Starting phenix.real_space_refine on Mon Mar 11 01:40:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv2_27731/03_2024/8dv2_27731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv2_27731/03_2024/8dv2_27731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv2_27731/03_2024/8dv2_27731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv2_27731/03_2024/8dv2_27731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv2_27731/03_2024/8dv2_27731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dv2_27731/03_2024/8dv2_27731.pdb" } resolution = 3.5 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= 0.029 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 37 5.16 5 C 4186 2.51 5 N 1075 2.21 5 O 1247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6545 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" 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: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.06, per 1000 atoms: 0.62 Number of scatterers: 6545 At special positions: 0 Unit cell: (76.608, 88.704, 122.976, 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 37 16.00 O 1247 8.00 N 1075 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.06 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D1101 " - " ASN D 322 " " NAG D1102 " - " ASN D 103 " " NAG D1103 " - " ASN D 432 " " NAG D1104 " - " ASN D 546 " " NAG D1105 " - " ASN D 90 " " NAG D1106 " - " ASN D 53 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 57.2% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.623A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.367A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.645A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.268A pdb=" N ASP D 38 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.605A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 194 Proline residue: D 178 - end of helix removed outlier: 3.790A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 249 removed outlier: 4.248A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 414 removed outlier: 3.685A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.107A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix removed outlier: 3.617A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.709A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.082A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 350 322 hydrogen bonds defined for protein. 909 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: 1.77 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1305 1.32 - 1.45: 2125 1.45 - 1.58: 3229 1.58 - 1.71: 10 1.71 - 1.84: 58 Bond restraints: 6727 Sorted by residual: bond pdb=" CB HIS D 265 " pdb=" CG HIS D 265 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.68e+01 bond pdb=" CB HIS D 535 " pdb=" CG HIS D 535 " ideal model delta sigma weight residual 1.497 1.425 0.072 1.40e-02 5.10e+03 2.64e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.50e+01 bond pdb=" CZ ARG D 460 " pdb=" NH2 ARG D 460 " ideal model delta sigma weight residual 1.330 1.274 0.056 1.30e-02 5.92e+03 1.83e+01 bond pdb=" CZ ARG D 161 " pdb=" NH2 ARG D 161 " ideal model delta sigma weight residual 1.330 1.278 0.052 1.30e-02 5.92e+03 1.60e+01 ... (remaining 6722 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.35: 118 104.35 - 111.89: 2827 111.89 - 119.43: 2740 119.43 - 126.97: 3365 126.97 - 134.51: 93 Bond angle restraints: 9143 Sorted by residual: angle pdb=" N SER D 170 " pdb=" CA SER D 170 " pdb=" C SER D 170 " ideal model delta sigma weight residual 110.35 98.98 11.37 1.38e+00 5.25e-01 6.79e+01 angle pdb=" C GLU D 489 " pdb=" N PRO D 490 " pdb=" CA PRO D 490 " ideal model delta sigma weight residual 119.87 128.34 -8.47 1.04e+00 9.25e-01 6.63e+01 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CA PRO A 527 " ideal model delta sigma weight residual 119.85 127.88 -8.03 1.01e+00 9.80e-01 6.33e+01 angle pdb=" CB ASN D 90 " pdb=" CG ASN D 90 " pdb=" ND2 ASN D 90 " ideal model delta sigma weight residual 116.40 128.07 -11.67 1.50e+00 4.44e-01 6.05e+01 angle pdb=" N TYR A 380 " pdb=" CA TYR A 380 " pdb=" C TYR A 380 " ideal model delta sigma weight residual 114.31 104.49 9.82 1.29e+00 6.01e-01 5.80e+01 ... (remaining 9138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3878 17.29 - 34.58: 140 34.58 - 51.88: 25 51.88 - 69.17: 15 69.17 - 86.46: 5 Dihedral angle restraints: 4063 sinusoidal: 1728 harmonic: 2335 Sorted by residual: dihedral pdb=" C TYR A 421 " pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual -122.60 -134.06 11.46 0 2.50e+00 1.60e-01 2.10e+01 dihedral pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual 122.80 133.46 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" CA PRO D 389 " pdb=" C PRO D 389 " pdb=" N PHE D 390 " pdb=" CA PHE D 390 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 739 0.114 - 0.229: 209 0.229 - 0.343: 21 0.343 - 0.457: 7 0.457 - 0.572: 1 Chirality restraints: 977 Sorted by residual: chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.17e+00 chirality pdb=" C1 NAG D1102 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D1102 " pdb=" O5 NAG D1102 " both_signs ideal model delta sigma weight residual False -2.40 -2.84 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" C1 NAG D1104 " pdb=" ND2 ASN D 546 " pdb=" C2 NAG D1104 " pdb=" O5 NAG D1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 974 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 53 " 0.015 2.00e-02 2.50e+03 7.67e-02 7.35e+01 pdb=" CG ASN D 53 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN D 53 " -0.076 2.00e-02 2.50e+03 pdb=" ND2 ASN D 53 " 0.125 2.00e-02 2.50e+03 pdb=" C1 NAG D1106 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " -0.013 2.00e-02 2.50e+03 4.66e-02 2.71e+01 pdb=" CG ASN D 103 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG D1102 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 432 " -0.008 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN D 432 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN D 432 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN D 432 " -0.069 2.00e-02 2.50e+03 pdb=" C1 NAG D1103 " 0.048 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1264 2.76 - 3.29: 6404 3.29 - 3.83: 11299 3.83 - 4.36: 14413 4.36 - 4.90: 22737 Nonbonded interactions: 56117 Sorted by model distance: nonbonded pdb=" O4 NAG D1102 " pdb=" O6 NAG D1102 " model vdw 2.222 2.440 nonbonded pdb=" O4 NAG D1101 " pdb=" O6 NAG D1101 " model vdw 2.241 2.440 nonbonded pdb=" N SER D 170 " pdb=" O SER D 170 " model vdw 2.348 2.496 nonbonded pdb=" O4 NAG D1104 " pdb=" O6 NAG D1104 " model vdw 2.372 2.440 nonbonded pdb=" N TYR A 380 " pdb=" N GLY A 381 " model vdw 2.385 2.560 ... (remaining 56112 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 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: 13.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 19.510 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.018 0.125 6727 Z= 1.143 Angle : 1.678 11.668 9143 Z= 1.145 Chirality : 0.104 0.572 977 Planarity : 0.009 0.067 1177 Dihedral : 10.740 86.458 2544 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.89 % Favored : 97.98 % Rotamer: Outliers : 0.14 % Allowed : 1.00 % Favored : 98.86 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.28), residues: 792 helix: -0.42 (0.23), residues: 391 sheet: 0.78 (0.73), residues: 61 loop : 0.38 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP D 349 HIS 0.014 0.003 HIS D 535 PHE 0.028 0.006 PHE D 390 TYR 0.059 0.008 TYR D 199 ARG 0.010 0.001 ARG D 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 ASN cc_start: 0.7073 (t0) cc_final: 0.6510 (m110) REVERT: A 418 ILE cc_start: 0.9251 (mm) cc_final: 0.8602 (mm) REVERT: D 119 ILE cc_start: 0.8518 (mt) cc_final: 0.8257 (mt) REVERT: D 155 SER cc_start: 0.8440 (t) cc_final: 0.8027 (p) REVERT: D 291 ILE cc_start: 0.8495 (pt) cc_final: 0.7995 (mp) REVERT: D 362 THR cc_start: 0.7357 (m) cc_final: 0.6892 (m) REVERT: D 441 LYS cc_start: 0.8693 (tttt) cc_final: 0.8471 (tptp) REVERT: D 474 MET cc_start: 0.8360 (mmp) cc_final: 0.8030 (mmm) REVERT: D 480 MET cc_start: 0.8661 (mtp) cc_final: 0.8432 (mtt) outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.2287 time to fit residues: 59.8359 Evaluate side-chains 117 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 414 GLN A 493 GLN A 498 GLN D 60 GLN D 154 ASN D 401 HIS D 508 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6727 Z= 0.242 Angle : 0.703 12.844 9143 Z= 0.363 Chirality : 0.057 0.757 977 Planarity : 0.005 0.053 1177 Dihedral : 8.300 89.768 1013 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.02 % Favored : 97.73 % Rotamer: Outliers : 2.29 % Allowed : 9.44 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.29), residues: 792 helix: 1.11 (0.26), residues: 389 sheet: 0.05 (0.71), residues: 61 loop : 0.37 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 478 HIS 0.004 0.001 HIS D 535 PHE 0.018 0.002 PHE D 369 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.758 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: D 206 ASP cc_start: 0.8524 (t0) cc_final: 0.8283 (t0) REVERT: D 270 MET cc_start: 0.7799 (tpp) cc_final: 0.7446 (tpp) REVERT: D 441 LYS cc_start: 0.8893 (tttt) cc_final: 0.8622 (tptp) REVERT: D 483 GLU cc_start: 0.8359 (tp30) cc_final: 0.8109 (tp30) outliers start: 16 outliers final: 9 residues processed: 154 average time/residue: 0.2196 time to fit residues: 44.5741 Evaluate side-chains 112 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.0370 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 0.0980 chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN A 506 GLN D 154 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6727 Z= 0.191 Angle : 0.632 10.042 9143 Z= 0.321 Chirality : 0.051 0.562 977 Planarity : 0.004 0.048 1177 Dihedral : 7.542 80.999 1013 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.53 % Favored : 97.22 % Rotamer: Outliers : 2.43 % Allowed : 11.87 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.30), residues: 792 helix: 1.37 (0.26), residues: 393 sheet: 0.02 (0.69), residues: 60 loop : 0.40 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 478 HIS 0.003 0.001 HIS D 535 PHE 0.022 0.001 PHE D 31 TYR 0.020 0.001 TYR A 380 ARG 0.002 0.000 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 ASP cc_start: 0.8509 (t0) cc_final: 0.7999 (t0) REVERT: D 406 GLU cc_start: 0.8077 (tp30) cc_final: 0.7701 (tp30) REVERT: D 441 LYS cc_start: 0.8899 (tttt) cc_final: 0.8628 (tptp) REVERT: D 470 LYS cc_start: 0.7655 (mmmm) cc_final: 0.7292 (mmmm) REVERT: D 601 ASN cc_start: 0.8072 (t0) cc_final: 0.7836 (t0) outliers start: 17 outliers final: 12 residues processed: 127 average time/residue: 0.1778 time to fit residues: 30.6379 Evaluate side-chains 115 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN D 60 GLN D 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6727 Z= 0.213 Angle : 0.615 10.252 9143 Z= 0.311 Chirality : 0.050 0.488 977 Planarity : 0.004 0.045 1177 Dihedral : 6.730 53.546 1013 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.47 % Rotamer: Outliers : 3.29 % Allowed : 12.73 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.30), residues: 792 helix: 1.47 (0.26), residues: 401 sheet: -0.23 (0.70), residues: 60 loop : 0.37 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.003 0.001 HIS D 535 PHE 0.022 0.001 PHE D 31 TYR 0.018 0.001 TYR A 380 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 360 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.6992 (tmm) REVERT: D 375 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8297 (mm-30) REVERT: D 406 GLU cc_start: 0.8019 (tp30) cc_final: 0.7557 (tp30) REVERT: D 410 LEU cc_start: 0.8733 (mt) cc_final: 0.8424 (mt) REVERT: D 441 LYS cc_start: 0.8911 (tttt) cc_final: 0.8642 (tptp) REVERT: D 488 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8205 (m) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.1783 time to fit residues: 29.9162 Evaluate side-chains 119 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 68 optimal weight: 0.0470 chunk 19 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6727 Z= 0.173 Angle : 0.573 6.360 9143 Z= 0.292 Chirality : 0.048 0.448 977 Planarity : 0.004 0.048 1177 Dihedral : 6.424 57.328 1013 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 3.43 % Allowed : 14.31 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.30), residues: 792 helix: 1.63 (0.26), residues: 397 sheet: 0.03 (0.78), residues: 50 loop : 0.36 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.003 0.001 HIS D 540 PHE 0.021 0.001 PHE D 31 TYR 0.022 0.001 TYR D 497 ARG 0.002 0.000 ARG D 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6384 (p90) REVERT: D 123 MET cc_start: 0.7713 (mpp) cc_final: 0.7381 (mpp) REVERT: D 237 TYR cc_start: 0.8593 (t80) cc_final: 0.8385 (t80) REVERT: D 360 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6753 (tmm) REVERT: D 375 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 441 LYS cc_start: 0.8856 (tttt) cc_final: 0.8621 (tptp) REVERT: D 488 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8348 (m) outliers start: 24 outliers final: 16 residues processed: 124 average time/residue: 0.1963 time to fit residues: 32.0833 Evaluate side-chains 123 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN D 417 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6727 Z= 0.244 Angle : 0.638 13.681 9143 Z= 0.321 Chirality : 0.050 0.456 977 Planarity : 0.004 0.044 1177 Dihedral : 6.386 58.785 1013 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.16 % Favored : 96.72 % Rotamer: Outliers : 3.29 % Allowed : 14.88 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.31), residues: 792 helix: 1.59 (0.26), residues: 398 sheet: -0.51 (0.71), residues: 60 loop : 0.31 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 478 HIS 0.003 0.001 HIS A 519 PHE 0.030 0.002 PHE D 327 TYR 0.023 0.002 TYR D 497 ARG 0.004 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 TYR cc_start: 0.8562 (p90) cc_final: 0.8215 (p90) REVERT: A 518 LEU cc_start: 0.8146 (mt) cc_final: 0.7946 (mp) REVERT: D 237 TYR cc_start: 0.8703 (t80) cc_final: 0.8499 (t80) REVERT: D 360 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7217 (tmm) REVERT: D 375 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8335 (mm-30) REVERT: D 406 GLU cc_start: 0.8030 (tp30) cc_final: 0.7651 (tp30) REVERT: D 441 LYS cc_start: 0.8904 (tttt) cc_final: 0.8670 (tptp) REVERT: D 488 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8566 (m) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.1803 time to fit residues: 30.1517 Evaluate side-chains 128 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.0980 chunk 64 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6727 Z= 0.172 Angle : 0.604 14.107 9143 Z= 0.297 Chirality : 0.047 0.424 977 Planarity : 0.004 0.044 1177 Dihedral : 6.026 57.906 1013 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 3.15 % Allowed : 15.88 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.30), residues: 792 helix: 1.73 (0.26), residues: 398 sheet: 0.18 (0.79), residues: 49 loop : 0.32 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.002 0.001 HIS D 535 PHE 0.027 0.001 PHE D 327 TYR 0.016 0.001 TYR D 497 ARG 0.002 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 441 LYS cc_start: 0.8852 (tttt) cc_final: 0.8547 (tptp) outliers start: 22 outliers final: 17 residues processed: 126 average time/residue: 0.1717 time to fit residues: 29.4429 Evaluate side-chains 124 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.0010 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6727 Z= 0.185 Angle : 0.617 11.990 9143 Z= 0.306 Chirality : 0.048 0.420 977 Planarity : 0.004 0.044 1177 Dihedral : 5.927 55.866 1013 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.86 % Allowed : 16.74 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.31), residues: 792 helix: 1.82 (0.26), residues: 398 sheet: -0.49 (0.70), residues: 60 loop : 0.39 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.003 0.001 HIS A 519 PHE 0.028 0.001 PHE D 327 TYR 0.018 0.001 TYR A 365 ARG 0.002 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 518 LEU cc_start: 0.8287 (mt) cc_final: 0.7735 (mt) REVERT: D 152 MET cc_start: 0.6839 (mmm) cc_final: 0.6638 (mmm) REVERT: D 332 MET cc_start: 0.8211 (mmm) cc_final: 0.8006 (tpp) REVERT: D 375 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8274 (mm-30) REVERT: D 441 LYS cc_start: 0.8859 (tttt) cc_final: 0.8556 (tptp) outliers start: 20 outliers final: 16 residues processed: 122 average time/residue: 0.1873 time to fit residues: 30.8774 Evaluate side-chains 123 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6727 Z= 0.202 Angle : 0.605 10.315 9143 Z= 0.305 Chirality : 0.049 0.425 977 Planarity : 0.004 0.045 1177 Dihedral : 5.971 53.319 1013 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.22 % Rotamer: Outliers : 2.72 % Allowed : 16.60 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 792 helix: 1.85 (0.27), residues: 398 sheet: -0.42 (0.70), residues: 59 loop : 0.29 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.004 0.001 HIS D 493 PHE 0.029 0.002 PHE D 327 TYR 0.019 0.002 TYR D 237 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 152 MET cc_start: 0.6817 (mmm) cc_final: 0.6545 (mmm) REVERT: D 375 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8286 (mm-30) REVERT: D 406 GLU cc_start: 0.7981 (tp30) cc_final: 0.7647 (tp30) REVERT: D 441 LYS cc_start: 0.8868 (tttt) cc_final: 0.8572 (tptp) REVERT: D 493 HIS cc_start: 0.5642 (m-70) cc_final: 0.5103 (m90) REVERT: D 497 TYR cc_start: 0.6642 (m-80) cc_final: 0.6145 (m-10) outliers start: 19 outliers final: 18 residues processed: 118 average time/residue: 0.1980 time to fit residues: 31.8124 Evaluate side-chains 120 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 493 GLN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6727 Z= 0.246 Angle : 0.649 8.491 9143 Z= 0.328 Chirality : 0.051 0.440 977 Planarity : 0.005 0.045 1177 Dihedral : 6.127 53.000 1013 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.66 % Favored : 96.21 % Rotamer: Outliers : 3.15 % Allowed : 16.88 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.31), residues: 792 helix: 1.77 (0.26), residues: 398 sheet: -0.37 (0.71), residues: 59 loop : 0.19 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.003 0.001 HIS A 519 PHE 0.030 0.002 PHE D 327 TYR 0.030 0.002 TYR D 237 ARG 0.003 0.000 ARG A 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: D 285 PHE cc_start: 0.6416 (m-80) cc_final: 0.6165 (m-80) REVERT: D 375 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8296 (mm-30) REVERT: D 406 GLU cc_start: 0.8019 (tp30) cc_final: 0.7677 (tp30) REVERT: D 441 LYS cc_start: 0.8887 (tttt) cc_final: 0.8586 (tptp) REVERT: D 493 HIS cc_start: 0.5948 (m-70) cc_final: 0.5281 (m170) REVERT: D 497 TYR cc_start: 0.6790 (m-80) cc_final: 0.6191 (m-10) outliers start: 22 outliers final: 18 residues processed: 116 average time/residue: 0.1760 time to fit residues: 27.7504 Evaluate side-chains 117 residues out of total 699 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 261 CYS Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 478 TRP Chi-restraints excluded: chain D residue 498 CYS Chi-restraints excluded: chain D residue 522 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081849 restraints weight = 18704.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084166 restraints weight = 8919.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085663 restraints weight = 5285.155| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6727 Z= 0.213 Angle : 0.659 8.879 9143 Z= 0.328 Chirality : 0.050 0.433 977 Planarity : 0.004 0.046 1177 Dihedral : 6.060 52.711 1013 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 2.43 % Allowed : 18.88 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 792 helix: 1.75 (0.26), residues: 398 sheet: -0.39 (0.72), residues: 59 loop : 0.14 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 478 HIS 0.003 0.001 HIS D 493 PHE 0.029 0.002 PHE D 327 TYR 0.026 0.002 TYR D 158 ARG 0.003 0.000 ARG A 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1970.91 seconds wall clock time: 37 minutes 1.75 seconds (2221.75 seconds total)