Starting phenix.real_space_refine on Thu Nov 16 15:46:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/11_2023/7l8w_23238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/11_2023/7l8w_23238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/11_2023/7l8w_23238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/11_2023/7l8w_23238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/11_2023/7l8w_23238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8w_23238/11_2023/7l8w_23238_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 105 5.16 5 C 9845 2.51 5 N 2677 2.21 5 O 3176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3485 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3460 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 20, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1060 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 2, 'TRANS': 130} Chain breaks: 1 Chain: "E" Number of atoms: 3466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3466 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 20, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1052 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 1 Chain: "H" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 515 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'TRANS': 102} Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'UNK:plan-1': 103} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "K" 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 chiralities: 5 Chain: "M" 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 chiralities: 2 Chain: "N" 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 chiralities: 2 Chain: "O" 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 chiralities: 5 Chain: "P" 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 chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen chiralities: 17 Chain: "B" 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 chiralities: 2 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen chiralities: 16 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.64, per 1000 atoms: 0.55 Number of scatterers: 15803 At special positions: 0 Unit cell: (127.72, 136.99, 118.45, 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 105 16.00 O 3176 8.00 N 2677 7.00 C 9845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.07 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.10 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 8 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 9 " " BMA K 3 " - " MAN K 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 386 " " NAG A 607 " - " ASN A 339 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 160 " " NAG A 613 " - " ASN A 197 " " NAG A 614 " - " ASN A 133 " " NAG A 615 " - " ASN A 289 " " NAG A 616 " - " ASN A 137 " " NAG A 617 " - " ASN A 363 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 448 " " NAG C 610 " - " ASN C 301 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 197 " " NAG C 613 " - " ASN C 133 " " NAG C 614 " - " ASN C 355 " " NAG C 615 " - " ASN C 289 " " NAG C 616 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 386 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 618 " " NAG F 702 " - " ASN F 637 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN C 262 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN E 332 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 156 " Time building additional restraints: 6.61 Conformation dependent library (CDL) restraints added in 2.6 seconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 32 sheets defined 28.9% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.732A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.158A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.890A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'B' and resid 532 through 544 removed outlier: 5.138A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 622 No H-bonds generated for 'chain 'B' and resid 619 through 622' Processing helix chain 'B' and resid 628 through 660 removed outlier: 3.514A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.743A pdb=" N ASN C 197 " --> pdb=" O ILE C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.631A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 483 " --> pdb=" O ARG C 480 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.345A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 530 through 545 removed outlier: 4.385A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL D 539 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 619 through 623 Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 662 removed outlier: 5.443A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR D 643 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU D 661 " --> pdb=" O GLN D 658 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 662 " --> pdb=" O ASP D 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.762A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 475 through 485 removed outlier: 3.659A pdb=" N ARG E 480 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 483 " --> pdb=" O ARG E 480 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 527 removed outlier: 4.117A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 524 through 527' Processing helix chain 'F' and resid 532 through 545 removed outlier: 3.954A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 567 Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 628 through 662 removed outlier: 6.277A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR F 639 " --> pdb=" O ILE F 635 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLN F 640 " --> pdb=" O SER F 636 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 39 Processing sheet with id= B, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'A' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.665A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.315A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.351A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.445A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= N, first strand: chain 'C' and resid 130 through 132 Processing sheet with id= O, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= P, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= Q, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.795A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.694A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 304 through 307 Processing sheet with id= T, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= U, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= V, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= X, first strand: chain 'E' and resid 169 through 177 removed outlier: 4.720A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 200 through 203 Processing sheet with id= Z, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.320A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.136A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 304 through 307 Processing sheet with id= AC, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.778A pdb=" N UNK H 18 " --> pdb=" O UNK H 79 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 106 through 109 Processing sheet with id= AE, first strand: chain 'L' and resid 6 through 8 Processing sheet with id= AF, first strand: chain 'L' and resid 36 through 40 removed outlier: 3.605A pdb=" N UNK L 86 " --> pdb=" O UNK L 40 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3102 1.32 - 1.46: 5297 1.46 - 1.60: 7510 1.60 - 1.74: 30 1.74 - 1.88: 133 Bond restraints: 16072 Sorted by residual: bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.43e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.36e+01 bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.404 -0.078 1.10e-02 8.26e+03 4.98e+01 bond pdb=" NE ARG C 550 " pdb=" CZ ARG C 550 " ideal model delta sigma weight residual 1.326 1.393 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.651 -0.121 2.00e-02 2.50e+03 3.64e+01 ... (remaining 16067 not shown) Histogram of bond angle deviations from ideal: 95.23 - 103.10: 152 103.10 - 110.98: 6444 110.98 - 118.86: 7248 118.86 - 126.74: 7760 126.74 - 134.62: 248 Bond angle restraints: 21852 Sorted by residual: angle pdb=" C PHE C 53 " pdb=" N CYS C 54 " pdb=" CA CYS C 54 " ideal model delta sigma weight residual 122.19 133.63 -11.44 1.41e+00 5.03e-01 6.59e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.67 -8.11 1.01e+00 9.80e-01 6.44e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.47 103.05 7.42 9.60e-01 1.09e+00 5.98e+01 angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 113.23 122.33 -9.10 1.24e+00 6.50e-01 5.39e+01 angle pdb=" C CYS C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.56 126.89 -7.33 1.02e+00 9.61e-01 5.16e+01 ... (remaining 21847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 8678 17.16 - 34.33: 245 34.33 - 51.49: 73 51.49 - 68.65: 30 68.65 - 85.82: 12 Dihedral angle restraints: 9038 sinusoidal: 3449 harmonic: 5589 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 166.12 -73.12 1 1.00e+01 1.00e-02 6.81e+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 93.00 164.19 -71.19 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 ... (remaining 9035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2395 0.188 - 0.376: 311 0.376 - 0.565: 64 0.565 - 0.753: 1 0.753 - 0.941: 2 Chirality restraints: 2773 Sorted by residual: chirality pdb=" C1 MAN G 8 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 8 " pdb=" O5 MAN G 8 " both_signs ideal model delta sigma weight residual False 2.40 1.46 0.94 2.00e-02 2.50e+03 2.21e+03 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.07e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 2770 not shown) Planarity restraints: 2744 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 602 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 602 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E 602 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 602 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 602 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 607 " -0.332 2.00e-02 2.50e+03 2.83e-01 9.99e+02 pdb=" C7 NAG A 607 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A 607 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG A 607 " 0.496 2.00e-02 2.50e+03 pdb=" O7 NAG A 607 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 612 " 0.322 2.00e-02 2.50e+03 2.74e-01 9.39e+02 pdb=" C7 NAG A 612 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG A 612 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG A 612 " -0.479 2.00e-02 2.50e+03 pdb=" O7 NAG A 612 " 0.060 2.00e-02 2.50e+03 ... (remaining 2741 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 5764 2.88 - 3.39: 14426 3.39 - 3.89: 25578 3.89 - 4.40: 29240 4.40 - 4.90: 45970 Nonbonded interactions: 120978 Sorted by model distance: nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.378 2.496 nonbonded pdb=" O3 NAG D 703 " pdb=" O7 NAG D 703 " model vdw 2.383 2.440 nonbonded pdb=" O ASN A 80 " pdb=" NE2 GLN A 82 " model vdw 2.436 2.520 nonbonded pdb=" OD1 ASN E 234 " pdb=" N GLY E 235 " model vdw 2.451 2.520 nonbonded pdb=" N ASP C 167 " pdb=" OD1 ASP C 167 " model vdw 2.488 2.520 ... (remaining 120973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 57 or resid 64 through 503 or resid 601 through \ 616)) selection = (chain 'C' and (resid 33 through 185 or resid 189 through 457 or resid 461 throu \ gh 550 or resid 601 through 616)) selection = (chain 'E' and (resid 33 through 57 or resid 64 through 457 or resid 461 through \ 503 or resid 601 through 616)) } ncs_group { reference = (chain 'B' and (resid 521 through 546 or resid 558 through 662 or resid 701 thro \ ugh 702)) selection = (chain 'D' and (resid 521 through 662 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 662 or resid 702 through 703)) } ncs_group { reference = (chain 'H' and resid 8 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'O' } 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: 6.040 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: 0.000 Extract box with map and model: 11.960 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 43.660 Find NCS groups from input model: 1.130 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.021 0.121 16072 Z= 1.338 Angle : 1.709 11.444 21852 Z= 1.104 Chirality : 0.137 0.941 2773 Planarity : 0.018 0.291 2679 Dihedral : 10.044 85.817 5290 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1678 helix: 0.58 (0.22), residues: 427 sheet: 1.21 (0.23), residues: 465 loop : 0.77 (0.22), residues: 786 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3228 time to fit residues: 233.2526 Evaluate side-chains 239 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 422 GLN C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 HIS C 302 ASN C 422 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16072 Z= 0.251 Angle : 0.760 10.376 21852 Z= 0.387 Chirality : 0.051 0.696 2773 Planarity : 0.004 0.041 2679 Dihedral : 5.007 26.911 2025 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % Rotamer: Outliers : 0.20 % Allowed : 2.10 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1678 helix: 1.44 (0.25), residues: 423 sheet: 1.20 (0.23), residues: 453 loop : 0.22 (0.21), residues: 802 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 366 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 367 average time/residue: 0.2746 time to fit residues: 148.6020 Evaluate side-chains 242 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 153 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 58 optimal weight: 0.0980 chunk 137 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS B 562 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 249 HIS ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 16072 Z= 0.422 Angle : 0.812 12.637 21852 Z= 0.407 Chirality : 0.051 0.412 2773 Planarity : 0.005 0.057 2679 Dihedral : 5.252 27.858 2025 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 0.33 % Allowed : 3.67 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1678 helix: 0.88 (0.25), residues: 425 sheet: 0.88 (0.24), residues: 442 loop : -0.13 (0.21), residues: 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 313 average time/residue: 0.2982 time to fit residues: 136.6025 Evaluate side-chains 208 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1387 time to fit residues: 2.5873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 0.0870 chunk 115 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 90 optimal weight: 0.5980 chunk 163 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN C 352 HIS D 653 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16072 Z= 0.193 Angle : 0.637 15.424 21852 Z= 0.318 Chirality : 0.046 0.421 2773 Planarity : 0.004 0.046 2679 Dihedral : 4.846 22.957 2025 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.55 % Favored : 98.39 % Rotamer: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1678 helix: 1.07 (0.26), residues: 423 sheet: 0.86 (0.24), residues: 443 loop : -0.10 (0.21), residues: 812 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.2962 time to fit residues: 125.8535 Evaluate side-chains 218 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 462 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16072 Z= 0.417 Angle : 0.793 14.065 21852 Z= 0.392 Chirality : 0.051 0.453 2773 Planarity : 0.005 0.064 2679 Dihedral : 5.169 23.674 2025 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1678 helix: 0.66 (0.26), residues: 421 sheet: 0.51 (0.24), residues: 462 loop : -0.35 (0.21), residues: 795 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 262 average time/residue: 0.2980 time to fit residues: 116.1430 Evaluate side-chains 196 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.5980 chunk 164 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 182 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN C 352 HIS E 99 ASN E 195 ASN E 249 HIS E 293 GLN E 425 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16072 Z= 0.182 Angle : 0.637 15.694 21852 Z= 0.314 Chirality : 0.046 0.401 2773 Planarity : 0.004 0.043 2679 Dihedral : 4.798 24.226 2025 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.97 % Favored : 97.97 % Rotamer: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1678 helix: 0.93 (0.27), residues: 420 sheet: 0.64 (0.24), residues: 459 loop : -0.36 (0.21), residues: 799 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 286 average time/residue: 0.2926 time to fit residues: 124.7817 Evaluate side-chains 210 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 114 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN E 99 ASN E 249 HIS F 563 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16072 Z= 0.240 Angle : 0.653 15.815 21852 Z= 0.327 Chirality : 0.047 0.382 2773 Planarity : 0.004 0.051 2679 Dihedral : 4.831 25.195 2025 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.38 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1678 helix: 0.92 (0.27), residues: 422 sheet: 0.53 (0.24), residues: 447 loop : -0.45 (0.21), residues: 809 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.2879 time to fit residues: 119.6991 Evaluate side-chains 208 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 99 ASN E 195 ASN E 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16072 Z= 0.235 Angle : 0.649 15.391 21852 Z= 0.325 Chirality : 0.046 0.370 2773 Planarity : 0.004 0.049 2679 Dihedral : 4.797 27.835 2025 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1678 helix: 0.82 (0.27), residues: 423 sheet: 0.33 (0.24), residues: 460 loop : -0.42 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.2879 time to fit residues: 113.6497 Evaluate side-chains 207 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN E 99 ASN E 195 ASN E 249 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16072 Z= 0.257 Angle : 0.654 15.366 21852 Z= 0.328 Chirality : 0.047 0.425 2773 Planarity : 0.004 0.051 2679 Dihedral : 4.845 28.973 2025 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1678 helix: 0.86 (0.27), residues: 421 sheet: 0.27 (0.24), residues: 432 loop : -0.58 (0.21), residues: 825 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2769 time to fit residues: 111.1090 Evaluate side-chains 207 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 149 optimal weight: 0.0470 chunk 15 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 overall best weight: 1.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN E 99 ASN E 249 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16072 Z= 0.256 Angle : 0.653 15.303 21852 Z= 0.330 Chirality : 0.047 0.478 2773 Planarity : 0.004 0.051 2679 Dihedral : 4.857 29.965 2025 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.20), residues: 1678 helix: 0.79 (0.27), residues: 422 sheet: 0.19 (0.24), residues: 436 loop : -0.67 (0.21), residues: 820 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.2728 time to fit residues: 104.9176 Evaluate side-chains 209 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 82 GLN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN E 99 ASN E 195 ASN E 249 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.104546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087149 restraints weight = 35991.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089536 restraints weight = 21717.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.091139 restraints weight = 15374.522| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16072 Z= 0.223 Angle : 0.639 15.545 21852 Z= 0.320 Chirality : 0.047 0.454 2773 Planarity : 0.004 0.050 2679 Dihedral : 4.787 30.187 2025 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1678 helix: 0.77 (0.27), residues: 421 sheet: 0.21 (0.24), residues: 436 loop : -0.66 (0.21), residues: 821 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3230.89 seconds wall clock time: 59 minutes 53.52 seconds (3593.52 seconds total)