Starting phenix.real_space_refine on Wed Nov 20 00:37:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/11_2024/8sav_40281_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/11_2024/8sav_40281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/11_2024/8sav_40281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/11_2024/8sav_40281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/11_2024/8sav_40281_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sav_40281/11_2024/8sav_40281_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 138 5.16 5 C 12771 2.51 5 N 3528 2.21 5 O 4014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20451 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "B" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3782 Classifications: {'peptide': 480} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 22, 'TRANS': 455} Chain breaks: 1 Chain: "J" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1067 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 132} Chain breaks: 1 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 112} Chain: "L" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 767 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "O" 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: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "T" 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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 Chain: "Y" 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: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" 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: "E" 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: "I" 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 Time building chain proxies: 13.30, per 1000 atoms: 0.65 Number of scatterers: 20451 At special positions: 0 Unit cell: (142.844, 149.24, 121.524, 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 138 16.00 O 4014 8.00 N 3528 7.00 C 12771 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA P 3 " - " MAN P 5 " " BMA U 3 " - " MAN U 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG A 602 " - " ASN A 392 " " NAG E 601 " - " ASN E 138 " " NAG E 602 " - " ASN E 392 " " NAG I 601 " - " ASN I 138 " " NAG I 602 " - " ASN I 392 " " NAG M 1 " - " ASN A 386 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 396 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 156 " " NAG U 1 " - " ASN E 262 " " NAG V 1 " - " ASN E 396 " " NAG W 1 " - " ASN I 386 " " NAG X 1 " - " ASN I 332 " " NAG Y 1 " - " ASN I 156 " " NAG Z 1 " - " ASN I 262 " " NAG a 1 " - " ASN I 396 " Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 2.5 seconds 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4638 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 42 sheets defined 20.1% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.500A pdb=" N THR A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.841A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.882A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.106A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.506A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.974A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 461 through 464 removed outlier: 3.664A pdb=" N LYS E 463 " --> pdb=" O ASN E 461 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 464 " --> pdb=" O SER E 461l" (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 461 through 464' Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.508A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 544 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.833A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 removed outlier: 4.333A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.512A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 4.026A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR F 643 " --> pdb=" O THR F 639 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.725A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.616A pdb=" N PHE H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 353 removed outlier: 3.582A pdb=" N HIS I 352 " --> pdb=" O GLU I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 461 through 464 removed outlier: 3.532A pdb=" N LYS I 463 " --> pdb=" O ASN I 461 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR I 464 " --> pdb=" O SER I 461l" (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 461 through 464' Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.542A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 Processing helix chain 'J' and resid 570 through 596 removed outlier: 3.889A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP J 596 " --> pdb=" O LEU J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 618 through 625 removed outlier: 4.246A pdb=" N ASP J 624 " --> pdb=" O SER J 620 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 635 removed outlier: 4.384A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.735A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.666A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.510A pdb=" N ASP L 82 " --> pdb=" O GLU L 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.442A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.619A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) 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 169 through 177 removed outlier: 3.807A pdb=" N ARG A 192 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.516A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 360 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.064A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N VAL A 292 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N LYS A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N ILE A 294 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 10.230A pdb=" N THR A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 421 removed outlier: 3.849A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 309 removed outlier: 6.125A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.536A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET C 18 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 82 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C 68 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.695A pdb=" N GLN C 10 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 109 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TRP C 36 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN C 58 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.803A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.551A pdb=" N VAL D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN D 89 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.548A pdb=" N GLN D 90 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.313A pdb=" N TRP E 35 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 46 removed outlier: 3.616A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.804A pdb=" N ARG E 192 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.623A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 360 through 361 Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.065A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.666A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.363A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL E 292 " --> pdb=" O LYS E 446 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N LYS E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.598A pdb=" N ILE E 294 " --> pdb=" O THR E 444 " (cutoff:3.500A) removed outlier: 10.260A pdb=" N THR E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 421 removed outlier: 3.815A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 301 through 309 removed outlier: 6.237A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 423 through 425 Processing sheet with id=AC6, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.754A pdb=" N MET G 18 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.625A pdb=" N GLN G 10 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN G 58 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.216A pdb=" N ASP H 70 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TRP H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AD1, first strand: chain 'H' and resid 53 through 54 removed outlier: 5.849A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN H 89 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 494 through 499 removed outlier: 3.570A pdb=" N THR I 499 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TRP I 35 " --> pdb=" O THR I 499 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.618A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AD6, first strand: chain 'I' and resid 169 through 177 removed outlier: 3.844A pdb=" N ARG I 192 " --> pdb=" O VAL I 182 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.271A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 259 through 261 removed outlier: 10.239A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 360 through 361 Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.039A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.705A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.578A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 456 current: chain 'I' and resid 413 through 421 removed outlier: 3.842A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 301 through 309 removed outlier: 6.070A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.560A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET K 18 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 82 " --> pdb=" O MET K 18 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.718A pdb=" N GLN K 10 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP K 36 " --> pdb=" O GLY K 49 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.283A pdb=" N ASP L 70 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TRP L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.622A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN L 89 " --> pdb=" O ALA L 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.549A pdb=" N GLN L 90 " --> pdb=" O PHE L 97 " (cutoff:3.500A) 686 hydrogen bonds defined for protein. 1788 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: 6.95 Time building geometry restraints manager: 6.20 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: 6597 1.34 - 1.46: 4987 1.46 - 1.58: 9086 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 20856 Sorted by residual: bond pdb=" C TRP C 100B" pdb=" N ASP C 100C" ideal model delta sigma weight residual 1.333 1.375 -0.042 1.38e-02 5.25e+03 9.44e+00 bond pdb=" C TRP K 100B" pdb=" N ASP K 100C" ideal model delta sigma weight residual 1.333 1.367 -0.034 1.38e-02 5.25e+03 6.12e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 20851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 27552 2.49 - 4.99: 653 4.99 - 7.48: 73 7.48 - 9.98: 12 9.98 - 12.47: 6 Bond angle restraints: 28296 Sorted by residual: angle pdb=" C ASP G 100C" pdb=" N PHE G 100D" pdb=" CA PHE G 100D" ideal model delta sigma weight residual 121.70 134.17 -12.47 1.80e+00 3.09e-01 4.80e+01 angle pdb=" C ASP C 100C" pdb=" N PHE C 100D" pdb=" CA PHE C 100D" ideal model delta sigma weight residual 121.70 133.88 -12.18 1.80e+00 3.09e-01 4.58e+01 angle pdb=" C ASP K 100C" pdb=" N PHE K 100D" pdb=" CA PHE K 100D" ideal model delta sigma weight residual 121.70 133.20 -11.50 1.80e+00 3.09e-01 4.08e+01 angle pdb=" C THR A 460 " pdb=" N ASN A 461 " pdb=" CA ASN A 461 " ideal model delta sigma weight residual 121.70 132.14 -10.44 1.80e+00 3.09e-01 3.37e+01 angle pdb=" C THR E 460 " pdb=" N ASN E 461 " pdb=" CA ASN E 461 " ideal model delta sigma weight residual 121.70 131.99 -10.29 1.80e+00 3.09e-01 3.27e+01 ... (remaining 28291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 12304 21.99 - 43.98: 708 43.98 - 65.98: 105 65.98 - 87.97: 105 87.97 - 109.96: 50 Dihedral angle restraints: 13272 sinusoidal: 6048 harmonic: 7224 Sorted by residual: dihedral pdb=" CB CYS I 126 " pdb=" SG CYS I 126 " pdb=" SG CYS I 196 " pdb=" CB CYS I 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.62 -65.62 1 1.00e+01 1.00e-02 5.64e+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 93.00 158.23 -65.23 1 1.00e+01 1.00e-02 5.58e+01 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 93.00 157.99 -64.99 1 1.00e+01 1.00e-02 5.54e+01 ... (remaining 13269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2649 0.057 - 0.114: 491 0.114 - 0.172: 139 0.172 - 0.229: 8 0.229 - 0.286: 16 Chirality restraints: 3303 Sorted by residual: chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3300 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 100D" -0.030 2.00e-02 2.50e+03 2.91e-02 1.48e+01 pdb=" CG PHE G 100D" 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE G 100D" -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE G 100D" -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE G 100D" 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 100D" -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE G 100D" -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 50 " 0.018 2.00e-02 2.50e+03 1.89e-02 8.89e+00 pdb=" CG TRP K 50 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP K 50 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP K 50 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP K 50 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP K 50 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 50 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 50 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 50 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP K 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 58 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO D 59 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 59 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 59 " -0.035 5.00e-02 4.00e+02 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 160 2.58 - 3.16: 17230 3.16 - 3.74: 29491 3.74 - 4.32: 41034 4.32 - 4.90: 69523 Nonbonded interactions: 157438 Sorted by model distance: nonbonded pdb=" O ASP G 100C" pdb=" OH TYR H 36 " model vdw 2.003 3.040 nonbonded pdb=" O ASP K 100C" pdb=" OH TYR L 36 " model vdw 2.042 3.040 nonbonded pdb=" O ASP C 100C" pdb=" OH TYR D 36 " model vdw 2.044 3.040 nonbonded pdb=" O ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.108 3.040 nonbonded pdb=" OD1 ASN A 461 " pdb=" OG1 THR A 464 " model vdw 2.192 3.040 ... (remaining 157433 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 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: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 46.350 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.005 0.047 20856 Z= 0.332 Angle : 0.918 12.470 28296 Z= 0.491 Chirality : 0.053 0.286 3303 Planarity : 0.005 0.064 3570 Dihedral : 17.297 109.962 8508 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Rotamer: Outliers : 0.14 % Allowed : 0.09 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.16), residues: 2478 helix: 0.26 (0.25), residues: 411 sheet: -0.74 (0.18), residues: 759 loop : -1.63 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP K 50 HIS 0.004 0.001 HIS E 249 PHE 0.067 0.002 PHE G 100D TYR 0.025 0.002 TYR L 91 ARG 0.010 0.001 ARG E 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 2.356 Fit side-chains revert: symmetry clash REVERT: C 48 MET cc_start: 0.8084 (mtm) cc_final: 0.7766 (mtt) REVERT: E 434 MET cc_start: 0.7848 (ttp) cc_final: 0.7394 (mtm) REVERT: F 586 TYR cc_start: 0.9354 (t80) cc_final: 0.9124 (t80) REVERT: G 72 ASP cc_start: 0.8365 (t0) cc_final: 0.7965 (t0) REVERT: H 82 ASP cc_start: 0.6924 (m-30) cc_final: 0.6379 (m-30) REVERT: K 32 CYS cc_start: 0.5703 (t) cc_final: 0.5426 (t) outliers start: 3 outliers final: 0 residues processed: 200 average time/residue: 0.2951 time to fit residues: 96.4102 Evaluate side-chains 133 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 195 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 145 optimal weight: 0.3980 chunk 226 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 105 HIS E 72 HIS F 540 GLN F 658 GLN G 102 HIS I 72 HIS J 540 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20856 Z= 0.342 Angle : 0.819 14.312 28296 Z= 0.425 Chirality : 0.052 0.368 3303 Planarity : 0.005 0.055 3570 Dihedral : 13.820 85.539 3837 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.26 % Favored : 92.41 % Rotamer: Outliers : 1.01 % Allowed : 6.48 % Favored : 92.51 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2478 helix: 0.37 (0.26), residues: 399 sheet: -0.64 (0.19), residues: 681 loop : -1.76 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 571 HIS 0.004 0.001 HIS A 374 PHE 0.056 0.003 PHE G 100D TYR 0.032 0.002 TYR H 91 ARG 0.004 0.001 ARG I 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7868 (mtm) cc_final: 0.7561 (mtt) REVERT: C 69 MET cc_start: 0.7558 (mtm) cc_final: 0.7246 (mtp) REVERT: E 434 MET cc_start: 0.8103 (ttp) cc_final: 0.7656 (ttp) REVERT: E 461 ASN cc_start: 0.6625 (t0) cc_final: 0.6358 (t0) REVERT: F 535 MET cc_start: 0.5940 (mpp) cc_final: 0.5572 (tpp) REVERT: G 72 ASP cc_start: 0.8330 (t0) cc_final: 0.8035 (t0) REVERT: I 434 MET cc_start: 0.8003 (ttp) cc_final: 0.7773 (ttp) REVERT: K 32 CYS cc_start: 0.6005 (t) cc_final: 0.5694 (t) outliers start: 22 outliers final: 14 residues processed: 154 average time/residue: 0.2753 time to fit residues: 71.7186 Evaluate side-chains 136 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 244 optimal weight: 0.0050 chunk 201 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 147 ASN H 90 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20856 Z= 0.237 Angle : 0.738 13.951 28296 Z= 0.381 Chirality : 0.050 0.476 3303 Planarity : 0.004 0.048 3570 Dihedral : 11.815 88.368 3837 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.05 % Favored : 93.62 % Rotamer: Outliers : 1.20 % Allowed : 9.38 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2478 helix: 0.28 (0.25), residues: 429 sheet: -0.46 (0.19), residues: 684 loop : -1.71 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 100B HIS 0.004 0.001 HIS G 102 PHE 0.044 0.002 PHE G 100D TYR 0.025 0.002 TYR H 91 ARG 0.003 0.000 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 50 TRP cc_start: 0.5170 (m100) cc_final: 0.4946 (m100) REVERT: E 369 MET cc_start: 0.7749 (ttm) cc_final: 0.7122 (ttm) REVERT: E 434 MET cc_start: 0.8221 (ttp) cc_final: 0.7667 (ttp) REVERT: E 461 ASN cc_start: 0.6621 (t0) cc_final: 0.6361 (t0) REVERT: F 530 MET cc_start: 0.6278 (mtm) cc_final: 0.5755 (mtm) REVERT: F 535 MET cc_start: 0.5987 (mpp) cc_final: 0.5655 (tpp) REVERT: G 72 ASP cc_start: 0.8300 (t0) cc_final: 0.7984 (t0) REVERT: H 96 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7268 (pm20) REVERT: J 535 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6445 (mmp) REVERT: K 32 CYS cc_start: 0.5891 (t) cc_final: 0.5576 (t) outliers start: 26 outliers final: 20 residues processed: 155 average time/residue: 0.2831 time to fit residues: 74.3248 Evaluate side-chains 143 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN E 428 GLN I 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20856 Z= 0.298 Angle : 0.747 14.367 28296 Z= 0.387 Chirality : 0.050 0.477 3303 Planarity : 0.005 0.048 3570 Dihedral : 10.447 87.524 3837 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.14 % Favored : 92.49 % Rotamer: Outliers : 2.02 % Allowed : 11.03 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2478 helix: 0.51 (0.26), residues: 393 sheet: -0.58 (0.19), residues: 693 loop : -1.85 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 100B HIS 0.005 0.001 HIS G 102 PHE 0.038 0.002 PHE G 100D TYR 0.026 0.002 TYR H 91 ARG 0.003 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 THR cc_start: 0.8227 (p) cc_final: 0.7984 (t) REVERT: B 535 MET cc_start: 0.6847 (mpp) cc_final: 0.6416 (mmp) REVERT: B 586 TYR cc_start: 0.9295 (t80) cc_final: 0.9053 (t80) REVERT: E 188 THR cc_start: 0.8140 (p) cc_final: 0.7933 (t) REVERT: E 369 MET cc_start: 0.7752 (ttm) cc_final: 0.7087 (ttm) REVERT: E 434 MET cc_start: 0.8460 (ttp) cc_final: 0.7815 (ttp) REVERT: E 461 ASN cc_start: 0.6667 (t0) cc_final: 0.6410 (t0) REVERT: F 535 MET cc_start: 0.6442 (mpp) cc_final: 0.6091 (mpp) REVERT: G 72 ASP cc_start: 0.8300 (t0) cc_final: 0.8024 (t0) REVERT: J 535 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6973 (mmp) REVERT: K 32 CYS cc_start: 0.5808 (t) cc_final: 0.5560 (t) outliers start: 44 outliers final: 31 residues processed: 173 average time/residue: 0.2718 time to fit residues: 79.4237 Evaluate side-chains 157 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20856 Z= 0.334 Angle : 0.764 14.202 28296 Z= 0.397 Chirality : 0.050 0.409 3303 Planarity : 0.005 0.049 3570 Dihedral : 9.978 85.709 3837 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.59 % Favored : 92.05 % Rotamer: Outliers : 2.80 % Allowed : 11.68 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2478 helix: 0.21 (0.25), residues: 429 sheet: -0.69 (0.19), residues: 690 loop : -1.92 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 571 HIS 0.007 0.001 HIS K 102 PHE 0.037 0.003 PHE G 100D TYR 0.026 0.002 TYR H 91 ARG 0.003 0.000 ARG G 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 2.540 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (tp) REVERT: B 530 MET cc_start: 0.6644 (mtm) cc_final: 0.6088 (mtm) REVERT: E 461 ASN cc_start: 0.6813 (t0) cc_final: 0.6573 (t0) REVERT: F 535 MET cc_start: 0.6675 (mpp) cc_final: 0.6316 (mpp) REVERT: I 443 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8815 (tp) REVERT: J 535 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7251 (mmp) REVERT: K 32 CYS cc_start: 0.5835 (t) cc_final: 0.5623 (t) outliers start: 61 outliers final: 42 residues processed: 181 average time/residue: 0.2738 time to fit residues: 84.2692 Evaluate side-chains 167 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 240 optimal weight: 0.8980 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20856 Z= 0.207 Angle : 0.691 13.562 28296 Z= 0.359 Chirality : 0.047 0.404 3303 Planarity : 0.004 0.049 3570 Dihedral : 9.354 78.599 3837 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.26 % Favored : 93.42 % Rotamer: Outliers : 2.02 % Allowed : 12.92 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2478 helix: 0.56 (0.25), residues: 411 sheet: -0.47 (0.19), residues: 684 loop : -1.83 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP K 50 HIS 0.005 0.001 HIS K 102 PHE 0.031 0.002 PHE G 100D TYR 0.019 0.001 TYR H 91 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 2.265 Fit side-chains REVERT: C 16 GLU cc_start: 0.7669 (tt0) cc_final: 0.7362 (tt0) REVERT: E 100 MET cc_start: 0.7212 (mtm) cc_final: 0.6908 (mtm) REVERT: F 530 MET cc_start: 0.6370 (mtm) cc_final: 0.5596 (mtm) REVERT: F 535 MET cc_start: 0.6593 (mpp) cc_final: 0.6166 (mpp) REVERT: H 96 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: I 188 THR cc_start: 0.8104 (p) cc_final: 0.7866 (t) REVERT: I 290 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9035 (t) REVERT: J 535 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6952 (mmp) REVERT: K 32 CYS cc_start: 0.5787 (t) cc_final: 0.5566 (t) outliers start: 44 outliers final: 30 residues processed: 165 average time/residue: 0.2828 time to fit residues: 79.1705 Evaluate side-chains 149 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 96 GLU Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20856 Z= 0.215 Angle : 0.685 13.260 28296 Z= 0.355 Chirality : 0.047 0.390 3303 Planarity : 0.004 0.047 3570 Dihedral : 9.005 69.654 3837 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.38 % Favored : 93.34 % Rotamer: Outliers : 2.53 % Allowed : 12.97 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.16), residues: 2478 helix: 0.64 (0.26), residues: 411 sheet: -0.41 (0.19), residues: 690 loop : -1.74 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 50 HIS 0.005 0.001 HIS G 102 PHE 0.028 0.002 PHE G 100D TYR 0.019 0.001 TYR H 91 ARG 0.004 0.000 ARG J 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 2.551 Fit side-chains REVERT: A 443 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8817 (tp) REVERT: B 530 MET cc_start: 0.6391 (mtm) cc_final: 0.5958 (mtm) REVERT: B 535 MET cc_start: 0.6816 (mmp) cc_final: 0.6401 (mmp) REVERT: C 16 GLU cc_start: 0.7634 (tt0) cc_final: 0.7282 (tt0) REVERT: E 100 MET cc_start: 0.7343 (mtm) cc_final: 0.7011 (mtm) REVERT: E 434 MET cc_start: 0.8480 (ttp) cc_final: 0.8205 (ttp) REVERT: F 535 MET cc_start: 0.6770 (mpp) cc_final: 0.6343 (mpp) REVERT: I 188 THR cc_start: 0.8144 (p) cc_final: 0.7920 (t) REVERT: J 535 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6781 (mmp) REVERT: K 32 CYS cc_start: 0.5726 (t) cc_final: 0.5512 (t) outliers start: 55 outliers final: 41 residues processed: 173 average time/residue: 0.2917 time to fit residues: 84.4152 Evaluate side-chains 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 5.9990 chunk 95 optimal weight: 0.0770 chunk 143 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 188 optimal weight: 0.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20856 Z= 0.258 Angle : 0.713 12.955 28296 Z= 0.369 Chirality : 0.048 0.401 3303 Planarity : 0.004 0.048 3570 Dihedral : 8.927 60.934 3837 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.10 % Favored : 92.62 % Rotamer: Outliers : 2.48 % Allowed : 13.84 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.16), residues: 2478 helix: 0.60 (0.26), residues: 411 sheet: -0.42 (0.20), residues: 690 loop : -1.77 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 50 HIS 0.006 0.001 HIS K 102 PHE 0.028 0.002 PHE G 100D TYR 0.038 0.002 TYR H 91 ARG 0.003 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 123 time to evaluate : 2.489 Fit side-chains REVERT: A 443 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8790 (tp) REVERT: B 530 MET cc_start: 0.6499 (mtm) cc_final: 0.6102 (mtm) REVERT: B 535 MET cc_start: 0.7176 (mmp) cc_final: 0.6858 (mmp) REVERT: C 16 GLU cc_start: 0.7762 (tt0) cc_final: 0.7446 (tt0) REVERT: F 530 MET cc_start: 0.6233 (mtm) cc_final: 0.5679 (mtm) REVERT: F 535 MET cc_start: 0.7010 (mpp) cc_final: 0.6665 (mpp) REVERT: G 10 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.5660 (mp10) REVERT: I 188 THR cc_start: 0.8183 (p) cc_final: 0.7945 (t) REVERT: J 535 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7134 (mmp) REVERT: K 32 CYS cc_start: 0.5755 (t) cc_final: 0.5540 (t) outliers start: 54 outliers final: 46 residues processed: 166 average time/residue: 0.2857 time to fit residues: 79.1750 Evaluate side-chains 163 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 114 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 610 TRP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 222 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20856 Z= 0.237 Angle : 0.702 13.221 28296 Z= 0.363 Chirality : 0.047 0.395 3303 Planarity : 0.004 0.048 3570 Dihedral : 8.778 59.514 3837 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.34 % Favored : 93.38 % Rotamer: Outliers : 2.57 % Allowed : 14.07 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2478 helix: 0.66 (0.26), residues: 411 sheet: -0.37 (0.20), residues: 690 loop : -1.75 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP C 100B HIS 0.005 0.001 HIS G 102 PHE 0.028 0.002 PHE G 100D TYR 0.020 0.001 TYR H 91 ARG 0.003 0.000 ARG E 59 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 2.612 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8781 (tp) REVERT: B 530 MET cc_start: 0.6573 (mtm) cc_final: 0.6194 (mtm) REVERT: B 535 MET cc_start: 0.7150 (mmp) cc_final: 0.6515 (mmp) REVERT: C 16 GLU cc_start: 0.7780 (tt0) cc_final: 0.7451 (tt0) REVERT: D 71 TYR cc_start: 0.5460 (t80) cc_final: 0.4684 (t80) REVERT: E 434 MET cc_start: 0.8531 (ttp) cc_final: 0.8259 (mtm) REVERT: F 530 MET cc_start: 0.6337 (mtm) cc_final: 0.5737 (mtm) REVERT: F 535 MET cc_start: 0.7021 (mpp) cc_final: 0.6673 (mpp) REVERT: G 10 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.5657 (mp10) REVERT: J 535 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7093 (mmp) outliers start: 56 outliers final: 49 residues processed: 163 average time/residue: 0.2750 time to fit residues: 76.9693 Evaluate side-chains 165 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20856 Z= 0.307 Angle : 0.740 13.099 28296 Z= 0.383 Chirality : 0.048 0.403 3303 Planarity : 0.005 0.049 3570 Dihedral : 8.882 59.743 3837 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.95 % Favored : 91.73 % Rotamer: Outliers : 2.62 % Allowed : 14.02 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.16), residues: 2478 helix: 0.56 (0.26), residues: 411 sheet: -0.49 (0.20), residues: 690 loop : -1.85 (0.16), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP G 50 HIS 0.006 0.001 HIS I 374 PHE 0.031 0.002 PHE G 100D TYR 0.025 0.002 TYR H 91 ARG 0.003 0.000 ARG E 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4956 Ramachandran restraints generated. 2478 Oldfield, 0 Emsley, 2478 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 118 time to evaluate : 2.433 Fit side-chains revert: symmetry clash REVERT: A 416 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7954 (mt) REVERT: A 443 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8796 (tp) REVERT: B 530 MET cc_start: 0.6839 (mtm) cc_final: 0.6341 (mtm) REVERT: B 535 MET cc_start: 0.7301 (mmp) cc_final: 0.6560 (mmp) REVERT: C 16 GLU cc_start: 0.7783 (tt0) cc_final: 0.7528 (tt0) REVERT: D 71 TYR cc_start: 0.5822 (t80) cc_final: 0.4990 (t80) REVERT: E 434 MET cc_start: 0.8595 (ttp) cc_final: 0.8347 (ttp) REVERT: F 530 MET cc_start: 0.6504 (mtm) cc_final: 0.5845 (mtm) REVERT: F 535 MET cc_start: 0.7198 (mpp) cc_final: 0.6909 (mpp) REVERT: G 10 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.5751 (mp10) REVERT: I 151 MET cc_start: 0.7915 (mmt) cc_final: 0.7391 (mmp) REVERT: J 535 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7307 (mmp) outliers start: 57 outliers final: 48 residues processed: 166 average time/residue: 0.2931 time to fit residues: 81.1715 Evaluate side-chains 161 residues out of total 2181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 109 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 210 PHE Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 416 LEU Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 484 TYR Chi-restraints excluded: chain I residue 508 ARG Chi-restraints excluded: chain J residue 534 SER Chi-restraints excluded: chain J residue 535 MET Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 610 TRP Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 18 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 HIS K 100AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.078011 restraints weight = 68424.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079340 restraints weight = 51692.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080185 restraints weight = 39739.939| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20856 Z= 0.182 Angle : 0.678 13.126 28296 Z= 0.349 Chirality : 0.046 0.397 3303 Planarity : 0.004 0.048 3570 Dihedral : 8.465 59.440 3837 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.97 % Favored : 93.74 % Rotamer: Outliers : 2.21 % Allowed : 14.57 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.75 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2478 helix: 0.59 (0.25), residues: 429 sheet: -0.24 (0.19), residues: 723 loop : -1.79 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP G 50 HIS 0.005 0.001 HIS G 102 PHE 0.026 0.001 PHE G 100D TYR 0.018 0.001 TYR E 142 ARG 0.004 0.000 ARG E 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2993.05 seconds wall clock time: 57 minutes 14.64 seconds (3434.64 seconds total)