Starting phenix.real_space_refine on Thu Feb 15 14:37:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/02_2024/8hfy_34728.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/02_2024/8hfy_34728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/02_2024/8hfy_34728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/02_2024/8hfy_34728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/02_2024/8hfy_34728.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfy_34728/02_2024/8hfy_34728.pdb" } resolution = 3.21 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6024 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 38 5.16 5 C 4195 2.51 5 N 1075 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6568 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4886 Classifications: {'peptide': 595} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 570} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.16, per 1000 atoms: 0.63 Number of scatterers: 6568 At special positions: 0 Unit cell: (85, 88.4, 120.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 38 16.00 O 1259 8.00 N 1075 7.00 C 4195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 701 " - " ASN A 432 " " NAG A 702 " - " ASN A 299 " " NAG A 703 " - " ASN A 91 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 54 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 378 " 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1496 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 54.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.749A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.090A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.508A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'A' and resid 21 through 54 removed outlier: 3.677A pdb=" N HIS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 82 removed outlier: 3.724A pdb=" N LYS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 103 removed outlier: 3.559A pdb=" N GLN A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 4.243A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 removed outlier: 3.585A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 139 removed outlier: 3.831A pdb=" N GLN A 139 " --> pdb=" O PRO A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 139' Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.705A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.959A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.647A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 4.110A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.948A pdb=" N ILE A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.909A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.687A pdb=" N ARG A 393 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.136A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 448 Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.194A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 516 through 533 removed outlier: 3.575A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS A 530 " --> pdb=" O HIS A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.047A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.723A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.626A pdb=" N THR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 134 Processing sheet with id=AA6, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.114A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.368A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 843 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: 1.90 Time building geometry restraints manager: 2.80 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: 2075 1.34 - 1.46: 1522 1.46 - 1.58: 3091 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6748 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.557 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.444 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 6743 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.15: 222 107.15 - 113.86: 3662 113.86 - 120.57: 2772 120.57 - 127.28: 2408 127.28 - 133.99: 92 Bond angle restraints: 9156 Sorted by residual: angle pdb=" N ILE A 55 " pdb=" CA ILE A 55 " pdb=" C ILE A 55 " ideal model delta sigma weight residual 106.55 110.56 -4.01 1.45e+00 4.76e-01 7.66e+00 angle pdb=" C PHE B 375 " pdb=" N THR B 376 " pdb=" CA THR B 376 " ideal model delta sigma weight residual 122.41 118.51 3.90 1.47e+00 4.63e-01 7.04e+00 angle pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " pdb=" C5 NAG D 1 " ideal model delta sigma weight residual 113.21 121.03 -7.82 3.00e+00 1.11e-01 6.79e+00 angle pdb=" C ALA A 384 " pdb=" N TYR A 385 " pdb=" CA TYR A 385 " ideal model delta sigma weight residual 122.65 118.46 4.19 1.66e+00 3.63e-01 6.36e+00 angle pdb=" N GLY A 537 " pdb=" CA GLY A 537 " pdb=" C GLY A 537 " ideal model delta sigma weight residual 110.46 113.97 -3.51 1.43e+00 4.89e-01 6.04e+00 ... (remaining 9151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.82: 3926 24.82 - 49.64: 135 49.64 - 74.46: 18 74.46 - 99.28: 14 99.28 - 124.10: 15 Dihedral angle restraints: 4108 sinusoidal: 1778 harmonic: 2330 Sorted by residual: dihedral pdb=" C2 NAG A 701 " pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " pdb=" C5 NAG A 701 " ideal model delta sinusoidal sigma weight residual -62.96 61.14 -124.10 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" O4 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 288.71 173.99 114.72 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C3 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sinusoidal sigma weight residual 47.62 -65.53 113.15 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 4105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 812 0.053 - 0.107: 146 0.107 - 0.160: 19 0.160 - 0.214: 1 0.214 - 0.267: 1 Chirality restraints: 979 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.58e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.48e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 976 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO B 373 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 444 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C LEU A 444 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 444 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 445 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.62e+00 pdb=" N PRO A 146 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.021 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 68 2.64 - 3.21: 5868 3.21 - 3.77: 9628 3.77 - 4.34: 13493 4.34 - 4.90: 22737 Nonbonded interactions: 51794 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 704 " model vdw 2.081 2.230 nonbonded pdb=" OG1 THR B 500 " pdb=" OH TYR A 42 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.224 2.440 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.225 2.440 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.257 2.440 ... (remaining 51789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 18.910 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 23.300 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.003 0.073 6748 Z= 0.194 Angle : 0.554 7.817 9156 Z= 0.288 Chirality : 0.042 0.267 979 Planarity : 0.004 0.049 1166 Dihedral : 15.549 124.095 2600 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 6.47 % Favored : 92.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.29 (0.30), residues: 785 helix: 1.41 (0.27), residues: 392 sheet: 0.52 (0.80), residues: 44 loop : -1.30 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 606 HIS 0.004 0.001 HIS A 378 PHE 0.017 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7229 (t0) cc_final: 0.6988 (t0) REVERT: A 149 ASP cc_start: 0.8409 (t0) cc_final: 0.8204 (t0) REVERT: A 152 MET cc_start: 0.9148 (mmm) cc_final: 0.8644 (mmt) outliers start: 10 outliers final: 3 residues processed: 130 average time/residue: 0.2296 time to fit residues: 38.0477 Evaluate side-chains 76 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6748 Z= 0.352 Angle : 0.656 10.731 9156 Z= 0.330 Chirality : 0.046 0.231 979 Planarity : 0.005 0.055 1166 Dihedral : 13.836 106.091 1061 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.73 % Allowed : 11.49 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.30), residues: 785 helix: 1.35 (0.27), residues: 396 sheet: 0.53 (0.81), residues: 44 loop : -1.41 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.009 0.001 HIS B 519 PHE 0.021 0.002 PHE A 369 TYR 0.019 0.002 TYR B 365 ARG 0.002 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: B 370 ASN cc_start: 0.7231 (t0) cc_final: 0.7024 (t0) REVERT: A 552 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7848 (mp-120) outliers start: 19 outliers final: 10 residues processed: 93 average time/residue: 0.1699 time to fit residues: 21.9377 Evaluate side-chains 77 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6748 Z= 0.193 Angle : 0.560 8.430 9156 Z= 0.282 Chirality : 0.042 0.233 979 Planarity : 0.004 0.052 1166 Dihedral : 11.978 102.431 1060 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.30 % Allowed : 12.50 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.28 (0.30), residues: 785 helix: 1.38 (0.27), residues: 387 sheet: 0.51 (0.80), residues: 44 loop : -1.24 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR B 365 ARG 0.003 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 149 ASP cc_start: 0.8548 (t0) cc_final: 0.8278 (t0) outliers start: 16 outliers final: 10 residues processed: 82 average time/residue: 0.1969 time to fit residues: 22.3644 Evaluate side-chains 75 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6748 Z= 0.274 Angle : 0.569 8.819 9156 Z= 0.289 Chirality : 0.044 0.233 979 Planarity : 0.005 0.059 1166 Dihedral : 10.284 96.859 1060 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.01 % Allowed : 14.22 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.31 (0.30), residues: 785 helix: 1.37 (0.27), residues: 391 sheet: 0.64 (0.81), residues: 44 loop : -1.24 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 PHE 0.017 0.002 PHE A 369 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.794 Fit side-chains REVERT: A 151 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 332 MET cc_start: 0.8409 (ttm) cc_final: 0.8189 (ttt) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1746 time to fit residues: 19.4206 Evaluate side-chains 74 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6748 Z= 0.386 Angle : 0.630 9.588 9156 Z= 0.321 Chirality : 0.045 0.177 979 Planarity : 0.005 0.081 1166 Dihedral : 9.198 87.357 1060 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.87 % Allowed : 13.79 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.30), residues: 785 helix: 1.23 (0.27), residues: 396 sheet: 0.67 (0.82), residues: 44 loop : -1.26 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.007 0.001 HIS B 519 PHE 0.019 0.002 PHE A 369 TYR 0.015 0.002 TYR B 365 ARG 0.005 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.6828 (t0) cc_final: 0.6623 (t0) REVERT: A 80 MET cc_start: 0.7973 (ttm) cc_final: 0.7755 (ttm) REVERT: A 552 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8208 (mp-120) outliers start: 20 outliers final: 17 residues processed: 81 average time/residue: 0.1801 time to fit residues: 20.0212 Evaluate side-chains 81 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 576 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6748 Z= 0.182 Angle : 0.520 9.362 9156 Z= 0.264 Chirality : 0.041 0.154 979 Planarity : 0.005 0.067 1166 Dihedral : 8.681 87.208 1060 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.87 % Allowed : 15.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.33 (0.30), residues: 785 helix: 1.40 (0.27), residues: 385 sheet: 0.55 (0.81), residues: 44 loop : -1.18 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 566 HIS 0.003 0.001 HIS B 519 PHE 0.012 0.001 PHE A 315 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.774 Fit side-chains REVERT: B 370 ASN cc_start: 0.6923 (t0) cc_final: 0.6683 (t0) REVERT: A 80 MET cc_start: 0.7961 (ttm) cc_final: 0.7747 (ttm) REVERT: A 151 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8512 (mp) REVERT: A 332 MET cc_start: 0.8423 (ttm) cc_final: 0.8222 (ttt) REVERT: A 408 MET cc_start: 0.8931 (mmt) cc_final: 0.8718 (mmt) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 0.1836 time to fit residues: 19.5556 Evaluate side-chains 71 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6748 Z= 0.222 Angle : 0.542 9.685 9156 Z= 0.276 Chirality : 0.042 0.155 979 Planarity : 0.005 0.061 1166 Dihedral : 8.310 81.380 1060 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.44 % Allowed : 15.52 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.33 (0.30), residues: 785 helix: 1.37 (0.27), residues: 384 sheet: 0.54 (0.82), residues: 44 loop : -1.12 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 168 HIS 0.004 0.001 HIS B 519 PHE 0.013 0.001 PHE A 369 TYR 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.6981 (t0) cc_final: 0.6733 (t0) REVERT: A 151 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 332 MET cc_start: 0.8437 (ttm) cc_final: 0.8228 (ttt) REVERT: A 365 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 408 MET cc_start: 0.8938 (mmt) cc_final: 0.8667 (mmt) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.1697 time to fit residues: 18.9248 Evaluate side-chains 77 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 601 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6748 Z= 0.181 Angle : 0.530 9.741 9156 Z= 0.271 Chirality : 0.041 0.149 979 Planarity : 0.004 0.059 1166 Dihedral : 7.759 75.618 1060 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.59 % Allowed : 15.66 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.39 (0.30), residues: 785 helix: 1.40 (0.27), residues: 384 sheet: 0.51 (0.81), residues: 44 loop : -1.07 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 566 HIS 0.003 0.001 HIS B 519 PHE 0.011 0.001 PHE A 315 TYR 0.024 0.001 TYR A 183 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.6927 (t0) cc_final: 0.6695 (t0) REVERT: B 375 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6173 (t80) REVERT: A 151 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8507 (mp) REVERT: A 365 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 408 MET cc_start: 0.8948 (mmt) cc_final: 0.8682 (mmt) outliers start: 18 outliers final: 12 residues processed: 85 average time/residue: 0.1646 time to fit residues: 19.7779 Evaluate side-chains 80 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6748 Z= 0.278 Angle : 0.566 9.641 9156 Z= 0.290 Chirality : 0.042 0.159 979 Planarity : 0.005 0.064 1166 Dihedral : 7.314 67.315 1058 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.01 % Allowed : 16.09 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.30), residues: 785 helix: 1.34 (0.27), residues: 383 sheet: 0.55 (0.83), residues: 44 loop : -1.10 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 PHE 0.014 0.001 PHE A 369 TYR 0.016 0.001 TYR A 183 ARG 0.004 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.6942 (t0) cc_final: 0.6707 (t0) REVERT: A 151 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8514 (mp) REVERT: A 365 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8175 (p) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 0.1776 time to fit residues: 19.4339 Evaluate side-chains 79 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.0030 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6748 Z= 0.164 Angle : 0.519 9.260 9156 Z= 0.264 Chirality : 0.040 0.147 979 Planarity : 0.004 0.056 1166 Dihedral : 6.773 58.949 1056 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.87 % Allowed : 16.09 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.42 (0.30), residues: 785 helix: 1.43 (0.27), residues: 383 sheet: 0.53 (0.80), residues: 44 loop : -1.05 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 566 HIS 0.003 0.001 HIS B 519 PHE 0.010 0.001 PHE A 315 TYR 0.018 0.001 TYR A 183 ARG 0.001 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 370 ASN cc_start: 0.6926 (t0) cc_final: 0.6702 (t0) REVERT: A 151 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8491 (mp) REVERT: A 365 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 408 MET cc_start: 0.8947 (mmt) cc_final: 0.8714 (mmt) outliers start: 13 outliers final: 11 residues processed: 78 average time/residue: 0.1746 time to fit residues: 19.0671 Evaluate side-chains 79 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 66 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ASP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088803 restraints weight = 11949.181| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.82 r_work: 0.3085 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6748 Z= 0.267 Angle : 0.558 8.306 9156 Z= 0.286 Chirality : 0.042 0.158 979 Planarity : 0.005 0.066 1166 Dihedral : 6.600 51.078 1056 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.38 (0.30), residues: 785 helix: 1.47 (0.27), residues: 377 sheet: 0.67 (0.81), residues: 44 loop : -1.14 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.005 0.001 HIS B 519 PHE 0.014 0.001 PHE A 369 TYR 0.016 0.001 TYR A 183 ARG 0.001 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.43 seconds wall clock time: 32 minutes 24.13 seconds (1944.13 seconds total)