Starting phenix.real_space_refine on Sun Apr 7 22:04:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/04_2024/7bwa_30231.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/04_2024/7bwa_30231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/04_2024/7bwa_30231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/04_2024/7bwa_30231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/04_2024/7bwa_30231.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwa_30231/04_2024/7bwa_30231.pdb" } resolution = 4.9 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= 0.001 sd= 0.004 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 94 5.16 5 C 7420 2.51 5 N 1998 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 19": "NH1" <-> "NH2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A ARG 554": "NH1" <-> "NH2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 695": "OE1" <-> "OE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 250": "OD1" <-> "OD2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 322": "OD1" <-> "OD2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 413": "OD1" <-> "OD2" Residue "C PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ASP 496": "OD1" <-> "OD2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C ASP 584": "OD1" <-> "OD2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 13": "OE1" <-> "OE2" Residue "D TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 13": "OE1" <-> "OE2" Residue "E TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11670 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5459 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 639} Chain breaks: 6 Chain: "C" Number of atoms: 5459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5459 Classifications: {'peptide': 674} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 639} Chain breaks: 6 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "E" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 7.05, per 1000 atoms: 0.60 Number of scatterers: 11670 At special positions: 0 Unit cell: (91.79, 152.07, 132.89, 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 94 16.00 O 2158 8.00 N 1998 7.00 C 7420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.02 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 26 " distance=2.04 Simple disulfide: pdb=" SG CYS C 192 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 216 " distance=2.02 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 241 " - pdb=" SG CYS C 253 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 284 " distance=2.04 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 312 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 435 " - pdb=" SG CYS C 468 " distance=2.02 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 62 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.86 Conformation dependent library (CDL) restraints added in 2.0 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2740 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 22 sheets defined 17.9% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 4.311A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 47 removed outlier: 4.153A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 358 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 435 through 445 Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 695 through 714 removed outlier: 4.182A pdb=" N SER A 699 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 700 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 712 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'C' and resid 16 through 23 removed outlier: 4.311A pdb=" N ARG C 19 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N HIS C 21 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.154A pdb=" N PHE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 435 through 445 Processing helix chain 'C' and resid 458 through 462 Processing helix chain 'C' and resid 638 through 642 Processing helix chain 'C' and resid 695 through 714 removed outlier: 4.182A pdb=" N SER C 699 " --> pdb=" O GLU C 695 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP C 707 " --> pdb=" O LYS C 703 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 712 " --> pdb=" O TYR C 708 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE C 714 " --> pdb=" O HIS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 813 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 67 through 73 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.538A pdb=" N MET A 11 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU A 36 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE A 13 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.944A pdb=" N ILE A 29 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 255 removed outlier: 7.719A pdb=" N CYS A 284 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 363 through 364 removed outlier: 3.798A pdb=" N ILE A 364 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 368 through 371 removed outlier: 5.331A pdb=" N TYR A 398 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE A 427 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE A 400 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N HIS A 429 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 474 through 479 removed outlier: 5.475A pdb=" N PHE A 475 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N GLU A 490 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 532 through 533 removed outlier: 3.602A pdb=" N VAL A 532 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 502 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 569 " --> pdb=" O GLY A 502 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 561 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR A 568 " --> pdb=" O LYS A 582 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LYS A 582 " --> pdb=" O THR A 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 604 removed outlier: 5.977A pdb=" N ASP A 600 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A 616 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 759 through 762 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.537A pdb=" N MET C 11 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU C 36 " --> pdb=" O MET C 11 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C 13 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU C 93 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N GLU C 120 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 95 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASN C 122 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN C 148 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.944A pdb=" N ILE C 29 " --> pdb=" O MET C 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AB6, first strand: chain 'C' and resid 252 through 255 removed outlier: 7.720A pdb=" N CYS C 284 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N HIS C 247 " --> pdb=" O CYS C 284 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.797A pdb=" N ILE C 364 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 368 through 371 removed outlier: 5.331A pdb=" N TYR C 398 " --> pdb=" O LYS C 425 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N PHE C 427 " --> pdb=" O TYR C 398 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N PHE C 400 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS C 429 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA C 402 " --> pdb=" O HIS C 429 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 474 through 479 removed outlier: 5.475A pdb=" N PHE C 475 " --> pdb=" O GLU C 490 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU C 490 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.602A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C 502 " --> pdb=" O LEU C 569 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 569 " --> pdb=" O GLY C 502 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN C 561 " --> pdb=" O ALA C 510 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL C 566 " --> pdb=" O ASP C 584 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASP C 584 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 568 " --> pdb=" O LYS C 582 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LYS C 582 " --> pdb=" O THR C 568 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 599 through 604 removed outlier: 5.976A pdb=" N ASP C 600 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 616 " --> pdb=" O ASP C 600 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 759 through 762 262 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 5.27 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: 3799 1.34 - 1.46: 2701 1.46 - 1.58: 5330 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 11944 Sorted by residual: bond pdb=" N TYR C 579 " pdb=" CA TYR C 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" CA ALA A 581 " pdb=" CB ALA A 581 " ideal model delta sigma weight residual 1.538 1.506 0.032 1.22e-02 6.72e+03 6.89e+00 bond pdb=" N TYR A 579 " pdb=" CA TYR A 579 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.31e-02 5.83e+03 6.30e+00 bond pdb=" N ARG C 576 " pdb=" CA ARG C 576 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.16e-02 7.43e+03 6.17e+00 bond pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 6.09e+00 ... (remaining 11939 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.12: 403 107.12 - 113.90: 6670 113.90 - 120.69: 4656 120.69 - 127.47: 4320 127.47 - 134.25: 125 Bond angle restraints: 16174 Sorted by residual: angle pdb=" N GLU A 575 " pdb=" CA GLU A 575 " pdb=" C GLU A 575 " ideal model delta sigma weight residual 113.28 108.49 4.79 1.22e+00 6.72e-01 1.54e+01 angle pdb=" N GLU C 575 " pdb=" CA GLU C 575 " pdb=" C GLU C 575 " ideal model delta sigma weight residual 113.20 108.64 4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" CA GLY C 580 " pdb=" C GLY C 580 " pdb=" O GLY C 580 " ideal model delta sigma weight residual 122.24 118.32 3.92 1.08e+00 8.57e-01 1.32e+01 angle pdb=" CA ARG C 577 " pdb=" C ARG C 577 " pdb=" O ARG C 577 " ideal model delta sigma weight residual 121.87 117.95 3.92 1.10e+00 8.26e-01 1.27e+01 angle pdb=" CA ARG C 576 " pdb=" C ARG C 576 " pdb=" O ARG C 576 " ideal model delta sigma weight residual 121.38 118.19 3.19 1.06e+00 8.90e-01 9.06e+00 ... (remaining 16169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6337 17.95 - 35.89: 732 35.89 - 53.84: 153 53.84 - 71.79: 22 71.79 - 89.74: 8 Dihedral angle restraints: 7252 sinusoidal: 3024 harmonic: 4228 Sorted by residual: dihedral pdb=" CB CYS D 7 " pdb=" SG CYS D 7 " pdb=" SG CYS D 62 " pdb=" CB CYS D 62 " ideal model delta sinusoidal sigma weight residual -86.00 -152.59 66.59 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS E 7 " pdb=" SG CYS E 7 " pdb=" SG CYS E 62 " pdb=" CB CYS E 62 " ideal model delta sinusoidal sigma weight residual -86.00 -152.58 66.58 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS A 312 " pdb=" SG CYS A 312 " pdb=" SG CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sinusoidal sigma weight residual 93.00 148.34 -55.34 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1038 0.036 - 0.072: 486 0.072 - 0.109: 182 0.109 - 0.145: 48 0.145 - 0.181: 16 Chirality restraints: 1770 Sorted by residual: chirality pdb=" CA ARG A 577 " pdb=" N ARG A 577 " pdb=" C ARG A 577 " pdb=" CB ARG A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA ARG C 577 " pdb=" N ARG C 577 " pdb=" C ARG C 577 " pdb=" CB ARG C 577 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE C 145 " pdb=" N ILE C 145 " pdb=" C ILE C 145 " pdb=" CB ILE C 145 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 1767 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 574 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.35e+00 pdb=" C ASP A 574 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP A 574 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 575 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 574 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.79e+00 pdb=" C ASP C 574 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP C 574 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU C 575 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 42 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 43 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.019 5.00e-02 4.00e+02 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 258 2.56 - 3.14: 10632 3.14 - 3.73: 20249 3.73 - 4.31: 27501 4.31 - 4.90: 40931 Nonbonded interactions: 99571 Sorted by model distance: nonbonded pdb=" O GLU C 469 " pdb=" NH2 ARG C 577 " model vdw 1.970 2.520 nonbonded pdb=" OD1 ASP C 221 " pdb=" OG1 THR C 223 " model vdw 2.122 2.440 nonbonded pdb=" OD1 ASP A 221 " pdb=" OG1 THR A 223 " model vdw 2.123 2.440 nonbonded pdb=" OH TYR C 628 " pdb=" OE2 GLU C 766 " model vdw 2.138 2.440 nonbonded pdb=" OH TYR A 628 " pdb=" OE2 GLU A 766 " model vdw 2.139 2.440 ... (remaining 99566 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'E' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.010 Extract box with map and model: 1.580 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 34.100 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 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 : 0.004 0.034 11944 Z= 0.279 Angle : 0.772 7.294 16174 Z= 0.439 Chirality : 0.049 0.181 1770 Planarity : 0.004 0.034 2076 Dihedral : 15.314 89.735 4416 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 41.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.20), residues: 1408 helix: -2.50 (0.34), residues: 166 sheet: -3.54 (0.32), residues: 178 loop : -2.89 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 632 HIS 0.007 0.002 HIS A 263 PHE 0.019 0.002 PHE C 89 TYR 0.018 0.002 TYR C 91 ARG 0.004 0.001 ARG C 702 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.638 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: A 109 LEU cc_start: 0.8593 (mm) cc_final: 0.8379 (mm) REVERT: A 250 ASP cc_start: 0.7958 (m-30) cc_final: 0.7721 (t70) REVERT: A 368 LEU cc_start: 0.8239 (mm) cc_final: 0.7935 (mm) REVERT: A 442 MET cc_start: 0.8113 (mmt) cc_final: 0.7504 (mmt) REVERT: A 477 TYR cc_start: 0.8328 (m-10) cc_final: 0.7880 (m-80) REVERT: A 575 GLU cc_start: 0.5698 (pp20) cc_final: 0.5451 (pp20) REVERT: A 706 GLU cc_start: 0.8874 (mp0) cc_final: 0.8410 (mp0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2264 time to fit residues: 32.7450 Evaluate side-chains 65 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.647 Evaluate side-chains 11 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.046 Fit side-chains REVERT: D 22 ARG cc_start: 0.7851 (mpp80) cc_final: 0.7118 (mmm160) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1348 time to fit residues: 1.5906 Evaluate side-chains 6 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 82 optimal weight: 0.0770 chunk 128 optimal weight: 1.9990 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 GLN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 470 ASN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11944 Z= 0.212 Angle : 0.726 8.020 16174 Z= 0.383 Chirality : 0.047 0.176 1770 Planarity : 0.005 0.060 2076 Dihedral : 6.699 22.190 1566 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 33.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.07 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.21), residues: 1408 helix: -2.35 (0.34), residues: 164 sheet: -3.49 (0.32), residues: 178 loop : -2.68 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 632 HIS 0.029 0.002 HIS E 10 PHE 0.072 0.002 PHE A 701 TYR 0.021 0.002 TYR A 587 ARG 0.006 0.001 ARG C 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.4334 (ttt) cc_final: 0.3792 (tpt) REVERT: A 101 LEU cc_start: 0.9191 (tp) cc_final: 0.8863 (tp) REVERT: A 263 HIS cc_start: 0.8539 (t70) cc_final: 0.7996 (t70) REVERT: A 368 LEU cc_start: 0.8304 (mm) cc_final: 0.8061 (mm) REVERT: A 419 LEU cc_start: 0.8169 (tt) cc_final: 0.7965 (mt) REVERT: A 442 MET cc_start: 0.8327 (mmt) cc_final: 0.7595 (mmt) REVERT: A 504 MET cc_start: 0.8777 (mmp) cc_final: 0.8350 (mmm) REVERT: A 706 GLU cc_start: 0.8674 (mp0) cc_final: 0.7940 (pm20) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1632 time to fit residues: 18.7122 Evaluate side-chains 57 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.627 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.046 Fit side-chains REVERT: D 22 ARG cc_start: 0.7619 (mpp80) cc_final: 0.7060 (mmm160) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1743 time to fit residues: 1.4953 Evaluate side-chains 6 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 87 optimal weight: 0.4980 chunk 35 optimal weight: 9.9990 chunk 129 optimal weight: 0.1980 chunk 139 optimal weight: 20.0000 chunk 115 optimal weight: 0.0470 chunk 128 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 0.0970 overall best weight: 1.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 25 ASN A 34 GLN A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11944 Z= 0.190 Angle : 0.704 6.868 16174 Z= 0.372 Chirality : 0.047 0.171 1770 Planarity : 0.005 0.051 2076 Dihedral : 6.240 20.428 1566 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 27.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.21), residues: 1408 helix: -1.72 (0.39), residues: 164 sheet: -3.29 (0.31), residues: 192 loop : -2.64 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 632 HIS 0.008 0.001 HIS E 10 PHE 0.037 0.002 PHE C 701 TYR 0.017 0.002 TYR A 587 ARG 0.007 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7789 (pt) cc_final: 0.7398 (pt) REVERT: A 38 MET cc_start: 0.3908 (ttt) cc_final: 0.3541 (tpt) REVERT: A 263 HIS cc_start: 0.8565 (t70) cc_final: 0.8050 (t70) REVERT: A 368 LEU cc_start: 0.8581 (mm) cc_final: 0.8325 (mm) REVERT: A 419 LEU cc_start: 0.8179 (tt) cc_final: 0.7978 (mt) REVERT: A 442 MET cc_start: 0.8295 (mmt) cc_final: 0.7682 (mmt) REVERT: A 488 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.7050 (mmt90) REVERT: A 504 MET cc_start: 0.8824 (mmp) cc_final: 0.8361 (mmm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1941 time to fit residues: 21.9291 Evaluate side-chains 61 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.660 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1602 time to fit residues: 1.3790 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 122 optimal weight: 30.0000 chunk 36 optimal weight: 0.0060 chunk 114 optimal weight: 7.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11944 Z= 0.187 Angle : 0.671 7.705 16174 Z= 0.354 Chirality : 0.046 0.186 1770 Planarity : 0.005 0.039 2076 Dihedral : 6.148 22.550 1566 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 27.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.21), residues: 1408 helix: -1.73 (0.38), residues: 166 sheet: -3.07 (0.32), residues: 192 loop : -2.60 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 133 HIS 0.004 0.001 HIS D 10 PHE 0.026 0.002 PHE C 701 TYR 0.014 0.001 TYR C 60 ARG 0.007 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.4283 (ttt) cc_final: 0.3892 (tpt) REVERT: A 98 MET cc_start: 0.7388 (tpt) cc_final: 0.7072 (tpp) REVERT: A 101 LEU cc_start: 0.9110 (tp) cc_final: 0.8591 (tp) REVERT: A 109 LEU cc_start: 0.8784 (mm) cc_final: 0.8545 (mm) REVERT: A 263 HIS cc_start: 0.8566 (t70) cc_final: 0.8050 (t70) REVERT: A 368 LEU cc_start: 0.8124 (mm) cc_final: 0.7776 (mm) REVERT: A 442 MET cc_start: 0.8014 (mmt) cc_final: 0.7764 (mmt) REVERT: A 488 ARG cc_start: 0.7416 (mmm-85) cc_final: 0.6858 (mmt90) REVERT: A 504 MET cc_start: 0.8756 (mmp) cc_final: 0.8224 (mmm) REVERT: A 551 TRP cc_start: 0.7598 (t-100) cc_final: 0.7267 (t-100) REVERT: A 579 TYR cc_start: 0.7788 (m-80) cc_final: 0.7565 (m-80) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1652 time to fit residues: 19.0607 Evaluate side-chains 65 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.616 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.045 Fit side-chains REVERT: D 22 ARG cc_start: 0.7394 (mpp80) cc_final: 0.6700 (mmm160) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1691 time to fit residues: 1.4467 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 94 optimal weight: 0.0050 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 0.0770 chunk 123 optimal weight: 10.0000 chunk 34 optimal weight: 0.0170 chunk 46 optimal weight: 6.9990 overall best weight: 2.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11944 Z= 0.182 Angle : 0.671 8.650 16174 Z= 0.354 Chirality : 0.046 0.215 1770 Planarity : 0.005 0.044 2076 Dihedral : 5.989 23.728 1566 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 26.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.21), residues: 1408 helix: -2.06 (0.34), residues: 170 sheet: -2.95 (0.32), residues: 192 loop : -2.54 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 133 HIS 0.004 0.001 HIS A 263 PHE 0.044 0.002 PHE C 701 TYR 0.014 0.001 TYR C 60 ARG 0.007 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.4284 (ttt) cc_final: 0.3702 (tpt) REVERT: A 109 LEU cc_start: 0.8703 (mm) cc_final: 0.8438 (mm) REVERT: A 368 LEU cc_start: 0.8551 (mm) cc_final: 0.8194 (mm) REVERT: A 419 LEU cc_start: 0.8348 (tt) cc_final: 0.8075 (mt) REVERT: A 442 MET cc_start: 0.8219 (mmt) cc_final: 0.7756 (mmt) REVERT: A 488 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6819 (mmt90) REVERT: A 504 MET cc_start: 0.8673 (mmp) cc_final: 0.8122 (mmm) REVERT: A 575 GLU cc_start: 0.6017 (mp0) cc_final: 0.5800 (pm20) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1825 time to fit residues: 20.4478 Evaluate side-chains 66 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.692 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: D 22 ARG cc_start: 0.7413 (mpp80) cc_final: 0.6755 (mmm160) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1641 time to fit residues: 1.4101 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 10.0000 chunk 27 optimal weight: 0.0570 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.0270 chunk 132 optimal weight: 0.0040 overall best weight: 0.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 152 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11944 Z= 0.176 Angle : 0.686 11.777 16174 Z= 0.352 Chirality : 0.047 0.188 1770 Planarity : 0.005 0.046 2076 Dihedral : 5.809 21.653 1566 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.21), residues: 1408 helix: -1.73 (0.36), residues: 168 sheet: -2.65 (0.34), residues: 192 loop : -2.44 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 133 HIS 0.004 0.001 HIS C 263 PHE 0.029 0.002 PHE C 701 TYR 0.013 0.001 TYR C 60 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.3970 (ttt) cc_final: 0.3491 (tpt) REVERT: A 98 MET cc_start: 0.7382 (tpp) cc_final: 0.6331 (tpp) REVERT: A 101 LEU cc_start: 0.9142 (tp) cc_final: 0.8580 (pt) REVERT: A 109 LEU cc_start: 0.8689 (mm) cc_final: 0.8298 (mm) REVERT: A 263 HIS cc_start: 0.8388 (t70) cc_final: 0.7721 (t-90) REVERT: A 368 LEU cc_start: 0.8488 (mm) cc_final: 0.8087 (mm) REVERT: A 419 LEU cc_start: 0.8318 (tt) cc_final: 0.8041 (mt) REVERT: A 442 MET cc_start: 0.8174 (mmt) cc_final: 0.7870 (mmm) REVERT: A 488 ARG cc_start: 0.7194 (mmm-85) cc_final: 0.6736 (mmt180) REVERT: A 504 MET cc_start: 0.8746 (mmp) cc_final: 0.8272 (mmm) REVERT: A 552 LEU cc_start: 0.8311 (pt) cc_final: 0.8067 (pt) REVERT: A 575 GLU cc_start: 0.5883 (mp0) cc_final: 0.5682 (pm20) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1546 time to fit residues: 18.1778 Evaluate side-chains 65 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.635 Evaluate side-chains 9 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.1569 time to fit residues: 1.5126 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.0370 chunk 78 optimal weight: 8.9990 chunk 100 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 115 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 136 optimal weight: 0.2980 chunk 85 optimal weight: 0.0040 chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 0.1980 chunk 84 optimal weight: 30.0000 overall best weight: 0.1268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 ASN A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11944 Z= 0.155 Angle : 0.653 8.091 16174 Z= 0.336 Chirality : 0.046 0.199 1770 Planarity : 0.005 0.046 2076 Dihedral : 5.524 19.956 1566 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.21), residues: 1408 helix: -2.02 (0.35), residues: 170 sheet: -2.44 (0.36), residues: 172 loop : -2.40 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 133 HIS 0.003 0.001 HIS A 263 PHE 0.037 0.002 PHE A 701 TYR 0.012 0.001 TYR C 60 ARG 0.004 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.3894 (ttt) cc_final: 0.3410 (tpt) REVERT: A 93 LEU cc_start: 0.7865 (tp) cc_final: 0.7566 (tp) REVERT: A 98 MET cc_start: 0.7909 (tpp) cc_final: 0.7380 (tpp) REVERT: A 101 LEU cc_start: 0.9094 (tp) cc_final: 0.8729 (tp) REVERT: A 109 LEU cc_start: 0.8364 (mm) cc_final: 0.8108 (mm) REVERT: A 368 LEU cc_start: 0.8443 (mm) cc_final: 0.8048 (mm) REVERT: A 419 LEU cc_start: 0.8314 (tt) cc_final: 0.8039 (mt) REVERT: A 442 MET cc_start: 0.8213 (mmt) cc_final: 0.7886 (mmm) REVERT: A 488 ARG cc_start: 0.7175 (mmm-85) cc_final: 0.6824 (mmt180) REVERT: A 504 MET cc_start: 0.8897 (mmp) cc_final: 0.8486 (mmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1630 time to fit residues: 18.1055 Evaluate side-chains 64 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.673 Evaluate side-chains 11 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.045 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1660 time to fit residues: 1.9323 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 0.0070 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11944 Z= 0.166 Angle : 0.654 8.914 16174 Z= 0.339 Chirality : 0.046 0.282 1770 Planarity : 0.005 0.045 2076 Dihedral : 5.521 20.073 1566 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.21), residues: 1408 helix: -1.63 (0.37), residues: 166 sheet: -2.42 (0.34), residues: 192 loop : -2.32 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 133 HIS 0.003 0.001 HIS C 263 PHE 0.019 0.002 PHE C 39 TYR 0.012 0.001 TYR D 74 ARG 0.006 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.7903 (tp) cc_final: 0.7523 (tp) REVERT: A 98 MET cc_start: 0.7916 (tpp) cc_final: 0.7326 (tpp) REVERT: A 101 LEU cc_start: 0.9112 (tp) cc_final: 0.8663 (tp) REVERT: A 109 LEU cc_start: 0.8670 (mm) cc_final: 0.7902 (mm) REVERT: A 110 MET cc_start: 0.7143 (mmp) cc_final: 0.6699 (ttt) REVERT: A 125 LEU cc_start: 0.8636 (tp) cc_final: 0.8316 (tp) REVERT: A 368 LEU cc_start: 0.8483 (mm) cc_final: 0.8030 (mm) REVERT: A 442 MET cc_start: 0.8214 (mmt) cc_final: 0.7858 (mmm) REVERT: A 488 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6900 (mmt180) REVERT: A 504 MET cc_start: 0.8787 (mmp) cc_final: 0.8451 (mmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1764 time to fit residues: 20.4225 Evaluate side-chains 62 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.697 Evaluate side-chains 8 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.047 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0630 time to fit residues: 0.6189 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 7.9990 chunk 127 optimal weight: 8.9990 chunk 131 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11944 Z= 0.233 Angle : 0.692 8.472 16174 Z= 0.361 Chirality : 0.047 0.248 1770 Planarity : 0.005 0.042 2076 Dihedral : 5.724 21.272 1566 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.21), residues: 1408 helix: -2.18 (0.33), residues: 172 sheet: -2.49 (0.34), residues: 192 loop : -2.24 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 133 HIS 0.005 0.001 HIS E 10 PHE 0.017 0.002 PHE C 76 TYR 0.020 0.002 TYR C 67 ARG 0.006 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7614 (tpp) cc_final: 0.7020 (tpp) REVERT: A 101 LEU cc_start: 0.9140 (tp) cc_final: 0.8723 (tp) REVERT: A 109 LEU cc_start: 0.8678 (mm) cc_final: 0.8026 (mm) REVERT: A 110 MET cc_start: 0.7222 (mmp) cc_final: 0.6742 (ttt) REVERT: A 368 LEU cc_start: 0.8411 (mm) cc_final: 0.7946 (mm) REVERT: A 442 MET cc_start: 0.8311 (mmt) cc_final: 0.7894 (mmm) REVERT: A 488 ARG cc_start: 0.7311 (mmm-85) cc_final: 0.6832 (mmt90) REVERT: A 504 MET cc_start: 0.8625 (mmp) cc_final: 0.8297 (mmm) REVERT: A 553 MET cc_start: 0.8071 (mpp) cc_final: 0.7862 (mpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1557 time to fit residues: 16.5367 Evaluate side-chains 61 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.635 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0548 time to fit residues: 0.4793 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.0870 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 0.0070 chunk 130 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11944 Z= 0.163 Angle : 0.693 12.666 16174 Z= 0.351 Chirality : 0.047 0.216 1770 Planarity : 0.005 0.041 2076 Dihedral : 5.478 20.590 1566 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1408 helix: -2.25 (0.32), residues: 184 sheet: -2.21 (0.34), residues: 188 loop : -2.19 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 133 HIS 0.004 0.001 HIS D 10 PHE 0.016 0.002 PHE C 39 TYR 0.013 0.001 TYR A 67 ARG 0.007 0.001 ARG A 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.690 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: A 23 LEU cc_start: 0.6817 (tt) cc_final: 0.6573 (mt) REVERT: A 81 VAL cc_start: 0.8423 (t) cc_final: 0.8186 (t) REVERT: A 93 LEU cc_start: 0.7812 (tp) cc_final: 0.7483 (tp) REVERT: A 98 MET cc_start: 0.7911 (tpp) cc_final: 0.7446 (tpp) REVERT: A 101 LEU cc_start: 0.9138 (tp) cc_final: 0.8766 (tp) REVERT: A 109 LEU cc_start: 0.8610 (mm) cc_final: 0.8319 (mm) REVERT: A 125 LEU cc_start: 0.8645 (tp) cc_final: 0.8286 (tp) REVERT: A 368 LEU cc_start: 0.8424 (mm) cc_final: 0.7957 (mm) REVERT: A 442 MET cc_start: 0.8228 (mmt) cc_final: 0.7839 (mmm) REVERT: A 488 ARG cc_start: 0.7142 (mmm-85) cc_final: 0.6813 (mmt180) REVERT: A 504 MET cc_start: 0.8760 (mmp) cc_final: 0.8411 (mmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1664 time to fit residues: 19.0567 Evaluate side-chains 66 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.776 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0588 time to fit residues: 0.5206 Evaluate side-chains 7 residues out of total 43 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.094424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.076604 restraints weight = 35128.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.078727 restraints weight = 24933.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.080249 restraints weight = 19415.450| |-----------------------------------------------------------------------------| r_work (final): 0.3756 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.072542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065516 restraints weight = 2326.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.067309 restraints weight = 1438.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068639 restraints weight = 951.825| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11944 Z= 0.163 Angle : 0.651 8.906 16174 Z= 0.333 Chirality : 0.046 0.226 1770 Planarity : 0.005 0.040 2076 Dihedral : 5.345 19.530 1566 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.21), residues: 1408 helix: -2.23 (0.32), residues: 174 sheet: -2.12 (0.34), residues: 188 loop : -2.13 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 133 HIS 0.003 0.001 HIS A 263 PHE 0.016 0.002 PHE A 39 TYR 0.014 0.001 TYR A 67 ARG 0.004 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.22 seconds wall clock time: 40 minutes 15.54 seconds (2415.54 seconds total)