Starting phenix.real_space_refine on Sat Jun 21 08:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f92_28941/06_2025/8f92_28941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f92_28941/06_2025/8f92_28941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f92_28941/06_2025/8f92_28941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f92_28941/06_2025/8f92_28941.map" model { file = "/net/cci-nas-00/data/ceres_data/8f92_28941/06_2025/8f92_28941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f92_28941/06_2025/8f92_28941.cif" } resolution = 3.14 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= 0.037 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 147 5.16 5 C 15606 2.51 5 N 4149 2.21 5 O 4980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24882 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3447 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 23, 'TRANS': 412} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 978 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100} Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: E, F, G, I, J, K, M, N, O, P, Q, R, V, Y, W, Z, X, a Time building chain proxies: 15.48, per 1000 atoms: 0.62 Number of scatterers: 24882 At special positions: 0 Unit cell: (158.7, 158.7, 177.1, 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 147 16.00 O 4980 8.00 N 4149 7.00 C 15606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN Y 4 " - " MAN Y 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 355 " " NAG A 611 " - " ASN A 448 " " NAG A 612 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 355 " " NAG E 611 " - " ASN E 448 " " NAG E 612 " - " ASN E 392 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 156 " " NAG F 603 " - " ASN F 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 301 " " NAG F 609 " - " ASN F 339 " " NAG F 610 " - " ASN F 355 " " NAG F 611 " - " ASN F 448 " " NAG F 612 " - " ASN F 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 386 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN F 332 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 386 " Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.2 seconds 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5604 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 45 sheets defined 16.2% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 123 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.448A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.621A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 removed outlier: 3.898A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.511A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 Processing helix chain 'E' and resid 123 through 126 Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 479 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.447A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 542 removed outlier: 3.621A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 622 Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 661 removed outlier: 3.898A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.512A pdb=" N PHE Q 83 " --> pdb=" O SER Q 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 116 Processing helix chain 'F' and resid 123 through 126 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 350 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 474 through 479 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.447A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.621A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 622 Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 661 removed outlier: 3.898A pdb=" N GLY I 644 " --> pdb=" O GLN I 640 " (cutoff:3.500A) Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.512A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.359A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.651A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.719A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 39 removed outlier: 7.076A pdb=" N MET C 34 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 9 through 13 current: chain 'D' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.510A pdb=" N TRP H 35 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 101 Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.524A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.155A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.359A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.650A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 169 through 176 Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.719A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 34 through 39 removed outlier: 7.076A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'M' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 9 through 13 current: chain 'M' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 96 through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'O' and resid 5 through 6 Processing sheet with id=AD1, first strand: chain 'O' and resid 33 through 39 removed outlier: 6.511A pdb=" N TRP O 35 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 101 Processing sheet with id=AD2, first strand: chain 'Q' and resid 4 through 7 removed outlier: 3.524A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 7.155A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Q 53 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.358A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.650A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA F 200 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR F 435 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 169 through 176 Processing sheet with id=AE1, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 6.719A pdb=" N ASN F 301 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323A current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 470 Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'K' and resid 34 through 39 removed outlier: 7.076A pdb=" N MET K 34 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'N' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 9 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE6, first strand: chain 'P' and resid 5 through 6 Processing sheet with id=AE7, first strand: chain 'P' and resid 33 through 39 removed outlier: 6.510A pdb=" N TRP P 35 " --> pdb=" O GLU P 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU P 50 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100H through 101 Processing sheet with id=AE8, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.523A pdb=" N THR R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 10 through 12 removed outlier: 7.155A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1710 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: 9.07 Time building geometry restraints manager: 8.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7833 1.34 - 1.47: 6613 1.47 - 1.60: 10745 1.60 - 1.72: 0 1.72 - 1.85: 204 Bond restraints: 25395 Sorted by residual: bond pdb=" CA SER A 365 " pdb=" C SER A 365 " ideal model delta sigma weight residual 1.519 1.530 -0.011 5.30e-03 3.56e+04 4.37e+00 bond pdb=" C1 NAG A 609 " pdb=" O5 NAG A 609 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" CA SER F 365 " pdb=" C SER F 365 " ideal model delta sigma weight residual 1.519 1.529 -0.011 5.30e-03 3.56e+04 4.12e+00 bond pdb=" CA SER E 365 " pdb=" C SER E 365 " ideal model delta sigma weight residual 1.519 1.529 -0.011 5.30e-03 3.56e+04 4.12e+00 bond pdb=" C1 NAG F 609 " pdb=" O5 NAG F 609 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 ... (remaining 25390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 31488 1.69 - 3.38: 2523 3.38 - 5.06: 384 5.06 - 6.75: 72 6.75 - 8.44: 9 Bond angle restraints: 34476 Sorted by residual: angle pdb=" N TRP F 69 " pdb=" CA TRP F 69 " pdb=" C TRP F 69 " ideal model delta sigma weight residual 110.17 102.89 7.28 1.61e+00 3.86e-01 2.05e+01 angle pdb=" N TRP A 69 " pdb=" CA TRP A 69 " pdb=" C TRP A 69 " ideal model delta sigma weight residual 110.17 102.90 7.27 1.61e+00 3.86e-01 2.04e+01 angle pdb=" N TRP E 69 " pdb=" CA TRP E 69 " pdb=" C TRP E 69 " ideal model delta sigma weight residual 110.17 102.90 7.27 1.61e+00 3.86e-01 2.04e+01 angle pdb=" N GLU F 482 " pdb=" CA GLU F 482 " pdb=" C GLU F 482 " ideal model delta sigma weight residual 112.72 107.36 5.36 1.28e+00 6.10e-01 1.75e+01 angle pdb=" N GLU E 482 " pdb=" CA GLU E 482 " pdb=" C GLU E 482 " ideal model delta sigma weight residual 112.72 107.38 5.34 1.28e+00 6.10e-01 1.74e+01 ... (remaining 34471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 15562 21.39 - 42.79: 377 42.79 - 64.18: 117 64.18 - 85.57: 54 85.57 - 106.97: 30 Dihedral angle restraints: 16140 sinusoidal: 7374 harmonic: 8766 Sorted by residual: dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.00 -59.00 1 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 ... (remaining 16137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3042 0.063 - 0.126: 879 0.126 - 0.188: 141 0.188 - 0.251: 12 0.251 - 0.314: 6 Chirality restraints: 4080 Sorted by residual: chirality pdb=" C5 BMA Z 3 " pdb=" C4 BMA Z 3 " pdb=" C6 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C5 BMA W 3 " pdb=" C4 BMA W 3 " pdb=" C6 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 4077 not shown) Planarity restraints: 4335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 652 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLN I 652 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN I 652 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN I 653 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 652 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLN G 652 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN G 652 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN G 653 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 652 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C GLN B 652 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN B 652 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN B 653 " 0.023 2.00e-02 2.50e+03 ... (remaining 4332 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4242 2.78 - 3.31: 21889 3.31 - 3.84: 40504 3.84 - 4.37: 49764 4.37 - 4.90: 84088 Nonbonded interactions: 200487 Sorted by model distance: nonbonded pdb=" OE1 GLN N 37 " pdb=" OH TYR N 86 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLN M 37 " pdb=" OH TYR M 86 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLN D 37 " pdb=" OH TYR D 86 " model vdw 2.245 3.040 nonbonded pdb=" O GLY J 96 " pdb=" OH TYR M 96 " model vdw 2.326 3.040 nonbonded pdb=" O GLY K 96 " pdb=" OH TYR N 96 " model vdw 2.326 3.040 ... (remaining 200482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'U' selection = chain 'X' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.650 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: 0.020 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 57.660 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.140 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.006 0.063 25521 Z= 0.275 Angle : 1.032 8.441 34809 Z= 0.569 Chirality : 0.059 0.314 4080 Planarity : 0.006 0.040 4281 Dihedral : 12.258 106.966 10401 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.35 (0.14), residues: 2997 helix: -0.14 (0.25), residues: 408 sheet: 0.91 (0.17), residues: 897 loop : 0.04 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP P 47 HIS 0.012 0.002 HIS R 90 PHE 0.032 0.003 PHE R 98 TYR 0.025 0.003 TYR R 49 ARG 0.008 0.001 ARG K 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 54) link_NAG-ASN : angle 2.69119 ( 162) link_ALPHA1-6 : bond 0.00337 ( 3) link_ALPHA1-6 : angle 1.87411 ( 9) link_BETA1-4 : bond 0.00458 ( 15) link_BETA1-4 : angle 2.47043 ( 45) link_ALPHA1-2 : bond 0.00122 ( 3) link_ALPHA1-2 : angle 1.38365 ( 9) link_ALPHA1-3 : bond 0.00323 ( 6) link_ALPHA1-3 : angle 1.38496 ( 18) hydrogen bonds : bond 0.15188 ( 684) hydrogen bonds : angle 7.08158 ( 1710) SS BOND : bond 0.00530 ( 45) SS BOND : angle 2.26112 ( 90) covalent geometry : bond 0.00598 (25395) covalent geometry : angle 1.00879 (34476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 681 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6878 (mm110) REVERT: A 141 MET cc_start: 0.8584 (mtp) cc_final: 0.8292 (mtp) REVERT: C 89 VAL cc_start: 0.8435 (t) cc_final: 0.8173 (p) REVERT: C 91 TYR cc_start: 0.8586 (m-80) cc_final: 0.8297 (m-80) REVERT: C 102 PHE cc_start: 0.7458 (m-80) cc_final: 0.7149 (m-80) REVERT: D 102 THR cc_start: 0.7547 (m) cc_final: 0.7019 (p) REVERT: B 616 ASN cc_start: 0.8465 (p0) cc_final: 0.8143 (t0) REVERT: H 17 THR cc_start: 0.7770 (m) cc_final: 0.7476 (t) REVERT: L 3 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8201 (mp10) REVERT: E 82 GLN cc_start: 0.7313 (mm-40) cc_final: 0.6654 (mm110) REVERT: E 100 MET cc_start: 0.9300 (mtp) cc_final: 0.9007 (mtm) REVERT: E 450 THR cc_start: 0.8415 (p) cc_final: 0.8209 (p) REVERT: M 52 THR cc_start: 0.8413 (p) cc_final: 0.8105 (t) REVERT: M 102 THR cc_start: 0.7577 (m) cc_final: 0.7102 (p) REVERT: Q 3 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8179 (mp10) REVERT: Q 24 ARG cc_start: 0.7312 (mmm-85) cc_final: 0.6835 (ttm-80) REVERT: F 82 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7185 (mm110) REVERT: F 111 LEU cc_start: 0.8868 (mt) cc_final: 0.8587 (mt) REVERT: F 215 ILE cc_start: 0.8511 (mt) cc_final: 0.8244 (mm) REVERT: K 102 PHE cc_start: 0.7540 (m-80) cc_final: 0.7232 (m-10) REVERT: R 24 ARG cc_start: 0.7047 (mmm-85) cc_final: 0.6768 (ttp80) REVERT: R 97 THR cc_start: 0.8949 (m) cc_final: 0.8686 (p) outliers start: 0 outliers final: 0 residues processed: 681 average time/residue: 0.4114 time to fit residues: 420.0750 Evaluate side-chains 447 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS D 6 GLN B 585 HIS H 33 ASN H 76 ASN E 170 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS M 6 GLN G 585 HIS G 625 ASN O 5 GLN Q 53 ASN Q 70 GLN Q 90 HIS F 170 GLN F 374 HIS N 6 GLN I 585 HIS ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 ASN P 76 ASN R 53 ASN R 90 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.128144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.098464 restraints weight = 38314.742| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.36 r_work: 0.3120 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 25521 Z= 0.170 Angle : 0.667 13.392 34809 Z= 0.343 Chirality : 0.048 0.633 4080 Planarity : 0.004 0.044 4281 Dihedral : 9.995 90.353 4947 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.15 % Allowed : 8.42 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.52 (0.15), residues: 2997 helix: 0.95 (0.27), residues: 405 sheet: 0.89 (0.17), residues: 906 loop : -0.05 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 PHE 0.018 0.002 PHE K 29 TYR 0.015 0.001 TYR F 217 ARG 0.007 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 54) link_NAG-ASN : angle 2.78867 ( 162) link_ALPHA1-6 : bond 0.00352 ( 3) link_ALPHA1-6 : angle 1.33539 ( 9) link_BETA1-4 : bond 0.00650 ( 15) link_BETA1-4 : angle 2.28864 ( 45) link_ALPHA1-2 : bond 0.00448 ( 3) link_ALPHA1-2 : angle 1.87868 ( 9) link_ALPHA1-3 : bond 0.01019 ( 6) link_ALPHA1-3 : angle 2.25281 ( 18) hydrogen bonds : bond 0.05137 ( 684) hydrogen bonds : angle 5.44587 ( 1710) SS BOND : bond 0.00713 ( 45) SS BOND : angle 1.81876 ( 90) covalent geometry : bond 0.00398 (25395) covalent geometry : angle 0.62664 (34476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 449 time to evaluate : 2.719 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7951 (mt0) cc_final: 0.7684 (tt0) REVERT: A 114 GLN cc_start: 0.8370 (mm110) cc_final: 0.8069 (mm110) REVERT: A 166 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7895 (ttp80) REVERT: C 72 ASP cc_start: 0.8506 (t70) cc_final: 0.7932 (t0) REVERT: C 89 VAL cc_start: 0.8301 (t) cc_final: 0.8053 (p) REVERT: B 616 ASN cc_start: 0.8857 (p0) cc_final: 0.8459 (t0) REVERT: H 66 ARG cc_start: 0.8067 (mtp180) cc_final: 0.6951 (ttp-170) REVERT: L 3 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8396 (mp10) REVERT: E 82 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7352 (mm-40) REVERT: E 450 THR cc_start: 0.8690 (p) cc_final: 0.8473 (p) REVERT: J 34 MET cc_start: 0.8952 (mmm) cc_final: 0.8333 (mtp) REVERT: J 81 GLN cc_start: 0.8255 (tp40) cc_final: 0.8019 (tm-30) REVERT: M 47 MET cc_start: 0.8736 (mmm) cc_final: 0.8529 (mmm) REVERT: O 32 ASN cc_start: 0.7850 (m-40) cc_final: 0.7297 (p0) REVERT: O 80 LEU cc_start: 0.8665 (tt) cc_final: 0.8411 (tp) REVERT: Q 3 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8488 (mp10) REVERT: F 215 ILE cc_start: 0.8720 (mt) cc_final: 0.8487 (mm) REVERT: K 34 MET cc_start: 0.9099 (mmm) cc_final: 0.8736 (mtp) REVERT: N 79 GLN cc_start: 0.8051 (mp10) cc_final: 0.7595 (mp10) REVERT: I 616 ASN cc_start: 0.8942 (p0) cc_final: 0.8448 (t0) REVERT: P 29 ILE cc_start: 0.8111 (pt) cc_final: 0.7573 (mt) REVERT: R 70 GLN cc_start: 0.8258 (tp40) cc_final: 0.7883 (mm-40) REVERT: R 97 THR cc_start: 0.9114 (m) cc_final: 0.8685 (p) outliers start: 57 outliers final: 31 residues processed: 473 average time/residue: 0.4035 time to fit residues: 295.2173 Evaluate side-chains 431 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 400 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 133 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 55 optimal weight: 0.0170 chunk 66 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN D 6 GLN B 585 HIS H 13 GLN ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN M 6 GLN M 95 GLN G 585 HIS G 625 ASN ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN F 82 GLN K 81 GLN N 6 GLN N 95 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 GLN R 53 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093337 restraints weight = 38789.839| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.63 r_work: 0.3038 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 25521 Z= 0.220 Angle : 0.671 12.842 34809 Z= 0.338 Chirality : 0.048 0.403 4080 Planarity : 0.004 0.036 4281 Dihedral : 9.359 91.218 4947 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 8.95 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.21 (0.15), residues: 2997 helix: 0.72 (0.27), residues: 408 sheet: 0.68 (0.17), residues: 873 loop : -0.24 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 479 HIS 0.004 0.001 HIS E 105 PHE 0.021 0.002 PHE F 317 TYR 0.022 0.002 TYR R 49 ARG 0.007 0.001 ARG E 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 54) link_NAG-ASN : angle 2.88933 ( 162) link_ALPHA1-6 : bond 0.00280 ( 3) link_ALPHA1-6 : angle 1.55726 ( 9) link_BETA1-4 : bond 0.00550 ( 15) link_BETA1-4 : angle 2.58381 ( 45) link_ALPHA1-2 : bond 0.00181 ( 3) link_ALPHA1-2 : angle 1.81975 ( 9) link_ALPHA1-3 : bond 0.01021 ( 6) link_ALPHA1-3 : angle 1.74947 ( 18) hydrogen bonds : bond 0.04890 ( 684) hydrogen bonds : angle 5.07722 ( 1710) SS BOND : bond 0.00504 ( 45) SS BOND : angle 1.99305 ( 90) covalent geometry : bond 0.00532 (25395) covalent geometry : angle 0.62674 (34476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 384 time to evaluate : 2.646 Fit side-chains revert: symmetry clash REVERT: A 103 GLN cc_start: 0.7882 (mt0) cc_final: 0.7682 (tt0) REVERT: A 114 GLN cc_start: 0.8382 (mm110) cc_final: 0.8076 (mm110) REVERT: C 34 MET cc_start: 0.9087 (mmm) cc_final: 0.8571 (mtp) REVERT: C 72 ASP cc_start: 0.8516 (t70) cc_final: 0.8116 (t0) REVERT: B 616 ASN cc_start: 0.8892 (p0) cc_final: 0.8434 (t0) REVERT: H 66 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7864 (mtp180) REVERT: H 110 THR cc_start: 0.8129 (t) cc_final: 0.7882 (m) REVERT: L 3 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8455 (mp10) REVERT: E 82 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7624 (mm-40) REVERT: E 100 MET cc_start: 0.9426 (mtp) cc_final: 0.9201 (mtm) REVERT: J 34 MET cc_start: 0.9108 (mmm) cc_final: 0.8777 (mtt) REVERT: J 81 GLN cc_start: 0.8191 (tp40) cc_final: 0.7946 (tp40) REVERT: J 87 THR cc_start: 0.7417 (p) cc_final: 0.7001 (p) REVERT: O 32 ASN cc_start: 0.7803 (m-40) cc_final: 0.7350 (p0) REVERT: O 80 LEU cc_start: 0.8713 (tt) cc_final: 0.8446 (tp) REVERT: Q 3 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8511 (mp10) REVERT: Q 83 PHE cc_start: 0.6956 (m-80) cc_final: 0.6669 (m-80) REVERT: K 34 MET cc_start: 0.9205 (mmm) cc_final: 0.8913 (mtt) REVERT: K 72 ASP cc_start: 0.8616 (t70) cc_final: 0.8233 (t0) REVERT: N 69 ASN cc_start: 0.8542 (m-40) cc_final: 0.7742 (t0) REVERT: N 79 GLN cc_start: 0.8107 (mp10) cc_final: 0.7657 (mp10) REVERT: P 29 ILE cc_start: 0.8263 (pt) cc_final: 0.7769 (mt) REVERT: R 70 GLN cc_start: 0.8512 (tp40) cc_final: 0.8119 (mm-40) outliers start: 61 outliers final: 48 residues processed: 411 average time/residue: 0.4252 time to fit residues: 271.8978 Evaluate side-chains 411 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 363 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain G residue 636 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 20 THR Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 244 optimal weight: 4.9990 chunk 204 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 195 ASN C 3 GLN D 6 GLN B 585 HIS L 53 ASN L 70 GLN L 90 HIS E 302 ASN M 95 GLN O 5 GLN O 33 ASN O 76 ASN Q 53 ASN N 6 GLN N 95 GLN I 607 ASN R 53 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.091884 restraints weight = 39454.713| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.80 r_work: 0.3011 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25521 Z= 0.227 Angle : 0.661 12.077 34809 Z= 0.331 Chirality : 0.048 0.397 4080 Planarity : 0.004 0.042 4281 Dihedral : 8.946 91.300 4947 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.68 % Allowed : 9.29 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.03 (0.15), residues: 2997 helix: 0.61 (0.28), residues: 408 sheet: 0.61 (0.17), residues: 852 loop : -0.38 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 479 HIS 0.006 0.001 HIS K 82A PHE 0.018 0.002 PHE F 317 TYR 0.021 0.002 TYR R 49 ARG 0.005 0.001 ARG A 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 54) link_NAG-ASN : angle 2.79764 ( 162) link_ALPHA1-6 : bond 0.00181 ( 3) link_ALPHA1-6 : angle 1.58067 ( 9) link_BETA1-4 : bond 0.00514 ( 15) link_BETA1-4 : angle 2.64446 ( 45) link_ALPHA1-2 : bond 0.00169 ( 3) link_ALPHA1-2 : angle 1.78560 ( 9) link_ALPHA1-3 : bond 0.00952 ( 6) link_ALPHA1-3 : angle 1.73232 ( 18) hydrogen bonds : bond 0.04715 ( 684) hydrogen bonds : angle 4.96040 ( 1710) SS BOND : bond 0.00532 ( 45) SS BOND : angle 1.77236 ( 90) covalent geometry : bond 0.00550 (25395) covalent geometry : angle 0.61978 (34476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 387 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8402 (mm110) cc_final: 0.8086 (mm110) REVERT: A 232 LYS cc_start: 0.9273 (mttp) cc_final: 0.8976 (mmmm) REVERT: C 72 ASP cc_start: 0.8525 (t70) cc_final: 0.8081 (t0) REVERT: H 66 ARG cc_start: 0.8260 (mtp180) cc_final: 0.8000 (mtp180) REVERT: H 110 THR cc_start: 0.8146 (t) cc_final: 0.7928 (m) REVERT: L 3 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8536 (mp10) REVERT: L 83 PHE cc_start: 0.6882 (m-80) cc_final: 0.6232 (m-80) REVERT: E 67 ASN cc_start: 0.7775 (t0) cc_final: 0.7570 (t0) REVERT: E 100 MET cc_start: 0.9488 (mtp) cc_final: 0.9201 (mtm) REVERT: E 121 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8519 (mmtt) REVERT: E 185 ASN cc_start: 0.6774 (m-40) cc_final: 0.6486 (m-40) REVERT: J 34 MET cc_start: 0.9131 (mmm) cc_final: 0.8786 (mtt) REVERT: J 81 GLN cc_start: 0.8288 (tp40) cc_final: 0.7973 (tp40) REVERT: G 542 ARG cc_start: 0.8977 (mtm110) cc_final: 0.8684 (mtm-85) REVERT: O 80 LEU cc_start: 0.8662 (tt) cc_final: 0.8413 (tp) REVERT: Q 3 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8555 (mp10) REVERT: Q 74 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8138 (ttpp) REVERT: Q 83 PHE cc_start: 0.6922 (m-80) cc_final: 0.6650 (m-80) REVERT: K 72 ASP cc_start: 0.8608 (t70) cc_final: 0.8298 (t70) REVERT: N 69 ASN cc_start: 0.8633 (m-40) cc_final: 0.7713 (t0) REVERT: N 79 GLN cc_start: 0.8120 (mp10) cc_final: 0.7669 (mp10) REVERT: P 29 ILE cc_start: 0.8250 (pt) cc_final: 0.7741 (mt) REVERT: R 61 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.7110 (ptt-90) REVERT: R 70 GLN cc_start: 0.8502 (tp40) cc_final: 0.8099 (mm-40) outliers start: 71 outliers final: 55 residues processed: 422 average time/residue: 0.3885 time to fit residues: 251.9453 Evaluate side-chains 424 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 369 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 107 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 282 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 166 optimal weight: 0.0570 chunk 125 optimal weight: 0.5980 chunk 263 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 3 GLN D 6 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 31 ASN M 95 GLN G 625 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN F 216 HIS K 81 GLN N 6 GLN N 95 GLN R 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.125378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093719 restraints weight = 39249.151| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.67 r_work: 0.3041 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25521 Z= 0.132 Angle : 0.584 10.939 34809 Z= 0.295 Chirality : 0.045 0.377 4080 Planarity : 0.004 0.041 4281 Dihedral : 8.441 88.449 4947 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Rotamer: Outliers : 2.11 % Allowed : 10.53 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.11 (0.15), residues: 2997 helix: 0.85 (0.28), residues: 408 sheet: 0.63 (0.17), residues: 876 loop : -0.38 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 479 HIS 0.004 0.001 HIS E 85 PHE 0.014 0.001 PHE O 78 TYR 0.029 0.001 TYR R 49 ARG 0.007 0.000 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 54) link_NAG-ASN : angle 2.53298 ( 162) link_ALPHA1-6 : bond 0.00304 ( 3) link_ALPHA1-6 : angle 1.43193 ( 9) link_BETA1-4 : bond 0.00538 ( 15) link_BETA1-4 : angle 2.28694 ( 45) link_ALPHA1-2 : bond 0.00349 ( 3) link_ALPHA1-2 : angle 1.63835 ( 9) link_ALPHA1-3 : bond 0.01016 ( 6) link_ALPHA1-3 : angle 1.51431 ( 18) hydrogen bonds : bond 0.04022 ( 684) hydrogen bonds : angle 4.70663 ( 1710) SS BOND : bond 0.00401 ( 45) SS BOND : angle 1.66226 ( 90) covalent geometry : bond 0.00309 (25395) covalent geometry : angle 0.54597 (34476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 382 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8403 (mm110) cc_final: 0.8107 (mm110) REVERT: C 72 ASP cc_start: 0.8495 (t70) cc_final: 0.8051 (t0) REVERT: H 66 ARG cc_start: 0.8364 (mtp180) cc_final: 0.8145 (mtp180) REVERT: L 3 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8530 (mp10) REVERT: L 83 PHE cc_start: 0.6846 (m-80) cc_final: 0.6208 (m-80) REVERT: E 67 ASN cc_start: 0.7740 (t0) cc_final: 0.7532 (t0) REVERT: E 121 LYS cc_start: 0.8796 (mmmt) cc_final: 0.8518 (mmtt) REVERT: E 185 ASN cc_start: 0.6879 (m-40) cc_final: 0.6612 (m-40) REVERT: J 81 GLN cc_start: 0.8272 (tp40) cc_final: 0.7919 (tp40) REVERT: G 542 ARG cc_start: 0.8961 (mtm110) cc_final: 0.8737 (mtm110) REVERT: Q 3 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8581 (mp10) REVERT: Q 74 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8124 (ttpp) REVERT: Q 83 PHE cc_start: 0.6923 (m-80) cc_final: 0.6636 (m-80) REVERT: Q 104 LEU cc_start: 0.7736 (tp) cc_final: 0.7145 (tp) REVERT: K 72 ASP cc_start: 0.8584 (t70) cc_final: 0.8088 (t0) REVERT: N 69 ASN cc_start: 0.8580 (m-40) cc_final: 0.7720 (t0) REVERT: N 79 GLN cc_start: 0.8077 (mp10) cc_final: 0.7549 (mp10) REVERT: R 70 GLN cc_start: 0.8512 (tp40) cc_final: 0.8079 (mm-40) outliers start: 56 outliers final: 44 residues processed: 412 average time/residue: 0.4093 time to fit residues: 261.4008 Evaluate side-chains 405 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 361 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 251 optimal weight: 0.9980 chunk 292 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 3 GLN D 6 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN K 81 GLN N 6 GLN N 39 HIS N 95 GLN R 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.124369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092672 restraints weight = 39086.874| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.65 r_work: 0.3022 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25521 Z= 0.169 Angle : 0.609 10.799 34809 Z= 0.305 Chirality : 0.046 0.381 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.330 88.723 4947 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 2.72 % Allowed : 9.85 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.05 (0.15), residues: 2997 helix: 0.82 (0.28), residues: 408 sheet: 0.62 (0.17), residues: 855 loop : -0.43 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 479 HIS 0.004 0.001 HIS N 39 PHE 0.016 0.002 PHE O 78 TYR 0.029 0.001 TYR R 49 ARG 0.008 0.000 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 54) link_NAG-ASN : angle 2.54392 ( 162) link_ALPHA1-6 : bond 0.00277 ( 3) link_ALPHA1-6 : angle 1.49663 ( 9) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 2.42454 ( 45) link_ALPHA1-2 : bond 0.00230 ( 3) link_ALPHA1-2 : angle 1.70386 ( 9) link_ALPHA1-3 : bond 0.00990 ( 6) link_ALPHA1-3 : angle 1.49983 ( 18) hydrogen bonds : bond 0.04186 ( 684) hydrogen bonds : angle 4.71049 ( 1710) SS BOND : bond 0.00432 ( 45) SS BOND : angle 1.96125 ( 90) covalent geometry : bond 0.00405 (25395) covalent geometry : angle 0.56914 (34476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 376 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8403 (mm110) cc_final: 0.8098 (mm110) REVERT: A 232 LYS cc_start: 0.9233 (mttp) cc_final: 0.8951 (mmmm) REVERT: C 72 ASP cc_start: 0.8501 (t70) cc_final: 0.8033 (t0) REVERT: L 3 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8539 (mp10) REVERT: L 83 PHE cc_start: 0.6939 (m-80) cc_final: 0.6334 (m-80) REVERT: E 121 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8490 (mmtt) REVERT: E 185 ASN cc_start: 0.6874 (m-40) cc_final: 0.6597 (m-40) REVERT: J 81 GLN cc_start: 0.8266 (tp40) cc_final: 0.7942 (tp40) REVERT: G 542 ARG cc_start: 0.8998 (mtm110) cc_final: 0.8776 (mtm110) REVERT: Q 3 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8585 (mp10) REVERT: Q 74 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8115 (ttpp) REVERT: Q 83 PHE cc_start: 0.6869 (m-80) cc_final: 0.6562 (m-80) REVERT: Q 104 LEU cc_start: 0.7730 (tp) cc_final: 0.7004 (tp) REVERT: F 232 LYS cc_start: 0.9289 (mttp) cc_final: 0.8964 (mmmm) REVERT: K 72 ASP cc_start: 0.8585 (t70) cc_final: 0.8281 (t70) REVERT: N 42 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7694 (pttm) REVERT: N 69 ASN cc_start: 0.8613 (m-40) cc_final: 0.7672 (t0) REVERT: N 79 GLN cc_start: 0.8142 (mp10) cc_final: 0.7608 (mp10) REVERT: P 29 ILE cc_start: 0.8213 (pt) cc_final: 0.7698 (mt) REVERT: R 70 GLN cc_start: 0.8519 (tp40) cc_final: 0.8065 (mm-40) outliers start: 72 outliers final: 64 residues processed: 416 average time/residue: 0.3836 time to fit residues: 251.6699 Evaluate side-chains 433 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 369 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 75 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 225 optimal weight: 0.2980 chunk 280 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 6 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 37 GLN M 39 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN K 81 GLN N 6 GLN N 31 ASN N 95 GLN R 53 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.115416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.082626 restraints weight = 39118.888| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.84 r_work: 0.2850 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25521 Z= 0.158 Angle : 0.598 10.635 34809 Z= 0.300 Chirality : 0.045 0.375 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.195 88.126 4947 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 2.79 % Allowed : 10.15 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.03 (0.15), residues: 2997 helix: 0.87 (0.28), residues: 408 sheet: 0.51 (0.17), residues: 891 loop : -0.42 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 479 HIS 0.003 0.001 HIS A 105 PHE 0.015 0.002 PHE O 78 TYR 0.030 0.001 TYR R 49 ARG 0.008 0.000 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 54) link_NAG-ASN : angle 2.48709 ( 162) link_ALPHA1-6 : bond 0.00278 ( 3) link_ALPHA1-6 : angle 1.50755 ( 9) link_BETA1-4 : bond 0.00484 ( 15) link_BETA1-4 : angle 2.39592 ( 45) link_ALPHA1-2 : bond 0.00243 ( 3) link_ALPHA1-2 : angle 1.68239 ( 9) link_ALPHA1-3 : bond 0.00988 ( 6) link_ALPHA1-3 : angle 1.42815 ( 18) hydrogen bonds : bond 0.04076 ( 684) hydrogen bonds : angle 4.64206 ( 1710) SS BOND : bond 0.00405 ( 45) SS BOND : angle 1.68360 ( 90) covalent geometry : bond 0.00378 (25395) covalent geometry : angle 0.56085 (34476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 365 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8376 (mm110) cc_final: 0.8025 (mm110) REVERT: A 132 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8870 (p) REVERT: C 72 ASP cc_start: 0.8377 (t70) cc_final: 0.7836 (t0) REVERT: D 42 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7629 (mtmm) REVERT: D 79 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7234 (mp10) REVERT: L 3 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8464 (mp10) REVERT: L 83 PHE cc_start: 0.6818 (m-80) cc_final: 0.6194 (m-80) REVERT: J 72 ASP cc_start: 0.8128 (t70) cc_final: 0.7808 (t70) REVERT: M 103 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7510 (mmm160) REVERT: G 542 ARG cc_start: 0.9003 (mtm110) cc_final: 0.8744 (mtm110) REVERT: O 110 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7893 (m) REVERT: Q 3 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8526 (mp10) REVERT: Q 24 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.6983 (ttp80) REVERT: Q 74 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8064 (ttpp) REVERT: Q 83 PHE cc_start: 0.6677 (m-80) cc_final: 0.6332 (m-80) REVERT: Q 104 LEU cc_start: 0.7561 (tp) cc_final: 0.6717 (tp) REVERT: K 72 ASP cc_start: 0.8520 (t70) cc_final: 0.8155 (t70) REVERT: N 69 ASN cc_start: 0.8568 (m-40) cc_final: 0.7539 (t0) REVERT: N 79 GLN cc_start: 0.8082 (mp10) cc_final: 0.7572 (mp10) REVERT: I 542 ARG cc_start: 0.9110 (mtm110) cc_final: 0.8893 (mtm110) REVERT: R 3 GLN cc_start: 0.8616 (mp10) cc_final: 0.8358 (mp10) REVERT: R 70 GLN cc_start: 0.8510 (tp40) cc_final: 0.8018 (mm-40) outliers start: 74 outliers final: 68 residues processed: 407 average time/residue: 0.4687 time to fit residues: 299.8656 Evaluate side-chains 431 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 361 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 6 GLN Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 251 optimal weight: 0.9990 chunk 266 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 247 optimal weight: 0.9990 chunk 172 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 3 GLN D 6 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 31 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN N 95 GLN P 5 GLN R 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.083287 restraints weight = 39069.500| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.87 r_work: 0.2854 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25521 Z= 0.188 Angle : 0.618 10.636 34809 Z= 0.309 Chirality : 0.046 0.371 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.231 88.590 4947 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 3.13 % Allowed : 10.04 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.05 (0.15), residues: 2997 helix: 0.83 (0.28), residues: 408 sheet: 0.53 (0.17), residues: 858 loop : -0.51 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 479 HIS 0.004 0.001 HIS E 105 PHE 0.016 0.002 PHE O 78 TYR 0.031 0.001 TYR R 49 ARG 0.009 0.000 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 54) link_NAG-ASN : angle 2.51757 ( 162) link_ALPHA1-6 : bond 0.00237 ( 3) link_ALPHA1-6 : angle 1.57303 ( 9) link_BETA1-4 : bond 0.00466 ( 15) link_BETA1-4 : angle 2.50668 ( 45) link_ALPHA1-2 : bond 0.00171 ( 3) link_ALPHA1-2 : angle 1.72440 ( 9) link_ALPHA1-3 : bond 0.00933 ( 6) link_ALPHA1-3 : angle 1.38247 ( 18) hydrogen bonds : bond 0.04228 ( 684) hydrogen bonds : angle 4.68819 ( 1710) SS BOND : bond 0.00435 ( 45) SS BOND : angle 1.80217 ( 90) covalent geometry : bond 0.00455 (25395) covalent geometry : angle 0.57994 (34476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 375 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8344 (mm110) cc_final: 0.8130 (mm-40) REVERT: A 132 THR cc_start: 0.9102 (OUTLIER) cc_final: 0.8854 (p) REVERT: L 3 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8464 (mp10) REVERT: J 81 GLN cc_start: 0.8322 (tp40) cc_final: 0.8000 (tp40) REVERT: J 82 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8118 (mtp) REVERT: M 103 ARG cc_start: 0.7738 (mmm160) cc_final: 0.7482 (mmm160) REVERT: G 542 ARG cc_start: 0.8972 (mtm110) cc_final: 0.8705 (mtm110) REVERT: O 110 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7896 (m) REVERT: Q 3 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8511 (mp10) REVERT: Q 24 ARG cc_start: 0.7569 (mmm-85) cc_final: 0.6963 (ttp80) REVERT: Q 74 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8060 (ttpp) REVERT: Q 83 PHE cc_start: 0.6673 (m-80) cc_final: 0.6376 (m-80) REVERT: Q 104 LEU cc_start: 0.7524 (tp) cc_final: 0.6708 (tp) REVERT: K 72 ASP cc_start: 0.8511 (t70) cc_final: 0.8127 (t70) REVERT: N 69 ASN cc_start: 0.8552 (m-40) cc_final: 0.7432 (t0) REVERT: N 79 GLN cc_start: 0.8095 (mp10) cc_final: 0.7498 (mp10) REVERT: I 542 ARG cc_start: 0.9102 (mtm110) cc_final: 0.8875 (mtm110) REVERT: R 3 GLN cc_start: 0.8592 (mp10) cc_final: 0.8298 (mp10) REVERT: R 61 ARG cc_start: 0.7756 (ptt-90) cc_final: 0.7196 (ptp90) REVERT: R 70 GLN cc_start: 0.8496 (tp40) cc_final: 0.7986 (mm-40) outliers start: 83 outliers final: 71 residues processed: 423 average time/residue: 0.4448 time to fit residues: 300.5252 Evaluate side-chains 438 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 2.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 274 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 31 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN K 81 GLN N 31 ASN N 95 GLN R 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.083176 restraints weight = 39240.816| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.83 r_work: 0.2848 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25521 Z= 0.152 Angle : 0.597 10.370 34809 Z= 0.299 Chirality : 0.045 0.361 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.138 87.541 4947 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 2.98 % Allowed : 10.27 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.15), residues: 2997 helix: 0.92 (0.28), residues: 408 sheet: 0.45 (0.17), residues: 891 loop : -0.45 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 479 HIS 0.004 0.001 HIS K 82A PHE 0.015 0.001 PHE O 78 TYR 0.031 0.001 TYR R 49 ARG 0.009 0.000 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00536 ( 54) link_NAG-ASN : angle 2.44551 ( 162) link_ALPHA1-6 : bond 0.00269 ( 3) link_ALPHA1-6 : angle 1.50218 ( 9) link_BETA1-4 : bond 0.00470 ( 15) link_BETA1-4 : angle 2.38167 ( 45) link_ALPHA1-2 : bond 0.00240 ( 3) link_ALPHA1-2 : angle 1.68256 ( 9) link_ALPHA1-3 : bond 0.00951 ( 6) link_ALPHA1-3 : angle 1.35714 ( 18) hydrogen bonds : bond 0.04012 ( 684) hydrogen bonds : angle 4.62186 ( 1710) SS BOND : bond 0.00447 ( 45) SS BOND : angle 1.79535 ( 90) covalent geometry : bond 0.00361 (25395) covalent geometry : angle 0.55989 (34476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 366 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8376 (mm110) cc_final: 0.8013 (mm110) REVERT: A 132 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8871 (p) REVERT: D 42 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7644 (mtmm) REVERT: D 79 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7395 (mp10) REVERT: D 103 ARG cc_start: 0.7287 (mmm160) cc_final: 0.6931 (mmm160) REVERT: L 3 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8506 (mp10) REVERT: L 83 PHE cc_start: 0.6653 (m-80) cc_final: 0.6121 (m-80) REVERT: J 81 GLN cc_start: 0.8325 (tp40) cc_final: 0.7924 (tp40) REVERT: J 82 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: M 103 ARG cc_start: 0.7758 (mmm160) cc_final: 0.7503 (mmm160) REVERT: G 542 ARG cc_start: 0.8988 (mtm110) cc_final: 0.8731 (mtm110) REVERT: O 110 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7968 (m) REVERT: Q 3 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8540 (mp10) REVERT: Q 24 ARG cc_start: 0.7608 (mmm-85) cc_final: 0.7011 (ttp80) REVERT: Q 74 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8076 (ttpp) REVERT: Q 83 PHE cc_start: 0.6695 (m-80) cc_final: 0.6475 (m-80) REVERT: Q 104 LEU cc_start: 0.7541 (tp) cc_final: 0.7086 (mp) REVERT: F 328 MET cc_start: 0.8947 (ttt) cc_final: 0.8664 (ttt) REVERT: K 72 ASP cc_start: 0.8520 (t70) cc_final: 0.8145 (t70) REVERT: N 42 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7801 (pttm) REVERT: N 69 ASN cc_start: 0.8614 (m-40) cc_final: 0.7556 (t0) REVERT: N 79 GLN cc_start: 0.8145 (mp10) cc_final: 0.7574 (mp10) REVERT: I 542 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8891 (mtm110) REVERT: I 626 MET cc_start: 0.9072 (ttt) cc_final: 0.8849 (ptm) REVERT: P 5 GLN cc_start: 0.7451 (mp-120) cc_final: 0.7116 (mp10) REVERT: R 3 GLN cc_start: 0.8613 (mp10) cc_final: 0.8311 (mp10) REVERT: R 61 ARG cc_start: 0.7780 (ptt-90) cc_final: 0.6960 (ptt-90) REVERT: R 70 GLN cc_start: 0.8518 (tp40) cc_final: 0.8018 (mm-40) outliers start: 79 outliers final: 67 residues processed: 412 average time/residue: 0.4661 time to fit residues: 304.3649 Evaluate side-chains 432 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 362 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 216 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 290 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 31 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN N 31 ASN N 95 GLN P 13 GLN R 53 ASN R 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090424 restraints weight = 38962.509| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.55 r_work: 0.2996 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25521 Z= 0.251 Angle : 0.686 11.088 34809 Z= 0.341 Chirality : 0.048 0.382 4080 Planarity : 0.005 0.043 4281 Dihedral : 8.472 89.092 4947 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.07 % Favored : 94.83 % Rotamer: Outliers : 2.94 % Allowed : 10.15 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.29 (0.15), residues: 2997 helix: 0.66 (0.28), residues: 408 sheet: 0.34 (0.17), residues: 888 loop : -0.67 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 479 HIS 0.005 0.001 HIS A 85 PHE 0.022 0.002 PHE K 29 TYR 0.032 0.002 TYR R 49 ARG 0.010 0.001 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00631 ( 54) link_NAG-ASN : angle 2.66943 ( 162) link_ALPHA1-6 : bond 0.00177 ( 3) link_ALPHA1-6 : angle 1.80701 ( 9) link_BETA1-4 : bond 0.00474 ( 15) link_BETA1-4 : angle 2.74517 ( 45) link_ALPHA1-2 : bond 0.00067 ( 3) link_ALPHA1-2 : angle 1.81892 ( 9) link_ALPHA1-3 : bond 0.00911 ( 6) link_ALPHA1-3 : angle 1.34531 ( 18) hydrogen bonds : bond 0.04705 ( 684) hydrogen bonds : angle 4.84463 ( 1710) SS BOND : bond 0.00526 ( 45) SS BOND : angle 2.06113 ( 90) covalent geometry : bond 0.00614 (25395) covalent geometry : angle 0.64688 (34476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5994 Ramachandran restraints generated. 2997 Oldfield, 0 Emsley, 2997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 370 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8420 (mm110) cc_final: 0.8207 (mm-40) REVERT: A 132 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8863 (p) REVERT: C 82 MET cc_start: 0.8856 (mtm) cc_final: 0.8609 (mtm) REVERT: D 79 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7744 (mp10) REVERT: D 103 ARG cc_start: 0.7455 (mmm160) cc_final: 0.7093 (mmm160) REVERT: L 3 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8587 (mp10) REVERT: J 81 GLN cc_start: 0.8337 (tp40) cc_final: 0.8028 (tp40) REVERT: M 103 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7603 (mmm160) REVERT: G 542 ARG cc_start: 0.8978 (mtm110) cc_final: 0.8495 (mtm-85) REVERT: O 110 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7956 (m) REVERT: Q 3 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8592 (mp10) REVERT: Q 24 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.7168 (ttp80) REVERT: Q 74 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8120 (ttpp) REVERT: Q 83 PHE cc_start: 0.6809 (m-80) cc_final: 0.6501 (m-80) REVERT: Q 104 LEU cc_start: 0.7615 (tp) cc_final: 0.6797 (tp) REVERT: F 232 LYS cc_start: 0.9294 (mttp) cc_final: 0.8974 (mmmm) REVERT: F 328 MET cc_start: 0.9034 (ttt) cc_final: 0.8703 (ttt) REVERT: K 72 ASP cc_start: 0.8610 (t70) cc_final: 0.8097 (t0) REVERT: N 79 GLN cc_start: 0.8278 (mp10) cc_final: 0.7654 (mp10) REVERT: I 542 ARG cc_start: 0.9077 (mtm110) cc_final: 0.8848 (mtm110) REVERT: I 626 MET cc_start: 0.9065 (ttt) cc_final: 0.8693 (ptt) REVERT: I 636 SER cc_start: 0.9143 (t) cc_final: 0.8863 (p) REVERT: P 5 GLN cc_start: 0.7470 (mp-120) cc_final: 0.7126 (mp10) REVERT: R 3 GLN cc_start: 0.8635 (mp10) cc_final: 0.8365 (mp10) REVERT: R 61 ARG cc_start: 0.7872 (ptt-90) cc_final: 0.7376 (ptp90) REVERT: R 70 GLN cc_start: 0.8537 (tp40) cc_final: 0.8067 (mm-40) outliers start: 78 outliers final: 71 residues processed: 418 average time/residue: 0.3797 time to fit residues: 247.3829 Evaluate side-chains 433 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 360 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain G residue 546 SER Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 21 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 25 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 74 CYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 21 ILE Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 25 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 213 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 242 optimal weight: 0.0040 chunk 128 optimal weight: 1.9990 chunk 224 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 216 optimal weight: 0.0770 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 585 HIS H 5 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 6 GLN M 31 ASN G 625 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN F 356 ASN N 95 GLN R 53 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083649 restraints weight = 39087.341| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.74 r_work: 0.2868 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25521 Z= 0.118 Angle : 0.601 12.201 34809 Z= 0.303 Chirality : 0.044 0.356 4080 Planarity : 0.004 0.043 4281 Dihedral : 8.153 85.810 4947 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 2.30 % Allowed : 11.06 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.15), residues: 2997 helix: 0.97 (0.28), residues: 408 sheet: 0.38 (0.17), residues: 894 loop : -0.52 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 479 HIS 0.005 0.001 HIS D 39 PHE 0.014 0.001 PHE O 78 TYR 0.031 0.001 TYR R 49 ARG 0.009 0.000 ARG O 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 54) link_NAG-ASN : angle 2.40302 ( 162) link_ALPHA1-6 : bond 0.00333 ( 3) link_ALPHA1-6 : angle 1.42723 ( 9) link_BETA1-4 : bond 0.00495 ( 15) link_BETA1-4 : angle 2.24465 ( 45) link_ALPHA1-2 : bond 0.00362 ( 3) link_ALPHA1-2 : angle 1.67304 ( 9) link_ALPHA1-3 : bond 0.00974 ( 6) link_ALPHA1-3 : angle 1.30625 ( 18) hydrogen bonds : bond 0.03838 ( 684) hydrogen bonds : angle 4.61795 ( 1710) SS BOND : bond 0.00464 ( 45) SS BOND : angle 1.82771 ( 90) covalent geometry : bond 0.00270 (25395) covalent geometry : angle 0.56626 (34476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17562.62 seconds wall clock time: 307 minutes 7.23 seconds (18427.23 seconds total)