain 'L' and resid 650 through 658 Processing helix chain 'L' and resid 682 through 686 Processing helix chain 'L' and resid 687 through 696 removed outlier: 4.361A pdb=" N ARG L 693 " --> pdb=" O ALA L 689 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR L 694 " --> pdb=" O PHE L 690 " (cutoff:3.500A) Processing helix chain 'L' and resid 705 through 709 removed outlier: 3.945A pdb=" N LYS L 709 " --> pdb=" O GLU L 706 " (cutoff:3.500A) Processing helix chain 'L' and resid 710 through 715 removed outlier: 3.746A pdb=" N SER L 715 " --> pdb=" O HIS L 712 " (cutoff:3.500A) Processing helix chain 'L' and resid 734 through 749 removed outlier: 4.165A pdb=" N THR L 738 " --> pdb=" O HIS L 734 " (cutoff:3.500A) Processing helix chain 'L' and resid 766 through 784 removed outlier: 3.654A pdb=" N GLU L 783 " --> pdb=" O ASN L 779 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS L 784 " --> pdb=" O PHE L 780 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 75 removed outlier: 3.882A pdb=" N LEU K 74 " --> pdb=" O THR K 70 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE K 75 " --> pdb=" O VAL K 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 75' Processing helix chain 'K' and resid 118 through 123 removed outlier: 3.820A pdb=" N LYS K 121 " --> pdb=" O GLU K 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE K 122 " --> pdb=" O GLY K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 234 Processing helix chain 'K' and resid 517 through 525 Processing helix chain 'K' and resid 582 through 591 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 620 through 635 removed outlier: 3.538A pdb=" N LYS K 624 " --> pdb=" O LEU K 620 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET K 627 " --> pdb=" O GLU K 623 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET K 633 " --> pdb=" O ALA K 629 " (cutoff:3.500A) Processing helix chain 'K' and resid 650 through 659 removed outlier: 3.887A pdb=" N TYR K 654 " --> pdb=" O ASP K 650 " (cutoff:3.500A) Processing helix chain 'K' and resid 682 through 686 Processing helix chain 'K' and resid 687 through 696 removed outlier: 3.695A pdb=" N ARG K 693 " --> pdb=" O ALA K 689 " (cutoff:3.500A) Processing helix chain 'K' and resid 735 through 748 removed outlier: 3.504A pdb=" N GLN K 744 " --> pdb=" O GLU K 740 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 786 removed outlier: 3.788A pdb=" N HIS K 772 " --> pdb=" O SER K 768 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU K 783 " --> pdb=" O ASN K 779 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS K 784 " --> pdb=" O PHE K 780 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 103 through 107 removed outlier: 6.253A pdb=" N LEU J 105 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL J 115 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN J 107 " --> pdb=" O SER J 113 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N SER J 113 " --> pdb=" O ASN J 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.745A pdb=" N ARG J 129 " --> pdb=" O SER J 142 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL J 145 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR J 154 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 192 through 195 removed outlier: 7.151A pdb=" N TYR J 202 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG J 212 " --> pdb=" O TYR J 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 305 through 307 removed outlier: 6.997A pdb=" N ALA J 241 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY J 225 " --> pdb=" O ALA J 241 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N TRP J 243 " --> pdb=" O TYR J 223 " (cutoff:3.500A) removed outlier: 16.168A pdb=" N TYR J 223 " --> pdb=" O TRP J 243 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY J 225 " --> pdb=" O ALA J 254 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA J 254 " --> pdb=" O GLY J 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 264 through 266 Processing sheet with id=AA6, first strand: chain 'J' and resid 319 through 325 removed outlier: 5.641A pdb=" N ILE J 321 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU J 337 " --> pdb=" O ILE J 321 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET J 323 " --> pdb=" O THR J 335 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL J 343 " --> pdb=" O ASN J 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N SER J 344 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU J 361 " --> pdb=" O SER J 344 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU J 346 " --> pdb=" O LYS J 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 384 through 390 Processing sheet with id=AA8, first strand: chain 'J' and resid 425 through 432 removed outlier: 3.705A pdb=" N LYS J 427 " --> pdb=" O LEU J 441 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR J 439 " --> pdb=" O LEU J 429 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N TYR J 431 " --> pdb=" O LYS J 437 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS J 437 " --> pdb=" O TYR J 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 478 through 481 removed outlier: 6.368A pdb=" N VAL J 502 " --> pdb=" O ASP J 513 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP J 513 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 531 through 534 removed outlier: 3.834A pdb=" N LYS J 597 " --> pdb=" O GLN J 547 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU J 549 " --> pdb=" O VAL J 595 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL J 595 " --> pdb=" O LEU J 549 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N CYS J 598 " --> pdb=" O VAL J 565 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS J 673 " --> pdb=" O VAL J 644 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER J 675 " --> pdb=" O VAL J 646 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY J 648 " --> pdb=" O SER J 675 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLN J 755 " --> pdb=" O PHE J 722 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE J 724 " --> pdb=" O GLN J 755 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N TYR J 757 " --> pdb=" O ILE J 724 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N HIS J 726 " --> pdb=" O TYR J 757 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 537 through 539 Processing sheet with id=AB3, first strand: chain 'I' and resid 103 through 107 removed outlier: 6.793A pdb=" N VAL I 103 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AB5, first strand: chain 'I' and resid 192 through 195 removed outlier: 7.083A pdb=" N TYR I 202 " --> pdb=" O ARG I 212 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG I 212 " --> pdb=" O TYR I 202 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AB7, first strand: chain 'I' and resid 222 through 224 removed outlier: 4.806A pdb=" N LEU I 294 " --> pdb=" O MET I 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 263 through 266 Processing sheet with id=AB9, first strand: chain 'I' and resid 319 through 326 removed outlier: 5.602A pdb=" N ILE I 321 " --> pdb=" O LEU I 337 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU I 337 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET I 323 " --> pdb=" O THR I 335 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL I 343 " --> pdb=" O ASN I 338 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER I 344 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU I 361 " --> pdb=" O SER I 344 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU I 346 " --> pdb=" O LYS I 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 384 through 390 Processing sheet with id=AC2, first strand: chain 'I' and resid 425 through 432 removed outlier: 6.640A pdb=" N TYR I 439 " --> pdb=" O LEU I 429 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR I 431 " --> pdb=" O LYS I 437 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS I 437 " --> pdb=" O TYR I 431 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 478 through 481 removed outlier: 6.845A pdb=" N VAL I 502 " --> pdb=" O ASP I 513 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP I 513 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 531 through 533 removed outlier: 3.585A pdb=" N LEU I 549 " --> pdb=" O VAL I 595 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL I 595 " --> pdb=" O LEU I 549 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYS I 598 " --> pdb=" O VAL I 565 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR I 560 " --> pdb=" O ASP I 640 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR I 642 " --> pdb=" O TYR I 560 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU I 562 " --> pdb=" O THR I 642 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL I 644 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N LEU I 564 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL I 646 " --> pdb=" O LEU I 564 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL I 566 " --> pdb=" O VAL I 646 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY I 648 " --> pdb=" O VAL I 566 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS I 673 " --> pdb=" O VAL I 644 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY I 648 " --> pdb=" O SER I 675 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE I 722 " --> pdb=" O SER I 753 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN I 755 " --> pdb=" O PHE I 722 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE I 724 " --> pdb=" O GLN I 755 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR I 757 " --> pdb=" O ILE I 724 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N HIS I 726 " --> pdb=" O TYR I 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 537 through 539 Processing sheet with id=AC6, first strand: chain 'L' and resid 103 through 107 removed outlier: 6.731A pdb=" N VAL L 103 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 129 through 132 removed outlier: 3.740A pdb=" N ARG L 129 " --> pdb=" O SER L 142 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL L 145 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR L 154 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 192 through 195 removed outlier: 7.155A pdb=" N TYR L 202 " --> pdb=" O ARG L 212 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG L 212 " --> pdb=" O TYR L 202 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 305 through 307 removed outlier: 6.984A pdb=" N ALA L 241 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY L 225 " --> pdb=" O ALA L 241 " (cutoff:3.500A) removed outlier: 11.617A pdb=" N TRP L 243 " --> pdb=" O TYR L 223 " (cutoff:3.500A) removed outlier: 16.174A pdb=" N TYR L 223 " --> pdb=" O TRP L 243 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY L 225 " --> pdb=" O ALA L 254 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA L 254 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 264 through 266 Processing sheet with id=AD2, first strand: chain 'L' and resid 319 through 325 removed outlier: 5.634A pdb=" N ILE L 321 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU L 337 " --> pdb=" O ILE L 321 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET L 323 " --> pdb=" O THR L 335 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL L 343 " --> pdb=" O ASN L 338 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER L 344 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU L 361 " --> pdb=" O SER L 344 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU L 346 " --> pdb=" O LYS L 359 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 384 through 390 Processing sheet with id=AD4, first strand: chain 'L' and resid 425 through 432 removed outlier: 3.675A pdb=" N LYS L 427 " --> pdb=" O LEU L 441 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR L 439 " --> pdb=" O LEU L 429 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR L 431 " --> pdb=" O LYS L 437 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS L 437 " --> pdb=" O TYR L 431 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 478 through 481 removed outlier: 6.363A pdb=" N VAL L 502 " --> pdb=" O ASP L 513 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASP L 513 " --> pdb=" O VAL L 502 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 531 through 534 removed outlier: 3.508A pdb=" N LYS L 597 " --> pdb=" O GLN L 547 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU L 549 " --> pdb=" O VAL L 595 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL L 595 " --> pdb=" O LEU L 549 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N CYS L 598 " --> pdb=" O VAL L 565 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS L 673 " --> pdb=" O VAL L 644 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER L 675 " --> pdb=" O VAL L 646 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY L 648 " --> pdb=" O SER L 675 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY L 674 " --> pdb=" O LEU L 723 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE L 725 " --> pdb=" O GLY L 674 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA L 676 " --> pdb=" O ILE L 725 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLN L 755 " --> pdb=" O PHE L 722 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE L 724 " --> pdb=" O GLN L 755 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR L 757 " --> pdb=" O ILE L 724 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N HIS L 726 " --> pdb=" O TYR L 757 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 537 through 539 Processing sheet with id=AD8, first strand: chain 'K' and resid 103 through 107 removed outlier: 7.009A pdb=" N VAL K 103 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AE1, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.974A pdb=" N ILE K 200 " --> pdb=" O VAL K 213 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 213 " --> pdb=" O ILE K 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AE3, first strand: chain 'K' and resid 222 through 224 Processing sheet with id=AE4, first strand: chain 'K' and resid 263 through 266 Processing sheet with id=AE5, first strand: chain 'K' and resid 319 through 326 removed outlier: 5.380A pdb=" N ILE K 321 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU K 337 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET K 323 " --> pdb=" O THR K 335 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL K 343 " --> pdb=" O ASN K 338 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LEU K 348 " --> pdb=" O LYS K 358 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS K 358 " --> pdb=" O LEU K 348 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASP K 350 " --> pdb=" O CYS K 356 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS K 356 " --> pdb=" O ASP K 350 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 384 through 390 Processing sheet with id=AE7, first strand: chain 'K' and resid 425 through 432 removed outlier: 5.180A pdb=" N ILE K 428 " --> pdb=" O LEU K 441 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU K 441 " --> pdb=" O ILE K 428 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS K 437 " --> pdb=" O ASP K 432 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 478 through 481 removed outlier: 6.539A pdb=" N VAL K 502 " --> pdb=" O ASP K 513 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP K 513 " --> pdb=" O VAL K 502 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N ASN K 504 " --> pdb=" O MET K 511 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N MET K 511 " --> pdb=" O ASN K 504 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 531 through 533 removed outlier: 3.557A pdb=" N LEU K 549 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL K 595 " --> pdb=" O LEU K 549 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS K 598 " --> pdb=" O VAL K 565 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N TYR K 560 " --> pdb=" O ARG K 643 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ALA K 645 " --> pdb=" O TYR K 560 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 562 " --> pdb=" O ALA K 645 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE K 647 " --> pdb=" O LEU K 562 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU K 564 " --> pdb=" O PHE K 647 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS K 673 " --> pdb=" O VAL K 644 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY K 648 " --> pdb=" O SER K 675 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N PHE K 722 " --> pdb=" O SER K 753 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN K 755 " --> pdb=" O PHE K 722 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE K 724 " --> pdb=" O GLN K 755 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N TYR K 757 " --> pdb=" O ILE K 724 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS K 726 " --> pdb=" O TYR K 757 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 537 through 539 694 hydrogen bonds defined for protein. 1812 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: 9.02 Time building geometry restraints manager: 9.84 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: 7628 1.34 - 1.46: 4973 1.46 - 1.58: 11375 1.58 - 1.70: 0 1.70 - 1.81: 152 Bond restraints: 24128 Sorted by residual: bond pdb=" C ILE I 162 " pdb=" N PRO I 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.80e+00 bond pdb=" C ILE K 162 " pdb=" N PRO K 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.79e+00 bond pdb=" N CYS K 468 " pdb=" CA CYS K 468 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C ILE J 162 " pdb=" N PRO J 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+00 bond pdb=" C ILE L 162 " pdb=" N PRO L 163 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.73e+00 ... (remaining 24123 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.67: 488 105.67 - 112.77: 12716 112.77 - 119.86: 7901 119.86 - 126.95: 11289 126.95 - 134.05: 330 Bond angle restraints: 32724 Sorted by residual: angle pdb=" C GLN I 626 " pdb=" N MET I 627 " pdb=" CA MET I 627 " ideal model delta sigma weight residual 120.28 115.47 4.81 1.34e+00 5.57e-01 1.29e+01 angle pdb=" N MET J 485 " pdb=" CA MET J 485 " pdb=" CB MET J 485 " ideal model delta sigma weight residual 113.65 109.09 4.56 1.47e+00 4.63e-01 9.60e+00 angle pdb=" C VAL I 586 " pdb=" N MET I 587 " pdb=" CA MET I 587 " ideal model delta sigma weight residual 121.66 116.23 5.43 1.76e+00 3.23e-01 9.51e+00 angle pdb=" N VAL J 714 " pdb=" CA VAL J 714 " pdb=" C VAL J 714 " ideal model delta sigma weight residual 111.88 108.98 2.90 1.06e+00 8.90e-01 7.47e+00 angle pdb=" N VAL L 714 " pdb=" CA VAL L 714 " pdb=" C VAL L 714 " ideal model delta sigma weight residual 111.88 108.99 2.89 1.06e+00 8.90e-01 7.45e+00 ... (remaining 32719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 13047 17.56 - 35.12: 1147 35.12 - 52.68: 182 52.68 - 70.25: 48 70.25 - 87.81: 20 Dihedral angle restraints: 14444 sinusoidal: 5888 harmonic: 8556 Sorted by residual: dihedral pdb=" CB CYS K 474 " pdb=" SG CYS K 474 " pdb=" SG CYS K 492 " pdb=" CB CYS K 492 " ideal model delta sinusoidal sigma weight residual -86.00 -12.82 -73.18 1 1.00e+01 1.00e-02 6.82e+01 dihedral pdb=" CB CYS L 465 " pdb=" SG CYS L 465 " pdb=" SG CYS L 468 " pdb=" CB CYS L 468 " ideal model delta sinusoidal sigma weight residual -86.00 -157.60 71.60 1 1.00e+01 1.00e-02 6.57e+01 dihedral pdb=" CB CYS J 465 " pdb=" SG CYS J 465 " pdb=" SG CYS J 468 " pdb=" CB CYS J 468 " ideal model delta sinusoidal sigma weight residual -86.00 -157.39 71.39 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 14441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2510 0.039 - 0.078: 704 0.078 - 0.118: 282 0.118 - 0.157: 37 0.157 - 0.196: 3 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CB ILE I 659 " pdb=" CA ILE I 659 " pdb=" CG1 ILE I 659 " pdb=" CG2 ILE I 659 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CB ILE I 438 " pdb=" CA ILE I 438 " pdb=" CG1 ILE I 438 " pdb=" CG2 ILE I 438 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CB ILE I 162 " pdb=" CA ILE I 162 " pdb=" CG1 ILE I 162 " pdb=" CG2 ILE I 162 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 3533 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 497 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO J 498 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO J 498 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 498 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 497 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO L 498 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 498 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 498 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP L 83 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO L 84 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.023 5.00e-02 4.00e+02 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 638 2.68 - 3.23: 23919 3.23 - 3.79: 38895 3.79 - 4.34: 52842 4.34 - 4.90: 83855 Nonbonded interactions: 200149 Sorted by model distance: nonbonded pdb=" O VAL K 69 " pdb=" OG SER K 590 " model vdw 2.124 2.440 nonbonded pdb=" O GLY L 696 " pdb=" OH TYR L 705 " model vdw 2.181 2.440 nonbonded pdb=" O GLY J 696 " pdb=" OH TYR J 705 " model vdw 2.182 2.440 nonbonded pdb=" OD1 ASN J 289 " pdb=" OG SER J 688 " model vdw 2.188 2.440 nonbonded pdb=" OG SER L 160 " pdb=" O GLY L 165 " model vdw 2.197 2.440 ... (remaining 200144 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 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.030 Extract box with map and model: 6.650 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 61.060 Find NCS groups from input model: 1.340 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: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 0.035 24128 Z= 0.173 Angle : 0.592 8.862 32724 Z= 0.328 Chirality : 0.043 0.196 3536 Planarity : 0.004 0.044 4216 Dihedral : 13.527 87.808 8908 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.18 % Favored : 91.75 % Rotamer: Outliers : 0.08 % Allowed : 0.42 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.30 (0.15), residues: 2908 helix: -0.31 (0.25), residues: 416 sheet: 0.12 (0.19), residues: 750 loop : -1.51 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 229 HIS 0.007 0.001 HIS I 151 PHE 0.016 0.001 PHE J 722 TYR 0.018 0.001 TYR K 763 ARG 0.004 0.000 ARG K 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5816 Ramachandran restraints generated. 2908 Oldfield, 0 Emsley, 2908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 707 MET cc_start: 0.6681 (pmm) cc_final: 0.6089 (pmm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2050 time to fit residues: 13.5940 Evaluate side-chains 28 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 0.0870 chunk 218 optimal weight: 10.0000 chunk 121 optimal weight: 0.0020 chunk 74 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 137 optimal weight: 0.0570 chunk 168 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 779 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24128 Z= 0.162 Angle : 0.617 8.842 32724 Z= 0.339 Chirality : 0.045 0.186 3536 Planarity : 0.004 0.055 4216 Dihedral : 4.603 25.174 3208 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.88 % Favored : 92.71 % Rotamer: Outliers : 0.46 % Allowed : 3.85 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.36 (0.15), residues: 2908 helix: -0.56 (0.24), residues: 492 sheet: 0.18 (0.18), residues: 856 loop : -1.68 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 229 HIS 0.006 0.001 HIS J 772 PHE 0.016 0.001 PHE J 764 TYR 0.015 0.001 TYR L 143 ARG 0.004 0.000 ARG J 616 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 97 ARG cc_start: 0.5837 (mtt180) cc_final: 0.5628 (mmt180) REVERT: I 449 ARG cc_start: 0.8224 (mtt180) cc_final: 0.7903 (mpt-90) REVERT: I 783 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7507 (mm-30) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.1929 time to fit residues: 12.8042 Evaluate side-chains 32 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 233 optimal weight: 0.5980 chunk 259 optimal weight: 0.0030 chunk 89 optimal weight: 0.0000 chunk 210 optimal weight: 4.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 289 ASN ** I 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24128 Z= 0.152 Angle : 0.552 8.413 32724 Z= 0.305 Chirality : 0.043 0.154 3536 Planarity : 0.003 0.028 4216 Dihedral : 4.090 22.174 3208 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.84 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.49 (0.15), residues: 2908 helix: -0.75 (0.23), residues: 496 sheet: 0.05 (0.18), residues: 848 loop : -1.69 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 229 HIS 0.003 0.001 HIS J 772 PHE 0.016 0.001 PHE K 764 TYR 0.012 0.001 TYR L 763 ARG 0.003 0.000 ARG J 775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 449 ARG cc_start: 0.8228 (mtt180) cc_final: 0.7915 (mpt-90) REVERT: I 707 MET cc_start: 0.7272 (pmm) cc_final: 0.6456 (pmm) REVERT: I 783 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7525 (mm-30) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2047 time to fit residues: 12.2434 Evaluate side-chains 31 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 20.0000 chunk 196 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 175 optimal weight: 0.5980 chunk 262 optimal weight: 5.9990 chunk 278 optimal weight: 0.0270 chunk 137 optimal weight: 0.0270 chunk 249 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24128 Z= 0.143 Angle : 0.559 8.855 32724 Z= 0.305 Chirality : 0.043 0.184 3536 Planarity : 0.003 0.030 4216 Dihedral : 3.933 20.350 3208 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.80 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.49 (0.15), residues: 2908 helix: -0.70 (0.23), residues: 496 sheet: 0.10 (0.18), residues: 816 loop : -1.71 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 336 HIS 0.002 0.000 HIS L 151 PHE 0.015 0.001 PHE I 764 TYR 0.017 0.001 TYR L 763 ARG 0.002 0.000 ARG K 775 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 449 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7933 (mpt-90) REVERT: I 499 MET cc_start: 0.6270 (mmm) cc_final: 0.5935 (mmm) REVERT: I 707 MET cc_start: 0.7341 (pmm) cc_final: 0.7049 (pmm) REVERT: I 783 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7544 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2111 time to fit residues: 12.0745 Evaluate side-chains 32 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.0010 chunk 158 optimal weight: 0.0870 chunk 4 optimal weight: 0.2980 chunk 207 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.6768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 289 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.6873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24128 Z= 0.142 Angle : 0.544 7.216 32724 Z= 0.301 Chirality : 0.042 0.159 3536 Planarity : 0.003 0.030 4216 Dihedral : 3.873 18.950 3208 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.94 % Favored : 90.92 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.51 (0.15), residues: 2908 helix: -0.62 (0.24), residues: 496 sheet: 0.10 (0.19), residues: 764 loop : -1.72 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 244 HIS 0.002 0.001 HIS I 281 PHE 0.012 0.001 PHE I 764 TYR 0.012 0.001 TYR I 763 ARG 0.002 0.000 ARG J 775 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 449 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7957 (mpt-90) REVERT: I 707 MET cc_start: 0.7411 (pmm) cc_final: 0.7151 (pmm) REVERT: I 783 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7577 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2338 time to fit residues: 12.0667 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.0470 chunk 250 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 163 optimal weight: 0.0010 chunk 68 optimal weight: 0.0070 chunk 278 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 146 optimal weight: 0.0040 overall best weight: 0.1714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.139 Angle : 0.559 8.508 32724 Z= 0.302 Chirality : 0.042 0.139 3536 Planarity : 0.003 0.030 4216 Dihedral : 3.790 17.295 3208 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.25 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.49 (0.15), residues: 2908 helix: -0.65 (0.23), residues: 496 sheet: 0.08 (0.18), residues: 808 loop : -1.72 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 243 HIS 0.002 0.000 HIS I 772 PHE 0.030 0.001 PHE I 785 TYR 0.012 0.001 TYR K 763 ARG 0.002 0.000 ARG I 775 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 449 ARG cc_start: 0.8340 (mtt180) cc_final: 0.7991 (mpt-90) REVERT: I 707 MET cc_start: 0.7434 (pmm) cc_final: 0.7155 (pmm) REVERT: I 783 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7582 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2307 time to fit residues: 12.9554 Evaluate side-chains 33 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.0570 chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 203 optimal weight: 0.0020 chunk 157 optimal weight: 9.9990 chunk 234 optimal weight: 0.0370 chunk 155 optimal weight: 8.9990 chunk 277 optimal weight: 0.3980 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.134 Angle : 0.549 7.381 32724 Z= 0.297 Chirality : 0.042 0.143 3536 Planarity : 0.003 0.029 4216 Dihedral : 3.666 16.088 3208 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.80 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.39 (0.15), residues: 2908 helix: -0.47 (0.24), residues: 492 sheet: 0.08 (0.18), residues: 808 loop : -1.65 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 336 HIS 0.002 0.000 HIS J 503 PHE 0.011 0.001 PHE L 764 TYR 0.011 0.001 TYR K 763 ARG 0.002 0.000 ARG K 775 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 264 MET cc_start: 0.7406 (mmp) cc_final: 0.7139 (mmp) REVERT: I 449 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8063 (mpt-90) REVERT: I 499 MET cc_start: 0.5632 (mmm) cc_final: 0.5081 (mmm) REVERT: I 707 MET cc_start: 0.7540 (pmm) cc_final: 0.7210 (pmm) REVERT: I 783 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7576 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2048 time to fit residues: 11.8238 Evaluate side-chains 31 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 54 optimal weight: 0.0770 chunk 53 optimal weight: 0.0020 chunk 176 optimal weight: 0.0270 chunk 189 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 25 optimal weight: 0.0970 chunk 218 optimal weight: 5.9990 overall best weight: 0.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.134 Angle : 0.578 10.243 32724 Z= 0.306 Chirality : 0.042 0.136 3536 Planarity : 0.003 0.031 4216 Dihedral : 3.587 15.106 3208 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.39 (0.15), residues: 2908 helix: -0.45 (0.24), residues: 492 sheet: 0.05 (0.18), residues: 808 loop : -1.63 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 336 HIS 0.002 0.000 HIS L 503 PHE 0.012 0.001 PHE K 79 TYR 0.010 0.001 TYR J 130 ARG 0.003 0.000 ARG J 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 499 MET cc_start: 0.5822 (mmm) cc_final: 0.5292 (mmm) REVERT: I 633 MET cc_start: 0.8431 (tpp) cc_final: 0.7889 (mmm) REVERT: I 707 MET cc_start: 0.7577 (pmm) cc_final: 0.7235 (pmm) REVERT: I 783 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7595 (mm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1973 time to fit residues: 11.0292 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.0670 chunk 265 optimal weight: 0.9990 chunk 242 optimal weight: 0.0670 chunk 258 optimal weight: 10.0000 chunk 155 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 257 optimal weight: 0.0270 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.137 Angle : 0.569 9.129 32724 Z= 0.302 Chirality : 0.042 0.134 3536 Planarity : 0.003 0.031 4216 Dihedral : 3.567 14.718 3208 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.35 (0.15), residues: 2908 helix: -0.36 (0.24), residues: 492 sheet: 0.04 (0.18), residues: 808 loop : -1.60 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 336 HIS 0.002 0.000 HIS J 503 PHE 0.011 0.001 PHE L 764 TYR 0.010 0.001 TYR I 763 ARG 0.002 0.000 ARG I 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 323 MET cc_start: 0.5415 (tmm) cc_final: 0.5007 (ptm) REVERT: I 499 MET cc_start: 0.5942 (mmm) cc_final: 0.5456 (mmm) REVERT: I 633 MET cc_start: 0.8317 (tpp) cc_final: 0.7995 (mmm) REVERT: I 701 ASP cc_start: 0.7668 (t0) cc_final: 0.7452 (t70) REVERT: I 707 MET cc_start: 0.7581 (pmm) cc_final: 0.6527 (pmm) REVERT: I 783 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7619 (mm-30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1977 time to fit residues: 10.7339 Evaluate side-chains 31 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 176 optimal weight: 0.0270 chunk 140 optimal weight: 4.9990 overall best weight: 1.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.7181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24128 Z= 0.147 Angle : 0.583 10.815 32724 Z= 0.308 Chirality : 0.043 0.199 3536 Planarity : 0.003 0.031 4216 Dihedral : 3.644 14.286 3208 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.53 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.34 (0.16), residues: 2908 helix: -0.31 (0.24), residues: 492 sheet: -0.10 (0.18), residues: 828 loop : -1.54 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 583 HIS 0.003 0.001 HIS J 737 PHE 0.010 0.001 PHE I 683 TYR 0.010 0.001 TYR J 130 ARG 0.002 0.000 ARG L 527 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4362 Ramachandran restraints generated. 2181 Oldfield, 0 Emsley, 2181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 499 MET cc_start: 0.6037 (mmm) cc_final: 0.5546 (mmm) REVERT: I 587 MET cc_start: 0.7860 (pmm) cc_final: 0.7635 (pmm) REVERT: I 633 MET cc_start: 0.8370 (tpp) cc_final: 0.8017 (mmm) REVERT: I 701 ASP cc_start: 0.7725 (t0) cc_final: 0.7457 (t70) REVERT: I 707 MET cc_start: 0.7709 (pmm) cc_final: 0.6988 (pmm) REVERT: I 783 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7660 (mm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1955 time to fit residues: 10.9478 Evaluate side-chains 30 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 6.9990 chunk 243 optimal weight: 0.0470 chunk 69 optimal weight: 0.0370 chunk 210 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 63 optimal weight: 7.9990 chunk 228 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.058046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.044476 restraints weight = 43645.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.045864 restraints weight = 27750.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.046754 restraints weight = 20756.185| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24128 Z= 0.132 Angle : 0.572 10.342 32724 Z= 0.301 Chirality : 0.043 0.211 3536 Planarity : 0.003 0.031 4216 Dihedral : 3.571 14.267 3208 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.39 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.34 (0.16), residues: 2908 helix: -0.31 (0.25), residues: 492 sheet: -0.09 (0.19), residues: 828 loop : -1.54 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 229 HIS 0.002 0.000 HIS K 281 PHE 0.010 0.001 PHE L 764 TYR 0.007 0.001 TYR J 130 ARG 0.002 0.000 ARG K 527 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2739.17 seconds wall clock time: 51 minutes 52.93 seconds (3112.93 seconds total)