Starting phenix.real_space_refine on Fri Dec 27 20:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dv2_27731/12_2024/8dv2_27731.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dv2_27731/12_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/cci-nas-00/data/ceres_data/8dv2_27731/12_2024/8dv2_27731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dv2_27731/12_2024/8dv2_27731.map" model { file = "/net/cci-nas-00/data/ceres_data/8dv2_27731/12_2024/8dv2_27731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dv2_27731/12_2024/8dv2_27731.cif" } 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. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.97, per 1000 atoms: 0.91 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 1.66 Conformation dependent library (CDL) restraints added in 938.0 milliseconds 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: 0.64 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: 1.89 Time building geometry restraints manager: 1.93 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: 0.00 - 2.33: 7882 2.33 - 4.67: 1070 4.67 - 7.00: 171 7.00 - 9.33: 15 9.33 - 11.67: 5 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 3.040 nonbonded pdb=" O4 NAG D1101 " pdb=" O6 NAG D1101 " model vdw 2.241 3.040 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 3.040 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 Time spend for trying shortcut: 0.00 ========== 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: 18.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.260 Find NCS groups from input model: 0.060 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.490 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.757 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: 0.2400 time to fit residues: 62.9376 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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: 0.0170 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 493 GLN A 498 GLN A 506 GLN D 154 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6727 Z= 0.207 Angle : 0.702 13.940 9143 Z= 0.360 Chirality : 0.056 0.767 977 Planarity : 0.005 0.055 1177 Dihedral : 8.090 88.017 1013 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.89 % Favored : 97.98 % Rotamer: Outliers : 2.00 % Allowed : 9.01 % Favored : 88.98 % 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: 0.96 (0.30), residues: 792 helix: 1.11 (0.26), residues: 390 sheet: 0.06 (0.72), residues: 61 loop : 0.36 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 PHE 0.017 0.001 PHE D 369 TYR 0.017 0.001 TYR D 385 ARG 0.003 0.000 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 163 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 ASP cc_start: 0.8466 (t0) cc_final: 0.8260 (t0) REVERT: D 441 LYS cc_start: 0.8855 (tttt) cc_final: 0.8589 (tptp) REVERT: D 483 GLU cc_start: 0.8322 (tp30) cc_final: 0.8042 (tp30) outliers start: 14 outliers final: 8 residues processed: 158 average time/residue: 0.1984 time to fit residues: 41.2117 Evaluate side-chains 108 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 HIS 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: 0.4980 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 71 optimal weight: 0.0970 chunk 77 optimal weight: 0.1980 chunk 64 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6727 Z= 0.185 Angle : 0.650 9.750 9143 Z= 0.331 Chirality : 0.052 0.586 977 Planarity : 0.004 0.051 1177 Dihedral : 7.728 88.016 1013 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 1.77 % Favored : 97.98 % Rotamer: Outliers : 2.29 % Allowed : 11.73 % Favored : 85.98 % 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: 1.13 (0.30), residues: 792 helix: 1.31 (0.26), residues: 393 sheet: 0.00 (0.70), residues: 60 loop : 0.38 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 478 HIS 0.004 0.001 HIS D 535 PHE 0.024 0.002 PHE D 327 TYR 0.020 0.001 TYR A 380 ARG 0.004 0.000 ARG A 466 *********************** 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 133 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 206 ASP cc_start: 0.8458 (t0) cc_final: 0.7989 (t0) REVERT: D 285 PHE cc_start: 0.6444 (m-80) cc_final: 0.6129 (m-80) REVERT: D 287 GLN cc_start: 0.6038 (pm20) cc_final: 0.5561 (mm-40) REVERT: D 406 GLU cc_start: 0.8074 (tp30) cc_final: 0.7690 (tp30) REVERT: D 441 LYS cc_start: 0.8875 (tttt) cc_final: 0.8607 (tptp) REVERT: D 483 GLU cc_start: 0.8294 (tp30) cc_final: 0.8046 (tp30) outliers start: 16 outliers final: 12 residues processed: 128 average time/residue: 0.1912 time to fit residues: 32.6623 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 73 LEU 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 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: 0.0870 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 ASN D 210 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 401 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6727 Z= 0.193 Angle : 0.620 10.821 9143 Z= 0.314 Chirality : 0.050 0.477 977 Planarity : 0.004 0.050 1177 Dihedral : 6.865 68.321 1013 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.02 % Favored : 97.85 % Rotamer: Outliers : 3.00 % Allowed : 13.59 % Favored : 83.40 % 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: 1.14 (0.30), residues: 792 helix: 1.33 (0.26), residues: 401 sheet: -0.05 (0.69), residues: 62 loop : 0.35 (0.36), residues: 329 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 0.025 0.001 PHE D 327 TYR 0.021 0.001 TYR D 497 ARG 0.003 0.000 ARG D 115 *********************** 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 136 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 270 MET cc_start: 0.7731 (tpp) cc_final: 0.7517 (tpp) REVERT: D 285 PHE cc_start: 0.6382 (m-80) cc_final: 0.6089 (m-80) REVERT: D 360 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7448 (ttt) REVERT: D 375 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8272 (mm-30) REVERT: D 406 GLU cc_start: 0.7998 (tp30) cc_final: 0.7575 (tp30) REVERT: D 441 LYS cc_start: 0.8888 (tttt) cc_final: 0.8649 (tptp) REVERT: D 488 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8226 (m) REVERT: D 601 ASN cc_start: 0.8087 (t0) cc_final: 0.7876 (t0) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.2093 time to fit residues: 35.6438 Evaluate side-chains 115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 439 LEU 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: 0.7980 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.0670 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8087 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6727 Z= 0.187 Angle : 0.610 9.002 9143 Z= 0.311 Chirality : 0.050 0.432 977 Planarity : 0.004 0.049 1177 Dihedral : 5.953 51.993 1013 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.53 % Favored : 97.35 % Rotamer: Outliers : 3.29 % Allowed : 13.88 % Favored : 82.83 % 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: 1.31 (0.30), residues: 792 helix: 1.51 (0.26), residues: 397 sheet: 0.31 (0.76), residues: 50 loop : 0.33 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 478 HIS 0.003 0.001 HIS D 535 PHE 0.026 0.001 PHE D 327 TYR 0.026 0.001 TYR D 497 ARG 0.003 0.000 ARG A 454 *********************** 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 133 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 PHE cc_start: 0.7529 (t80) cc_final: 0.7305 (t80) REVERT: D 323 MET cc_start: 0.9239 (tpp) cc_final: 0.8891 (mmm) REVERT: D 360 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7492 (ttt) REVERT: D 375 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8212 (mm-30) REVERT: D 406 GLU cc_start: 0.7984 (tp30) cc_final: 0.7620 (tp30) REVERT: D 441 LYS cc_start: 0.8871 (tttt) cc_final: 0.8631 (tptp) REVERT: D 488 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8397 (m) outliers start: 23 outliers final: 15 residues processed: 122 average time/residue: 0.2024 time to fit residues: 33.4413 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 385 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 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 439 LEU 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: 2.9990 chunk 76 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6727 Z= 0.222 Angle : 0.612 6.375 9143 Z= 0.315 Chirality : 0.051 0.422 977 Planarity : 0.004 0.045 1177 Dihedral : 5.662 52.635 1013 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 3.43 % Allowed : 14.16 % Favored : 82.40 % 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: 1.37 (0.30), residues: 792 helix: 1.56 (0.26), residues: 398 sheet: 0.26 (0.77), residues: 50 loop : 0.37 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 478 HIS 0.003 0.001 HIS A 519 PHE 0.023 0.001 PHE D 327 TYR 0.022 0.002 TYR D 497 ARG 0.002 0.000 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 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ILE cc_start: 0.9208 (mm) cc_final: 0.8973 (mm) REVERT: D 270 MET cc_start: 0.8118 (tpp) cc_final: 0.7914 (tpp) REVERT: D 323 MET cc_start: 0.9228 (tpp) cc_final: 0.8896 (mmm) REVERT: D 360 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7180 (tmm) REVERT: D 375 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 406 GLU cc_start: 0.7998 (tp30) cc_final: 0.7659 (tp30) REVERT: D 441 LYS cc_start: 0.8885 (tttt) cc_final: 0.8658 (tptp) REVERT: D 488 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8555 (m) outliers start: 24 outliers final: 19 residues processed: 116 average time/residue: 0.1864 time to fit residues: 29.2136 Evaluate side-chains 116 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 488 CYS 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 142 LEU 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 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 366 MET 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: 0.4980 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 0.0020 chunk 46 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8126 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6727 Z= 0.200 Angle : 0.610 12.600 9143 Z= 0.310 Chirality : 0.049 0.404 977 Planarity : 0.004 0.045 1177 Dihedral : 5.550 52.618 1013 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.22 % Rotamer: Outliers : 3.58 % Allowed : 15.59 % Favored : 80.83 % 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: 1.48 (0.30), residues: 792 helix: 1.67 (0.26), residues: 395 sheet: 0.30 (0.77), residues: 50 loop : 0.41 (0.35), residues: 347 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 0.023 0.001 PHE D 327 TYR 0.016 0.001 TYR D 497 ARG 0.003 0.000 ARG D 115 *********************** 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 132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 270 MET cc_start: 0.8204 (tpp) cc_final: 0.7955 (tpp) REVERT: D 323 MET cc_start: 0.9212 (tpp) cc_final: 0.8928 (mmm) REVERT: D 360 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7111 (tmm) REVERT: D 375 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8301 (mm-30) REVERT: D 441 LYS cc_start: 0.8861 (tttt) cc_final: 0.8565 (tptp) REVERT: D 488 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8671 (m) outliers start: 25 outliers final: 19 residues processed: 122 average time/residue: 0.1898 time to fit residues: 30.8511 Evaluate side-chains 117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 488 CYS 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 120 LEU Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 366 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6727 Z= 0.224 Angle : 0.634 10.021 9143 Z= 0.325 Chirality : 0.049 0.406 977 Planarity : 0.004 0.044 1177 Dihedral : 5.551 52.708 1013 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.22 % Rotamer: Outliers : 3.72 % Allowed : 15.74 % Favored : 80.54 % 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 (0.30), residues: 792 helix: 1.63 (0.26), residues: 398 sheet: 0.35 (0.77), residues: 50 loop : 0.23 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 478 HIS 0.003 0.001 HIS D 493 PHE 0.023 0.001 PHE D 327 TYR 0.016 0.001 TYR D 497 ARG 0.005 0.001 ARG D 482 *********************** 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 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 270 MET cc_start: 0.8219 (tpp) cc_final: 0.7949 (tpp) REVERT: D 323 MET cc_start: 0.9208 (tpp) cc_final: 0.8925 (mmm) REVERT: D 375 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8246 (mm-30) REVERT: D 441 LYS cc_start: 0.8887 (tttt) cc_final: 0.8582 (tptp) outliers start: 26 outliers final: 18 residues processed: 114 average time/residue: 0.2173 time to fit residues: 33.2459 Evaluate side-chains 113 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 CYS 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 123 MET Chi-restraints excluded: chain D residue 142 LEU 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 487 VAL 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: 0.8980 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8142 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6727 Z= 0.226 Angle : 0.687 9.512 9143 Z= 0.346 Chirality : 0.051 0.500 977 Planarity : 0.004 0.043 1177 Dihedral : 5.755 50.389 1013 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.78 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 17.17 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.30), residues: 792 helix: 1.63 (0.26), residues: 395 sheet: 0.36 (0.78), residues: 50 loop : 0.25 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 478 HIS 0.003 0.001 HIS A 519 PHE 0.022 0.001 PHE D 327 TYR 0.016 0.001 TYR D 497 ARG 0.003 0.000 ARG D 115 *********************** 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 123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 323 MET cc_start: 0.9205 (tpp) cc_final: 0.8939 (mmm) REVERT: D 332 MET cc_start: 0.8214 (mmm) cc_final: 0.7967 (tpp) REVERT: D 375 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8283 (mm-30) REVERT: D 441 LYS cc_start: 0.8874 (tttt) cc_final: 0.8580 (tptp) outliers start: 19 outliers final: 16 residues processed: 115 average time/residue: 0.2119 time to fit residues: 32.6187 Evaluate side-chains 115 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 LEU 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 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: 0.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8141 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6727 Z= 0.216 Angle : 0.654 8.851 9143 Z= 0.336 Chirality : 0.048 0.395 977 Planarity : 0.004 0.042 1177 Dihedral : 5.612 44.463 1013 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 2.58 % Allowed : 17.17 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.30), residues: 792 helix: 1.63 (0.26), residues: 397 sheet: 0.54 (0.80), residues: 50 loop : 0.10 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 473 HIS 0.002 0.001 HIS A 519 PHE 0.028 0.001 PHE D 327 TYR 0.017 0.001 TYR D 497 ARG 0.006 0.001 ARG D 482 ********************** 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 124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6744 (p90) REVERT: D 323 MET cc_start: 0.9262 (tpp) cc_final: 0.8806 (mmm) REVERT: D 332 MET cc_start: 0.8218 (mmm) cc_final: 0.8006 (tpp) REVERT: D 375 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8178 (mm-30) REVERT: D 406 GLU cc_start: 0.7981 (tp30) cc_final: 0.7656 (tp30) REVERT: D 441 LYS cc_start: 0.8877 (tttt) cc_final: 0.8577 (tptp) REVERT: D 470 LYS cc_start: 0.8473 (tptt) cc_final: 0.7821 (tptt) REVERT: D 479 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8165 (tm-30) outliers start: 18 outliers final: 17 residues processed: 117 average time/residue: 0.2098 time to fit residues: 32.3973 Evaluate side-chains 111 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 488 CYS 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 123 MET Chi-restraints excluded: chain D residue 142 LEU 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 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: 0.9980 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 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 493 GLN ** D 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082449 restraints weight = 18710.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084779 restraints weight = 9204.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.086313 restraints weight = 5604.723| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6727 Z= 0.231 Angle : 0.680 8.823 9143 Z= 0.347 Chirality : 0.049 0.396 977 Planarity : 0.005 0.042 1177 Dihedral : 5.422 40.720 1013 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 2.72 % Allowed : 17.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.30), residues: 792 helix: 1.57 (0.26), residues: 397 sheet: 0.54 (0.80), residues: 50 loop : 0.07 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 478 HIS 0.004 0.001 HIS D 493 PHE 0.031 0.002 PHE A 486 TYR 0.017 0.002 TYR D 497 ARG 0.005 0.001 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.46 seconds wall clock time: 39 minutes 54.58 seconds (2394.58 seconds total)