Starting phenix.real_space_refine on Mon Aug 25 02:34:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f92_28941/08_2025/8f92_28941.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f92_28941/08_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_28941/08_2025/8f92_28941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f92_28941/08_2025/8f92_28941.map" model { file = "/net/cci-nas-00/data/ceres_data/8f92_28941/08_2025/8f92_28941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f92_28941/08_2025/8f92_28941.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.19, per 1000 atoms: 0.17 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: 1.85 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.57 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: 3.28 Time building geometry restraints manager: 2.57 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: 0.03 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: 6.800 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.280 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG K 66 TYR 0.025 0.003 TYR R 49 PHE 0.032 0.003 PHE R 98 TRP 0.029 0.003 TRP P 47 HIS 0.012 0.002 HIS R 90 Details of bonding type rmsd covalent geometry : bond 0.00598 (25395) covalent geometry : angle 1.00879 (34476) SS BOND : bond 0.00530 ( 45) SS BOND : angle 2.26112 ( 90) hydrogen bonds : bond 0.15188 ( 684) hydrogen bonds : angle 7.08158 ( 1710) 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) 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_NAG-ASN : bond 0.00474 ( 54) link_NAG-ASN : angle 2.69119 ( 162) *********************** 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 : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6877 (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: 0.8174 (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: 0.7148 (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: 0.8144 (t0) REVERT: H 17 THR cc_start: 0.7770 (m) cc_final: 0.7463 (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: 0.6652 (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: 0.8210 (p) REVERT: M 52 THR cc_start: 0.8413 (p) cc_final: 0.8104 (t) REVERT: M 102 THR cc_start: 0.7577 (m) cc_final: 0.7105 (p) REVERT: Q 3 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8180 (mp10) REVERT: Q 24 ARG cc_start: 0.7312 (mmm-85) cc_final: 0.6780 (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: 0.8589 (mt) REVERT: F 215 ILE cc_start: 0.8511 (mt) cc_final: 0.8241 (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: 0.1651 time to fit residues: 169.2275 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 : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.0030 overall best weight: 0.4190 ------------------------------------------------------------------------------- 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 76 ASN Q 90 HIS F 170 GLN F 374 HIS N 6 GLN I 585 HIS I 607 ASN P 33 ASN P 76 ASN R 53 ASN R 90 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100479 restraints weight = 38866.569| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.47 r_work: 0.3148 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25521 Z= 0.137 Angle : 0.654 14.308 34809 Z= 0.335 Chirality : 0.047 0.613 4080 Planarity : 0.004 0.045 4281 Dihedral : 9.960 89.288 4947 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.74 % Allowed : 8.64 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.15), residues: 2997 helix: 1.01 (0.27), residues: 405 sheet: 0.96 (0.17), residues: 903 loop : -0.01 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 192 TYR 0.014 0.001 TYR F 217 PHE 0.017 0.002 PHE K 29 TRP 0.019 0.001 TRP A 479 HIS 0.004 0.001 HIS L 90 Details of bonding type rmsd covalent geometry : bond 0.00305 (25395) covalent geometry : angle 0.61224 (34476) SS BOND : bond 0.00459 ( 45) SS BOND : angle 1.90877 ( 90) hydrogen bonds : bond 0.04925 ( 684) hydrogen bonds : angle 5.45376 ( 1710) link_ALPHA1-2 : bond 0.00524 ( 3) link_ALPHA1-2 : angle 1.78884 ( 9) link_ALPHA1-3 : bond 0.00934 ( 6) link_ALPHA1-3 : angle 2.13421 ( 18) link_ALPHA1-6 : bond 0.00237 ( 3) link_ALPHA1-6 : angle 1.29736 ( 9) link_BETA1-4 : bond 0.00667 ( 15) link_BETA1-4 : angle 2.13851 ( 45) link_NAG-ASN : bond 0.00432 ( 54) link_NAG-ASN : angle 2.81635 ( 162) *********************** 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 504 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 458 time to evaluate : 0.782 Fit side-chains REVERT: A 82 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7399 (mm110) REVERT: A 103 GLN cc_start: 0.7930 (mt0) cc_final: 0.7651 (tt0) REVERT: C 72 ASP cc_start: 0.8488 (t70) cc_final: 0.7915 (t0) REVERT: C 89 VAL cc_start: 0.8302 (t) cc_final: 0.8066 (p) REVERT: B 616 ASN cc_start: 0.8867 (p0) cc_final: 0.8477 (t0) REVERT: H 66 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7001 (ttp-170) REVERT: L 3 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8376 (mp10) REVERT: L 70 GLN cc_start: 0.7907 (tt0) cc_final: 0.7702 (mm-40) REVERT: E 82 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7315 (mm-40) REVERT: E 450 THR cc_start: 0.8676 (p) cc_final: 0.8458 (p) REVERT: G 616 ASN cc_start: 0.8843 (p0) cc_final: 0.8434 (t0) REVERT: O 32 ASN cc_start: 0.7841 (m-40) cc_final: 0.7307 (p0) REVERT: O 80 LEU cc_start: 0.8592 (tt) cc_final: 0.8348 (tp) REVERT: Q 3 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8457 (mp10) REVERT: F 215 ILE cc_start: 0.8699 (mt) cc_final: 0.8468 (mm) REVERT: K 34 MET cc_start: 0.9052 (mmm) cc_final: 0.8662 (mtp) REVERT: N 79 GLN cc_start: 0.8015 (mp10) cc_final: 0.7575 (mp10) REVERT: I 616 ASN cc_start: 0.8919 (p0) cc_final: 0.8438 (t0) REVERT: P 29 ILE cc_start: 0.8051 (pt) cc_final: 0.7536 (mt) REVERT: R 97 THR cc_start: 0.9122 (m) cc_final: 0.8701 (p) outliers start: 46 outliers final: 27 residues processed: 478 average time/residue: 0.1598 time to fit residues: 117.1970 Evaluate side-chains 429 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 402 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS 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 22 THR 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 F residue 68 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 87 THR 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 R residue 13 VAL Chi-restraints excluded: chain R residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 233 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 G 585 HIS G 625 ASN ** O 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN Q 53 ASN F 82 GLN F 302 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092352 restraints weight = 39036.615| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.63 r_work: 0.3025 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25521 Z= 0.251 Angle : 0.706 13.473 34809 Z= 0.355 Chirality : 0.050 0.737 4080 Planarity : 0.005 0.042 4281 Dihedral : 9.415 91.561 4947 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 2.57 % Allowed : 8.83 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.15), residues: 2997 helix: 0.73 (0.27), residues: 405 sheet: 0.71 (0.17), residues: 885 loop : -0.21 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 192 TYR 0.021 0.002 TYR R 49 PHE 0.025 0.003 PHE F 317 TRP 0.018 0.002 TRP F 45 HIS 0.005 0.002 HIS Q 32 Details of bonding type rmsd covalent geometry : bond 0.00612 (25395) covalent geometry : angle 0.66459 (34476) SS BOND : bond 0.00530 ( 45) SS BOND : angle 1.86109 ( 90) hydrogen bonds : bond 0.05108 ( 684) hydrogen bonds : angle 5.12826 ( 1710) link_ALPHA1-2 : bond 0.00130 ( 3) link_ALPHA1-2 : angle 1.89455 ( 9) link_ALPHA1-3 : bond 0.00954 ( 6) link_ALPHA1-3 : angle 1.73726 ( 18) link_ALPHA1-6 : bond 0.00275 ( 3) link_ALPHA1-6 : angle 1.59216 ( 9) link_BETA1-4 : bond 0.00540 ( 15) link_BETA1-4 : angle 2.70606 ( 45) link_NAG-ASN : bond 0.00704 ( 54) link_NAG-ASN : angle 2.91277 ( 162) *********************** 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 456 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 388 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8382 (mtm110) cc_final: 0.7902 (ttp80) REVERT: A 232 LYS cc_start: 0.9214 (mttp) cc_final: 0.8908 (mmmm) REVERT: C 34 MET cc_start: 0.9106 (mmm) cc_final: 0.8613 (mtp) REVERT: C 72 ASP cc_start: 0.8533 (t70) cc_final: 0.7903 (t0) REVERT: B 616 ASN cc_start: 0.8902 (p0) cc_final: 0.8433 (t0) REVERT: H 66 ARG cc_start: 0.8247 (mtp180) cc_final: 0.7959 (mtp180) REVERT: L 3 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8447 (mp10) REVERT: L 83 PHE cc_start: 0.6877 (m-80) cc_final: 0.6259 (m-80) REVERT: E 82 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7648 (mm-40) REVERT: E 100 MET cc_start: 0.9444 (mtp) cc_final: 0.9236 (mtm) REVERT: E 103 GLN cc_start: 0.7753 (mt0) cc_final: 0.7470 (tt0) REVERT: J 87 THR cc_start: 0.7472 (p) cc_final: 0.7066 (p) REVERT: O 18 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7702 (mp) REVERT: O 32 ASN cc_start: 0.7804 (m-40) cc_final: 0.7383 (p0) REVERT: O 80 LEU cc_start: 0.8698 (tt) cc_final: 0.8430 (tp) REVERT: Q 3 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8518 (mp10) REVERT: Q 83 PHE cc_start: 0.6944 (m-80) cc_final: 0.6644 (m-80) REVERT: F 328 MET cc_start: 0.9051 (ttt) cc_final: 0.8806 (ttt) REVERT: K 34 MET cc_start: 0.9220 (mmm) cc_final: 0.8927 (mtt) REVERT: K 72 ASP cc_start: 0.8574 (t70) cc_final: 0.8247 (t0) REVERT: N 69 ASN cc_start: 0.8557 (m-40) cc_final: 0.7680 (t0) REVERT: N 79 GLN cc_start: 0.8054 (mp10) cc_final: 0.7629 (mp10) REVERT: P 29 ILE cc_start: 0.8293 (pt) cc_final: 0.7795 (mt) outliers start: 68 outliers final: 52 residues processed: 421 average time/residue: 0.1543 time to fit residues: 100.4360 Evaluate side-chains 417 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 364 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE 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 72 ASP 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 199 SER Chi-restraints excluded: chain E residue 355 ASN 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 18 LEU 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 111 LEU Chi-restraints excluded: chain F residue 150 MET 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 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 5 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 216 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 169 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 44 optimal weight: 0.0020 chunk 222 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 93 optimal weight: 0.1980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 53 ASN L 90 HIS ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 95 GLN G 585 HIS O 5 GLN O 33 ASN K 82AHIS N 6 GLN N 95 GLN R 53 ASN R 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.127348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096274 restraints weight = 38864.430| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.50 r_work: 0.3080 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25521 Z= 0.117 Angle : 0.581 11.266 34809 Z= 0.293 Chirality : 0.045 0.385 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.699 87.986 4947 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.81 % Allowed : 10.23 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.15), residues: 2997 helix: 0.91 (0.28), residues: 408 sheet: 0.95 (0.17), residues: 831 loop : -0.23 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 360 TYR 0.020 0.001 TYR R 49 PHE 0.014 0.001 PHE O 78 TRP 0.020 0.001 TRP E 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00263 (25395) covalent geometry : angle 0.54200 (34476) SS BOND : bond 0.00376 ( 45) SS BOND : angle 1.53837 ( 90) hydrogen bonds : bond 0.04005 ( 684) hydrogen bonds : angle 4.78691 ( 1710) link_ALPHA1-2 : bond 0.00451 ( 3) link_ALPHA1-2 : angle 1.61051 ( 9) link_ALPHA1-3 : bond 0.00990 ( 6) link_ALPHA1-3 : angle 1.67138 ( 18) link_ALPHA1-6 : bond 0.00302 ( 3) link_ALPHA1-6 : angle 1.41470 ( 9) link_BETA1-4 : bond 0.00580 ( 15) link_BETA1-4 : angle 2.19704 ( 45) link_NAG-ASN : bond 0.00585 ( 54) link_NAG-ASN : angle 2.61229 ( 162) *********************** 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 447 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 399 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6631 (m-40) cc_final: 0.6091 (m110) REVERT: A 232 LYS cc_start: 0.9190 (mttp) cc_final: 0.8895 (mmmm) REVERT: C 72 ASP cc_start: 0.8440 (t70) cc_final: 0.8016 (t0) REVERT: C 81 GLN cc_start: 0.8478 (tp40) cc_final: 0.8004 (tp40) REVERT: B 616 ASN cc_start: 0.8871 (p0) cc_final: 0.8421 (t0) REVERT: L 3 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8474 (mp10) REVERT: L 83 PHE cc_start: 0.6829 (m-80) cc_final: 0.6265 (m-80) REVERT: E 82 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7730 (mm-40) REVERT: J 78 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8186 (tp) REVERT: J 87 THR cc_start: 0.7347 (p) cc_final: 0.6913 (p) REVERT: G 542 ARG cc_start: 0.8956 (mtm110) cc_final: 0.8742 (mtm110) REVERT: O 32 ASN cc_start: 0.7558 (m-40) cc_final: 0.7328 (p0) REVERT: Q 3 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8497 (mp10) REVERT: Q 83 PHE cc_start: 0.6893 (m-80) cc_final: 0.6603 (m-80) REVERT: Q 104 LEU cc_start: 0.7778 (tp) cc_final: 0.6989 (tp) REVERT: K 72 ASP cc_start: 0.8564 (t70) cc_final: 0.8184 (t0) REVERT: N 69 ASN cc_start: 0.8450 (m-40) cc_final: 0.7685 (t0) REVERT: N 79 GLN cc_start: 0.8005 (mp10) cc_final: 0.7516 (mp10) REVERT: I 542 ARG cc_start: 0.9102 (mtm110) cc_final: 0.8877 (mtm110) REVERT: P 29 ILE cc_start: 0.8126 (pt) cc_final: 0.7657 (mt) REVERT: P 50 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7527 (mt-10) outliers start: 48 outliers final: 34 residues processed: 428 average time/residue: 0.1639 time to fit residues: 108.2650 Evaluate side-chains 401 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 366 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 ASP 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 H residue 56 ILE Chi-restraints excluded: chain H residue 82 VAL 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 J residue 28 THR Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 78 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 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 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 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 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 22 THR 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 100 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 201 optimal weight: 0.0270 chunk 63 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 242 optimal weight: 0.0980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN D 6 GLN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 31 ASN G 585 HIS O 5 GLN O 76 ASN F 82 GLN N 6 GLN N 95 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.094769 restraints weight = 38980.700| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.82 r_work: 0.3058 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 25521 Z= 0.147 Angle : 0.594 11.055 34809 Z= 0.298 Chirality : 0.045 0.379 4080 Planarity : 0.004 0.039 4281 Dihedral : 8.445 88.113 4947 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.15 % Allowed : 10.53 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 2997 helix: 0.93 (0.28), residues: 408 sheet: 0.90 (0.17), residues: 840 loop : -0.30 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 103 TYR 0.022 0.001 TYR R 49 PHE 0.016 0.002 PHE O 78 TRP 0.013 0.001 TRP E 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00350 (25395) covalent geometry : angle 0.55493 (34476) SS BOND : bond 0.00415 ( 45) SS BOND : angle 1.79108 ( 90) hydrogen bonds : bond 0.04069 ( 684) hydrogen bonds : angle 4.71421 ( 1710) link_ALPHA1-2 : bond 0.00316 ( 3) link_ALPHA1-2 : angle 1.66234 ( 9) link_ALPHA1-3 : bond 0.01029 ( 6) link_ALPHA1-3 : angle 1.60782 ( 18) link_ALPHA1-6 : bond 0.00297 ( 3) link_ALPHA1-6 : angle 1.46607 ( 9) link_BETA1-4 : bond 0.00517 ( 15) link_BETA1-4 : angle 2.31786 ( 45) link_NAG-ASN : bond 0.00532 ( 54) link_NAG-ASN : angle 2.54291 ( 162) *********************** 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 435 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 378 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6738 (m-40) cc_final: 0.6509 (m110) REVERT: A 232 LYS cc_start: 0.9243 (mttp) cc_final: 0.8909 (mmmm) REVERT: C 72 ASP cc_start: 0.8437 (t70) cc_final: 0.7999 (t0) REVERT: C 81 GLN cc_start: 0.8530 (tp40) cc_final: 0.8111 (tp40) REVERT: L 3 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8482 (mp10) REVERT: L 83 PHE cc_start: 0.6853 (m-80) cc_final: 0.6199 (m-80) REVERT: E 121 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8480 (mmtt) REVERT: G 542 ARG cc_start: 0.8979 (mtm110) cc_final: 0.8757 (mtm110) REVERT: O 32 ASN cc_start: 0.7643 (m-40) cc_final: 0.7374 (p0) REVERT: Q 3 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8503 (mp10) REVERT: Q 83 PHE cc_start: 0.6914 (m-80) cc_final: 0.6683 (m-80) REVERT: F 267 GLU cc_start: 0.7635 (pm20) cc_final: 0.7378 (pm20) REVERT: K 28 THR cc_start: 0.7988 (p) cc_final: 0.7754 (p) REVERT: K 72 ASP cc_start: 0.8559 (t70) cc_final: 0.8157 (t0) REVERT: N 69 ASN cc_start: 0.8524 (m-40) cc_final: 0.7724 (t0) REVERT: N 79 GLN cc_start: 0.8062 (mp10) cc_final: 0.7557 (mp10) REVERT: I 542 ARG cc_start: 0.9090 (mtm110) cc_final: 0.8854 (mtm110) REVERT: P 29 ILE cc_start: 0.8195 (pt) cc_final: 0.7678 (mt) outliers start: 57 outliers final: 45 residues processed: 408 average time/residue: 0.1584 time to fit residues: 100.9362 Evaluate side-chains 411 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 ASP 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 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 82 VAL 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 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 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 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain R residue 13 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 111 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 239 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 39 HIS B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN M 6 GLN M 31 ASN M 95 GLN G 625 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN N 95 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.123776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.092343 restraints weight = 39116.685| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.64 r_work: 0.3015 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25521 Z= 0.207 Angle : 0.644 11.065 34809 Z= 0.322 Chirality : 0.047 0.386 4080 Planarity : 0.004 0.041 4281 Dihedral : 8.439 89.597 4947 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 3.02 % Allowed : 10.27 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.15), residues: 2997 helix: 0.81 (0.28), residues: 408 sheet: 0.63 (0.17), residues: 858 loop : -0.40 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 81 TYR 0.030 0.002 TYR R 49 PHE 0.018 0.002 PHE K 29 TRP 0.024 0.002 TRP E 479 HIS 0.006 0.001 HIS M 39 Details of bonding type rmsd covalent geometry : bond 0.00502 (25395) covalent geometry : angle 0.60483 (34476) SS BOND : bond 0.00459 ( 45) SS BOND : angle 1.81869 ( 90) hydrogen bonds : bond 0.04464 ( 684) hydrogen bonds : angle 4.74881 ( 1710) link_ALPHA1-2 : bond 0.00163 ( 3) link_ALPHA1-2 : angle 1.76752 ( 9) link_ALPHA1-3 : bond 0.00964 ( 6) link_ALPHA1-3 : angle 1.52720 ( 18) link_ALPHA1-6 : bond 0.00272 ( 3) link_ALPHA1-6 : angle 1.60778 ( 9) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 2.56536 ( 45) link_NAG-ASN : bond 0.00568 ( 54) link_NAG-ASN : angle 2.62965 ( 162) *********************** 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 457 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 377 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.6666 (m-40) cc_final: 0.6459 (m110) REVERT: A 232 LYS cc_start: 0.9233 (mttp) cc_final: 0.8931 (mmmm) REVERT: C 72 ASP cc_start: 0.8478 (t70) cc_final: 0.7991 (t0) REVERT: D 79 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7403 (mp10) REVERT: L 3 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8529 (mp10) REVERT: L 83 PHE cc_start: 0.6939 (m-80) cc_final: 0.6318 (m-80) REVERT: E 53 PHE cc_start: 0.8514 (p90) cc_final: 0.8211 (p90) REVERT: E 185 ASN cc_start: 0.6875 (m-40) cc_final: 0.6615 (m-40) REVERT: G 542 ARG cc_start: 0.8942 (mtm110) cc_final: 0.8438 (mtm-85) REVERT: O 18 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7662 (mp) REVERT: O 32 ASN cc_start: 0.7823 (m-40) cc_final: 0.7446 (p0) REVERT: Q 3 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8274 (mp10) REVERT: Q 24 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7116 (ttp80) REVERT: Q 83 PHE cc_start: 0.6910 (m-80) cc_final: 0.6648 (m-80) REVERT: K 28 THR cc_start: 0.7989 (p) cc_final: 0.7726 (p) REVERT: K 72 ASP cc_start: 0.8597 (t70) cc_final: 0.8132 (t0) REVERT: N 69 ASN cc_start: 0.8587 (m-40) cc_final: 0.7685 (t0) REVERT: N 79 GLN cc_start: 0.8131 (mp10) cc_final: 0.7618 (mp10) REVERT: I 542 ARG cc_start: 0.9119 (mtm110) cc_final: 0.8850 (mtm110) REVERT: I 636 SER cc_start: 0.9149 (t) cc_final: 0.8870 (p) REVERT: P 29 ILE cc_start: 0.8211 (pt) cc_final: 0.7661 (mt) REVERT: R 61 ARG cc_start: 0.7837 (ptt-90) cc_final: 0.7329 (ptp90) outliers start: 80 outliers final: 63 residues processed: 425 average time/residue: 0.1813 time to fit residues: 118.4655 Evaluate side-chains 431 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 367 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE 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 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 100 GLN 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 82 VAL 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 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 J residue 94 THR 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 18 LEU Chi-restraints excluded: chain O residue 56 ILE Chi-restraints excluded: chain O residue 76 ASN 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 213 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 60 VAL Chi-restraints excluded: chain K residue 110 THR 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 P residue 17 THR Chi-restraints excluded: chain P residue 72 ASP 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 33 LEU Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 35 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 275 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 199 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 31 ASN M 39 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN N 31 ASN 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 = 0.3646 r_free = 0.3646 target = 0.123878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.093465 restraints weight = 38920.569| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.50 r_work: 0.3047 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25521 Z= 0.130 Angle : 0.586 10.566 34809 Z= 0.294 Chirality : 0.045 0.373 4080 Planarity : 0.004 0.039 4281 Dihedral : 8.134 87.111 4947 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 2.27 % Allowed : 11.10 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.15), residues: 2997 helix: 0.99 (0.28), residues: 408 sheet: 0.64 (0.17), residues: 858 loop : -0.37 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 81 TYR 0.029 0.001 TYR R 49 PHE 0.014 0.001 PHE O 78 TRP 0.019 0.001 TRP E 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00302 (25395) covalent geometry : angle 0.55121 (34476) SS BOND : bond 0.00376 ( 45) SS BOND : angle 1.59658 ( 90) hydrogen bonds : bond 0.03881 ( 684) hydrogen bonds : angle 4.60938 ( 1710) link_ALPHA1-2 : bond 0.00368 ( 3) link_ALPHA1-2 : angle 1.60396 ( 9) link_ALPHA1-3 : bond 0.00985 ( 6) link_ALPHA1-3 : angle 1.44649 ( 18) link_ALPHA1-6 : bond 0.00297 ( 3) link_ALPHA1-6 : angle 1.44841 ( 9) link_BETA1-4 : bond 0.00527 ( 15) link_BETA1-4 : angle 2.25930 ( 45) link_NAG-ASN : bond 0.00531 ( 54) link_NAG-ASN : angle 2.43211 ( 162) *********************** 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 437 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 377 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.9231 (mttp) cc_final: 0.8947 (mmmm) REVERT: C 72 ASP cc_start: 0.8460 (t70) cc_final: 0.7993 (t0) REVERT: D 103 ARG cc_start: 0.7504 (mmm160) cc_final: 0.7114 (mmm160) REVERT: L 3 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8574 (mp10) REVERT: L 61 ARG cc_start: 0.7654 (ptt-90) cc_final: 0.7140 (ptt-90) REVERT: L 83 PHE cc_start: 0.6957 (m-80) cc_final: 0.6311 (m-80) REVERT: E 53 PHE cc_start: 0.8546 (p90) cc_final: 0.8321 (p90) REVERT: E 185 ASN cc_start: 0.6857 (m-40) cc_final: 0.6577 (m-40) REVERT: J 72 ASP cc_start: 0.8442 (t70) cc_final: 0.8207 (t70) REVERT: O 32 ASN cc_start: 0.7714 (m-40) cc_final: 0.7416 (p0) REVERT: O 110 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7895 (m) REVERT: Q 3 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8234 (mp10) REVERT: Q 70 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8208 (tp-100) REVERT: Q 83 PHE cc_start: 0.6827 (m-80) cc_final: 0.6521 (m-80) REVERT: Q 104 LEU cc_start: 0.7688 (tp) cc_final: 0.6887 (tp) REVERT: K 28 THR cc_start: 0.7950 (p) cc_final: 0.7682 (p) REVERT: K 72 ASP cc_start: 0.8544 (t70) cc_final: 0.8116 (t0) REVERT: N 69 ASN cc_start: 0.8577 (m-40) cc_final: 0.7702 (t0) REVERT: N 79 GLN cc_start: 0.8162 (mp10) cc_final: 0.7650 (mp10) REVERT: I 542 ARG cc_start: 0.9136 (mtm110) cc_final: 0.8878 (mtm110) REVERT: R 61 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7211 (ptt-90) outliers start: 60 outliers final: 49 residues processed: 412 average time/residue: 0.1619 time to fit residues: 103.1666 Evaluate side-chains 419 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 369 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 GLN 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 82 VAL Chi-restraints excluded: chain L residue 22 THR 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 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 94 THR 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 O residue 56 ILE Chi-restraints excluded: chain O residue 76 ASN 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 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 N residue 106 LEU Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 72 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 293 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 275 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 296 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 31 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN N 31 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 = 0.3647 r_free = 0.3647 target = 0.123838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.093395 restraints weight = 38690.978| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.57 r_work: 0.3044 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25521 Z= 0.151 Angle : 0.599 10.505 34809 Z= 0.299 Chirality : 0.045 0.371 4080 Planarity : 0.004 0.039 4281 Dihedral : 8.074 87.260 4947 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 2.53 % Allowed : 10.87 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.15), residues: 2997 helix: 0.95 (0.28), residues: 408 sheet: 0.63 (0.17), residues: 855 loop : -0.41 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 81 TYR 0.030 0.001 TYR R 49 PHE 0.015 0.002 PHE O 78 TRP 0.015 0.001 TRP A 479 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00362 (25395) covalent geometry : angle 0.56413 (34476) SS BOND : bond 0.00396 ( 45) SS BOND : angle 1.61684 ( 90) hydrogen bonds : bond 0.03972 ( 684) hydrogen bonds : angle 4.61549 ( 1710) link_ALPHA1-2 : bond 0.00276 ( 3) link_ALPHA1-2 : angle 1.65359 ( 9) link_ALPHA1-3 : bond 0.00957 ( 6) link_ALPHA1-3 : angle 1.42200 ( 18) link_ALPHA1-6 : bond 0.00277 ( 3) link_ALPHA1-6 : angle 1.49670 ( 9) link_BETA1-4 : bond 0.00482 ( 15) link_BETA1-4 : angle 2.34055 ( 45) link_NAG-ASN : bond 0.00527 ( 54) link_NAG-ASN : angle 2.42890 ( 162) *********************** 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 441 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 374 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.9215 (mttp) cc_final: 0.8932 (mmmm) REVERT: C 72 ASP cc_start: 0.8445 (t70) cc_final: 0.7958 (t0) REVERT: D 79 GLN cc_start: 0.8285 (mm-40) cc_final: 0.7495 (mp10) REVERT: D 103 ARG cc_start: 0.7460 (mmm160) cc_final: 0.7065 (mmm160) REVERT: L 3 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8554 (mp10) REVERT: L 61 ARG cc_start: 0.7630 (ptt-90) cc_final: 0.7103 (ptt-90) REVERT: L 83 PHE cc_start: 0.6912 (m-80) cc_final: 0.6309 (m-80) REVERT: E 53 PHE cc_start: 0.8565 (p90) cc_final: 0.8320 (p90) REVERT: E 166 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8190 (mtm110) REVERT: E 185 ASN cc_start: 0.6889 (m-40) cc_final: 0.6637 (m-40) REVERT: O 32 ASN cc_start: 0.7675 (m-40) cc_final: 0.7351 (p0) REVERT: O 110 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7902 (m) REVERT: Q 3 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8469 (mp10) REVERT: Q 24 ARG cc_start: 0.7548 (mmm-85) cc_final: 0.7094 (ttp80) REVERT: Q 83 PHE cc_start: 0.6780 (m-80) cc_final: 0.6463 (m-80) REVERT: Q 104 LEU cc_start: 0.7608 (tp) cc_final: 0.6788 (tp) REVERT: K 72 ASP cc_start: 0.8534 (t70) cc_final: 0.8079 (t0) REVERT: N 69 ASN cc_start: 0.8568 (m-40) cc_final: 0.7672 (t0) REVERT: N 79 GLN cc_start: 0.8136 (mp10) cc_final: 0.7623 (mp10) REVERT: I 542 ARG cc_start: 0.9125 (mtm110) cc_final: 0.8869 (mtm110) REVERT: R 61 ARG cc_start: 0.7829 (ptt-90) cc_final: 0.7165 (ptt-90) outliers start: 67 outliers final: 58 residues processed: 412 average time/residue: 0.1825 time to fit residues: 116.1558 Evaluate side-chains 423 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 364 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 48 VAL 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 89 VAL 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 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 82 VAL Chi-restraints excluded: chain L residue 22 THR 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 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 94 THR 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 76 ASN 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 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 60 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 72 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 87 optimal weight: 0.1980 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 242 optimal weight: 0.4980 chunk 172 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 69 ASN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Q 70 GLN N 31 ASN N 95 GLN I 585 HIS R 53 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.084484 restraints weight = 38692.650| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.84 r_work: 0.2882 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25521 Z= 0.119 Angle : 0.577 10.164 34809 Z= 0.288 Chirality : 0.044 0.358 4080 Planarity : 0.004 0.040 4281 Dihedral : 7.898 85.636 4947 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 2.34 % Allowed : 11.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.15), residues: 2997 helix: 1.05 (0.28), residues: 408 sheet: 0.67 (0.17), residues: 855 loop : -0.39 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 81 TYR 0.029 0.001 TYR R 49 PHE 0.014 0.001 PHE O 78 TRP 0.017 0.001 TRP A 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00277 (25395) covalent geometry : angle 0.54432 (34476) SS BOND : bond 0.00363 ( 45) SS BOND : angle 1.52012 ( 90) hydrogen bonds : bond 0.03728 ( 684) hydrogen bonds : angle 4.55066 ( 1710) link_ALPHA1-2 : bond 0.00353 ( 3) link_ALPHA1-2 : angle 1.60093 ( 9) link_ALPHA1-3 : bond 0.00954 ( 6) link_ALPHA1-3 : angle 1.40725 ( 18) link_ALPHA1-6 : bond 0.00326 ( 3) link_ALPHA1-6 : angle 1.45594 ( 9) link_BETA1-4 : bond 0.00486 ( 15) link_BETA1-4 : angle 2.20301 ( 45) link_NAG-ASN : bond 0.00515 ( 54) link_NAG-ASN : angle 2.32783 ( 162) *********************** 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 437 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 375 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.9260 (mttp) cc_final: 0.8932 (mmmm) REVERT: C 72 ASP cc_start: 0.8348 (t70) cc_final: 0.7805 (t0) REVERT: C 81 GLN cc_start: 0.8393 (tp40) cc_final: 0.8153 (tt0) REVERT: D 69 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7954 (t0) REVERT: D 79 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7411 (mp10) REVERT: D 103 ARG cc_start: 0.7241 (mmm160) cc_final: 0.6887 (mmm160) REVERT: L 3 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8502 (mp10) REVERT: L 61 ARG cc_start: 0.7555 (ptt-90) cc_final: 0.6902 (ptt-90) REVERT: J 72 ASP cc_start: 0.8265 (t70) cc_final: 0.8022 (t70) REVERT: G 601 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8764 (mttt) REVERT: O 32 ASN cc_start: 0.7678 (m-40) cc_final: 0.7229 (p0) REVERT: O 110 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7900 (m) REVERT: Q 3 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8419 (mp10) REVERT: Q 104 LEU cc_start: 0.7480 (tp) cc_final: 0.7046 (mp) REVERT: K 72 ASP cc_start: 0.8433 (t70) cc_final: 0.7862 (t0) REVERT: K 81 GLN cc_start: 0.8308 (tt0) cc_final: 0.8002 (tm-30) REVERT: N 42 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7835 (pttm) REVERT: N 69 ASN cc_start: 0.8520 (m-40) cc_final: 0.7573 (t0) REVERT: N 79 GLN cc_start: 0.8079 (mp10) cc_final: 0.7571 (mp10) REVERT: I 542 ARG cc_start: 0.9129 (mtm110) cc_final: 0.8866 (mtm110) REVERT: P 5 GLN cc_start: 0.7448 (mp-120) cc_final: 0.7014 (mp10) REVERT: P 13 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.5968 (mp10) REVERT: R 3 GLN cc_start: 0.8691 (mp10) cc_final: 0.8448 (mp10) REVERT: R 61 ARG cc_start: 0.7738 (ptt-90) cc_final: 0.6980 (ptt-90) REVERT: R 83 PHE cc_start: 0.7038 (m-80) cc_final: 0.6819 (m-80) outliers start: 62 outliers final: 51 residues processed: 413 average time/residue: 0.1843 time to fit residues: 117.7303 Evaluate side-chains 416 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 362 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 78 LEU 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 82 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain E residue 74 CYS 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 505 VAL 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 98 SER 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 76 ASN 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 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 17 THR Chi-restraints excluded: chain P residue 72 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 246 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 266 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 D 69 ASN B 585 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN M 31 ASN G 625 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN N 31 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 = 0.3522 r_free = 0.3522 target = 0.115965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.082511 restraints weight = 39229.305| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.92 r_work: 0.2840 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25521 Z= 0.201 Angle : 0.639 10.432 34809 Z= 0.318 Chirality : 0.046 0.370 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.101 87.945 4947 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 2.34 % Allowed : 11.29 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.15), residues: 2997 helix: 0.83 (0.28), residues: 408 sheet: 0.55 (0.17), residues: 864 loop : -0.51 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 81 TYR 0.032 0.001 TYR R 49 PHE 0.018 0.002 PHE E 53 TRP 0.016 0.002 TRP A 479 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00489 (25395) covalent geometry : angle 0.60430 (34476) SS BOND : bond 0.00452 ( 45) SS BOND : angle 1.76750 ( 90) hydrogen bonds : bond 0.04277 ( 684) hydrogen bonds : angle 4.71702 ( 1710) link_ALPHA1-2 : bond 0.00147 ( 3) link_ALPHA1-2 : angle 1.74193 ( 9) link_ALPHA1-3 : bond 0.00894 ( 6) link_ALPHA1-3 : angle 1.36749 ( 18) link_ALPHA1-6 : bond 0.00236 ( 3) link_ALPHA1-6 : angle 1.61859 ( 9) link_BETA1-4 : bond 0.00460 ( 15) link_BETA1-4 : angle 2.55624 ( 45) link_NAG-ASN : bond 0.00562 ( 54) link_NAG-ASN : angle 2.46602 ( 162) ********************** 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 426 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 364 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 LYS cc_start: 0.9251 (mttp) cc_final: 0.8917 (mmmm) REVERT: C 81 GLN cc_start: 0.8374 (tp40) cc_final: 0.7747 (tm-30) REVERT: D 69 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.7659 (t0) REVERT: D 103 ARG cc_start: 0.7288 (mmm160) cc_final: 0.6927 (mmm160) REVERT: B 647 GLU cc_start: 0.8951 (tt0) cc_final: 0.8737 (tt0) REVERT: L 3 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8530 (mp10) REVERT: L 83 PHE cc_start: 0.6634 (m-80) cc_final: 0.6106 (m-80) REVERT: J 72 ASP cc_start: 0.8261 (t70) cc_final: 0.8012 (t70) REVERT: O 32 ASN cc_start: 0.7773 (m-40) cc_final: 0.7239 (p0) REVERT: O 110 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7917 (m) REVERT: Q 3 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8510 (mp10) REVERT: F 232 LYS cc_start: 0.9315 (mttp) cc_final: 0.8959 (mmmm) REVERT: K 72 ASP cc_start: 0.8467 (t70) cc_final: 0.7927 (t0) REVERT: N 42 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7776 (pttm) REVERT: N 69 ASN cc_start: 0.8556 (m-40) cc_final: 0.7475 (t0) REVERT: N 79 GLN cc_start: 0.8113 (mp10) cc_final: 0.7530 (mp10) REVERT: I 542 ARG cc_start: 0.9139 (mtm110) cc_final: 0.8843 (mtm110) REVERT: I 626 MET cc_start: 0.9078 (ttt) cc_final: 0.8817 (ptm) REVERT: P 5 GLN cc_start: 0.7464 (mp-120) cc_final: 0.7010 (mp10) REVERT: P 29 ILE cc_start: 0.8095 (pt) cc_final: 0.7542 (mt) REVERT: R 3 GLN cc_start: 0.8716 (mp10) cc_final: 0.8455 (mp10) REVERT: R 61 ARG cc_start: 0.7757 (ptt-90) cc_final: 0.7203 (ptp90) outliers start: 62 outliers final: 56 residues processed: 404 average time/residue: 0.1810 time to fit residues: 114.1178 Evaluate side-chains 412 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 78 LEU 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 82 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain E residue 74 CYS 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 60 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 94 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 76 ASN 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 213 ILE Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 505 VAL Chi-restraints excluded: chain K residue 5 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 17 THR Chi-restraints excluded: chain P residue 72 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 64 optimal weight: 2.9990 chunk 272 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 259 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 D 69 ASN B 585 HIS ** 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 K 81 GLN N 31 ASN N 95 GLN R 53 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.083525 restraints weight = 39008.258| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.88 r_work: 0.2858 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25521 Z= 0.179 Angle : 0.631 10.334 34809 Z= 0.313 Chirality : 0.046 0.368 4080 Planarity : 0.004 0.040 4281 Dihedral : 8.100 87.531 4947 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 2.34 % Allowed : 11.14 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.15), residues: 2997 helix: 0.85 (0.28), residues: 408 sheet: 0.54 (0.17), residues: 864 loop : -0.53 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 81 TYR 0.031 0.001 TYR R 49 PHE 0.017 0.002 PHE E 53 TRP 0.020 0.001 TRP E 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00433 (25395) covalent geometry : angle 0.59454 (34476) SS BOND : bond 0.00455 ( 45) SS BOND : angle 1.97660 ( 90) hydrogen bonds : bond 0.04178 ( 684) hydrogen bonds : angle 4.70199 ( 1710) link_ALPHA1-2 : bond 0.00209 ( 3) link_ALPHA1-2 : angle 1.69784 ( 9) link_ALPHA1-3 : bond 0.00931 ( 6) link_ALPHA1-3 : angle 1.35599 ( 18) link_ALPHA1-6 : bond 0.00241 ( 3) link_ALPHA1-6 : angle 1.56908 ( 9) link_BETA1-4 : bond 0.00461 ( 15) link_BETA1-4 : angle 2.48135 ( 45) link_NAG-ASN : bond 0.00551 ( 54) link_NAG-ASN : angle 2.44169 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7015.49 seconds wall clock time: 120 minutes 49.77 seconds (7249.77 seconds total)