Starting phenix.real_space_refine on Tue Feb 13 06:16:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/02_2024/7lx5_23566.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/02_2024/7lx5_23566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/02_2024/7lx5_23566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/02_2024/7lx5_23566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/02_2024/7lx5_23566.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lx5_23566/02_2024/7lx5_23566.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 19 5.16 5 C 2206 2.51 5 N 591 2.21 5 O 669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3485 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "C" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 951 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Time building chain proxies: 2.52, per 1000 atoms: 0.72 Number of scatterers: 3485 At special positions: 0 Unit cell: (61.92, 80.84, 99.76, 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 19 16.00 O 669 8.00 N 591 7.00 C 2206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 112 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 544.9 milliseconds 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 9 sheets defined 14.1% alpha, 47.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.526A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.313A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.330A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.776A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.577A pdb=" N MET C 117 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.971A pdb=" N ARG A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 28 through 32' Processing helix chain 'A' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.537A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 375 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 110 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 112 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 117 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 7.537A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N SER B 375 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 110 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 112 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 92 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 32 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR C 119 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.521A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N CYS C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 34 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 32 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.584A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 5 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 23 " --> pdb=" O GLN A 5 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 1.35 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1125 1.34 - 1.46: 961 1.46 - 1.58: 1465 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 3575 Sorted by residual: bond pdb=" CB VAL B 350 " pdb=" CG1 VAL B 350 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.76e-01 bond pdb=" CB TRP C 120 " pdb=" CG TRP C 120 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 7.91e-01 bond pdb=" CG LEU B 461 " pdb=" CD2 LEU B 461 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.71e-01 bond pdb=" CB TRP C 36 " pdb=" CG TRP C 36 " ideal model delta sigma weight residual 1.498 1.471 0.027 3.10e-02 1.04e+03 7.65e-01 bond pdb=" CB PRO A 106 " pdb=" CG PRO A 106 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.53e-01 ... (remaining 3570 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.30: 109 107.30 - 113.98: 1883 113.98 - 120.67: 1431 120.67 - 127.35: 1390 127.35 - 134.03: 35 Bond angle restraints: 4848 Sorted by residual: angle pdb=" CA LEU B 461 " pdb=" CB LEU B 461 " pdb=" CG LEU B 461 " ideal model delta sigma weight residual 116.30 125.54 -9.24 3.50e+00 8.16e-02 6.97e+00 angle pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " pdb=" CG ARG A 30 " ideal model delta sigma weight residual 114.10 108.92 5.18 2.00e+00 2.50e-01 6.70e+00 angle pdb=" N GLY B 485 " pdb=" CA GLY B 485 " pdb=" C GLY B 485 " ideal model delta sigma weight residual 113.18 108.49 4.69 2.37e+00 1.78e-01 3.92e+00 angle pdb=" C ARG A 30 " pdb=" N ARG A 31 " pdb=" CA ARG A 31 " ideal model delta sigma weight residual 123.24 120.36 2.88 1.54e+00 4.22e-01 3.49e+00 angle pdb=" N GLY A 15 " pdb=" CA GLY A 15 " pdb=" C GLY A 15 " ideal model delta sigma weight residual 115.36 112.93 2.43 1.33e+00 5.65e-01 3.34e+00 ... (remaining 4843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1968 16.02 - 32.04: 101 32.04 - 48.06: 16 48.06 - 64.07: 2 64.07 - 80.09: 3 Dihedral angle restraints: 2090 sinusoidal: 810 harmonic: 1280 Sorted by residual: dihedral pdb=" CA SER B 366 " pdb=" C SER B 366 " pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA TYR B 489 " pdb=" C TYR B 489 " pdb=" N PHE B 490 " pdb=" CA PHE B 490 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU B 471 " pdb=" CG GLU B 471 " pdb=" CD GLU B 471 " pdb=" OE1 GLU B 471 " ideal model delta sinusoidal sigma weight residual 0.00 80.09 -80.09 1 3.00e+01 1.11e-03 8.83e+00 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 311 0.031 - 0.063: 112 0.063 - 0.094: 48 0.094 - 0.126: 23 0.126 - 0.157: 7 Chirality restraints: 501 Sorted by residual: chirality pdb=" CG LEU B 461 " pdb=" CB LEU B 461 " pdb=" CD1 LEU B 461 " pdb=" CD2 LEU B 461 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA VAL A 40 " pdb=" N VAL A 40 " pdb=" C VAL A 40 " pdb=" CB VAL A 40 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ARG A 30 " pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CB ARG A 30 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 498 not shown) Planarity restraints: 633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 110 " -0.010 2.00e-02 2.50e+03 8.62e-03 1.30e+00 pdb=" CG PHE A 110 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 110 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 110 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 110 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 80 " 0.007 2.00e-02 2.50e+03 6.42e-03 8.25e-01 pdb=" CG TYR C 80 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 80 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 80 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 80 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 80 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 80 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 80 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 467 " -0.004 2.00e-02 2.50e+03 8.40e-03 7.06e-01 pdb=" C ASP B 467 " 0.015 2.00e-02 2.50e+03 pdb=" O ASP B 467 " -0.005 2.00e-02 2.50e+03 pdb=" N ILE B 468 " -0.005 2.00e-02 2.50e+03 ... (remaining 630 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 268 2.74 - 3.28: 3134 3.28 - 3.82: 5333 3.82 - 4.36: 6330 4.36 - 4.90: 11179 Nonbonded interactions: 26244 Sorted by model distance: nonbonded pdb=" OE1 GLN B 498 " pdb=" OG1 THR C 28 " model vdw 2.198 2.440 nonbonded pdb=" OH TYR A 52 " pdb=" O TRP A 105 " model vdw 2.256 2.440 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.258 2.440 nonbonded pdb=" O PHE A 29 " pdb=" NH2 ARG A 71 " model vdw 2.268 2.520 nonbonded pdb=" OE1 GLU B 406 " pdb=" OH TYR B 495 " model vdw 2.292 2.440 ... (remaining 26239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.430 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.005 0.043 3575 Z= 0.315 Angle : 0.616 9.238 4848 Z= 0.336 Chirality : 0.045 0.157 501 Planarity : 0.003 0.021 633 Dihedral : 10.099 80.092 1267 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % 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: -0.46 (0.38), residues: 442 helix: -4.06 (0.60), residues: 27 sheet: 0.79 (0.46), residues: 132 loop : -0.43 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 436 HIS 0.002 0.001 HIS B 519 PHE 0.020 0.002 PHE A 110 TYR 0.016 0.001 TYR C 80 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: B 357 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7165 (tmm-80) REVERT: B 469 SER cc_start: 0.8965 (t) cc_final: 0.8593 (p) REVERT: B 501 ASN cc_start: 0.8483 (m110) cc_final: 0.8133 (m110) REVERT: C 59 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8191 (mtpt) REVERT: C 73 ASP cc_start: 0.8733 (m-30) cc_final: 0.7297 (m-30) REVERT: C 76 LYS cc_start: 0.8240 (mmmt) cc_final: 0.8016 (mtmm) REVERT: C 80 TYR cc_start: 0.7863 (m-80) cc_final: 0.7638 (m-80) REVERT: C 87 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7734 (mmmt) REVERT: A 3 GLN cc_start: 0.8205 (pt0) cc_final: 0.7772 (pm20) REVERT: A 36 TRP cc_start: 0.8333 (m100) cc_final: 0.7580 (m100) REVERT: A 75 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7687 (mtpt) REVERT: A 84 SER cc_start: 0.7257 (m) cc_final: 0.6808 (p) REVERT: A 121 VAL cc_start: 0.8394 (t) cc_final: 0.8149 (t) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2049 time to fit residues: 34.3536 Evaluate side-chains 115 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3575 Z= 0.278 Angle : 0.632 9.048 4848 Z= 0.336 Chirality : 0.045 0.161 501 Planarity : 0.004 0.033 633 Dihedral : 4.527 20.659 500 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.85 % Allowed : 14.56 % Favored : 80.59 % 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: -0.17 (0.38), residues: 442 helix: -4.22 (0.54), residues: 27 sheet: 1.65 (0.45), residues: 127 loop : -0.53 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 113 HIS 0.001 0.000 HIS C 114 PHE 0.009 0.001 PHE B 392 TYR 0.020 0.001 TYR A 58 ARG 0.003 0.001 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8030 (mp0) REVERT: B 357 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7379 (tmm160) REVERT: B 383 SER cc_start: 0.5711 (OUTLIER) cc_final: 0.5466 (p) REVERT: B 465 GLU cc_start: 0.7934 (tt0) cc_final: 0.7657 (tt0) REVERT: B 469 SER cc_start: 0.9078 (t) cc_final: 0.8737 (p) REVERT: B 498 GLN cc_start: 0.8476 (mt0) cc_final: 0.8160 (mt0) REVERT: B 501 ASN cc_start: 0.8693 (m110) cc_final: 0.8279 (m110) REVERT: C 2 VAL cc_start: 0.7574 (OUTLIER) cc_final: 0.7074 (m) REVERT: C 27 PHE cc_start: 0.8951 (m-80) cc_final: 0.8308 (m-10) REVERT: C 32 TYR cc_start: 0.8852 (p90) cc_final: 0.8578 (p90) REVERT: C 59 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7932 (mtpt) REVERT: C 73 ASP cc_start: 0.8674 (m-30) cc_final: 0.7372 (m-30) REVERT: C 76 LYS cc_start: 0.8369 (mmmt) cc_final: 0.8140 (mtmm) REVERT: C 78 THR cc_start: 0.8938 (m) cc_final: 0.8447 (t) REVERT: C 80 TYR cc_start: 0.7851 (m-80) cc_final: 0.7321 (m-80) REVERT: C 81 LEU cc_start: 0.8327 (tt) cc_final: 0.8101 (tt) REVERT: C 87 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7761 (mmmt) REVERT: C 91 THR cc_start: 0.8589 (p) cc_final: 0.8180 (p) REVERT: C 124 THR cc_start: 0.8330 (p) cc_final: 0.8056 (p) REVERT: A 3 GLN cc_start: 0.8167 (pt0) cc_final: 0.7846 (pm20) REVERT: A 49 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8976 (p) REVERT: A 84 SER cc_start: 0.7382 (m) cc_final: 0.6953 (p) REVERT: A 98 ASP cc_start: 0.8357 (t70) cc_final: 0.8109 (t0) REVERT: A 100 MET cc_start: 0.8139 (mmm) cc_final: 0.7047 (mtm) outliers start: 18 outliers final: 8 residues processed: 140 average time/residue: 0.2100 time to fit residues: 33.8481 Evaluate side-chains 137 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 13 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN A 39 GLN A 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3575 Z= 0.212 Angle : 0.582 7.847 4848 Z= 0.307 Chirality : 0.043 0.152 501 Planarity : 0.003 0.022 633 Dihedral : 4.153 16.085 500 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.50 % Allowed : 16.98 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.38), residues: 442 helix: -4.01 (0.65), residues: 28 sheet: 1.76 (0.44), residues: 128 loop : -0.53 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 436 HIS 0.001 0.000 HIS C 114 PHE 0.007 0.001 PHE C 68 TYR 0.017 0.001 TYR A 58 ARG 0.003 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8000 (mp0) REVERT: B 357 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7325 (tmm160) REVERT: B 383 SER cc_start: 0.5592 (OUTLIER) cc_final: 0.5356 (p) REVERT: B 465 GLU cc_start: 0.7966 (tt0) cc_final: 0.7714 (tt0) REVERT: B 469 SER cc_start: 0.9144 (t) cc_final: 0.8844 (p) REVERT: B 474 GLN cc_start: 0.7638 (tt0) cc_final: 0.7260 (tp40) REVERT: B 498 GLN cc_start: 0.8494 (mt0) cc_final: 0.8191 (mt0) REVERT: B 501 ASN cc_start: 0.8723 (m110) cc_final: 0.8277 (m110) REVERT: C 2 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7289 (m) REVERT: C 27 PHE cc_start: 0.8912 (m-80) cc_final: 0.8554 (m-80) REVERT: C 67 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8318 (mtm-85) REVERT: C 68 PHE cc_start: 0.9133 (m-10) cc_final: 0.8873 (m-10) REVERT: C 73 ASP cc_start: 0.8585 (m-30) cc_final: 0.7330 (m-30) REVERT: C 76 LYS cc_start: 0.8367 (mmmt) cc_final: 0.8120 (mtmm) REVERT: C 78 THR cc_start: 0.8955 (m) cc_final: 0.8436 (t) REVERT: C 80 TYR cc_start: 0.7873 (m-80) cc_final: 0.7203 (m-80) REVERT: C 87 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7771 (mmmt) REVERT: C 91 THR cc_start: 0.8660 (p) cc_final: 0.8322 (p) REVERT: C 122 LYS cc_start: 0.9305 (mmmt) cc_final: 0.8784 (mmtt) REVERT: A 3 GLN cc_start: 0.8205 (pt0) cc_final: 0.7817 (pm20) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 0.2069 time to fit residues: 31.3018 Evaluate side-chains 128 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.0060 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3575 Z= 0.180 Angle : 0.570 8.721 4848 Z= 0.296 Chirality : 0.043 0.179 501 Planarity : 0.003 0.025 633 Dihedral : 3.869 14.087 500 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.04 % Allowed : 16.98 % Favored : 78.98 % 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: 0.04 (0.38), residues: 442 helix: -3.47 (1.03), residues: 21 sheet: 1.75 (0.43), residues: 128 loop : -0.53 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS B 519 PHE 0.005 0.001 PHE A 29 TYR 0.013 0.001 TYR C 32 ARG 0.002 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7974 (mp0) REVERT: B 357 ARG cc_start: 0.7732 (ttp80) cc_final: 0.7351 (tmm160) REVERT: B 461 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8034 (tt) REVERT: B 469 SER cc_start: 0.9211 (t) cc_final: 0.8976 (p) REVERT: B 474 GLN cc_start: 0.7671 (tt0) cc_final: 0.7247 (tp40) REVERT: B 498 GLN cc_start: 0.8480 (mt0) cc_final: 0.8201 (mt0) REVERT: B 501 ASN cc_start: 0.8709 (m110) cc_final: 0.8219 (m110) REVERT: C 2 VAL cc_start: 0.7709 (OUTLIER) cc_final: 0.7353 (m) REVERT: C 27 PHE cc_start: 0.8927 (m-80) cc_final: 0.8456 (m-80) REVERT: C 67 ARG cc_start: 0.8637 (mtm-85) cc_final: 0.8370 (mtm-85) REVERT: C 68 PHE cc_start: 0.9137 (m-10) cc_final: 0.8920 (m-10) REVERT: C 73 ASP cc_start: 0.8478 (m-30) cc_final: 0.7665 (m-30) REVERT: C 76 LYS cc_start: 0.8345 (mmmt) cc_final: 0.8097 (mtmm) REVERT: C 87 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7739 (mmmt) REVERT: C 91 THR cc_start: 0.8636 (p) cc_final: 0.8334 (p) REVERT: A 3 GLN cc_start: 0.8243 (pt0) cc_final: 0.7777 (pm20) REVERT: A 5 GLN cc_start: 0.7834 (mp10) cc_final: 0.7388 (mp10) REVERT: A 19 ARG cc_start: 0.8128 (mpp80) cc_final: 0.7829 (mpp80) REVERT: A 100 MET cc_start: 0.8249 (mmm) cc_final: 0.7278 (mtm) outliers start: 15 outliers final: 11 residues processed: 130 average time/residue: 0.2104 time to fit residues: 31.5376 Evaluate side-chains 130 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3575 Z= 0.189 Angle : 0.555 7.554 4848 Z= 0.289 Chirality : 0.043 0.146 501 Planarity : 0.003 0.025 633 Dihedral : 3.768 13.753 500 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.12 % Allowed : 17.79 % Favored : 77.09 % 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: 0.06 (0.39), residues: 442 helix: -3.37 (0.95), residues: 21 sheet: 1.81 (0.44), residues: 127 loop : -0.54 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS C 114 PHE 0.006 0.001 PHE A 29 TYR 0.012 0.001 TYR C 32 ARG 0.004 0.000 ARG A 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7992 (mp0) REVERT: B 357 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7373 (tmm160) REVERT: B 457 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7500 (ttt-90) REVERT: B 461 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7988 (tt) REVERT: B 466 ARG cc_start: 0.7816 (ptm160) cc_final: 0.7611 (ptm160) REVERT: B 469 SER cc_start: 0.9238 (t) cc_final: 0.9013 (p) REVERT: B 474 GLN cc_start: 0.7728 (tt0) cc_final: 0.7295 (tp40) REVERT: B 498 GLN cc_start: 0.8450 (mt0) cc_final: 0.8173 (mt0) REVERT: B 501 ASN cc_start: 0.8693 (m110) cc_final: 0.8203 (m110) REVERT: C 27 PHE cc_start: 0.8957 (m-80) cc_final: 0.8631 (m-80) REVERT: C 67 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8335 (mtm-85) REVERT: C 68 PHE cc_start: 0.9144 (m-10) cc_final: 0.8902 (m-10) REVERT: C 73 ASP cc_start: 0.8380 (m-30) cc_final: 0.7181 (m-30) REVERT: C 76 LYS cc_start: 0.8358 (mmmt) cc_final: 0.8034 (mtmm) REVERT: C 80 TYR cc_start: 0.7616 (m-80) cc_final: 0.7197 (m-80) REVERT: C 87 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7743 (mmmt) REVERT: C 91 THR cc_start: 0.8691 (p) cc_final: 0.8421 (p) REVERT: A 5 GLN cc_start: 0.7892 (mp10) cc_final: 0.7517 (mp10) REVERT: A 19 ARG cc_start: 0.8137 (mpp80) cc_final: 0.7836 (mpp80) outliers start: 19 outliers final: 17 residues processed: 133 average time/residue: 0.2072 time to fit residues: 31.9204 Evaluate side-chains 136 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3575 Z= 0.210 Angle : 0.557 7.684 4848 Z= 0.290 Chirality : 0.043 0.145 501 Planarity : 0.003 0.024 633 Dihedral : 3.796 13.905 500 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.20 % Allowed : 17.25 % Favored : 76.55 % 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: 0.08 (0.38), residues: 442 helix: -3.13 (1.04), residues: 21 sheet: 1.84 (0.44), residues: 126 loop : -0.54 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS C 114 PHE 0.007 0.001 PHE B 486 TYR 0.013 0.001 TYR C 32 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8013 (mp0) REVERT: B 357 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7382 (tmm160) REVERT: B 383 SER cc_start: 0.5688 (OUTLIER) cc_final: 0.5441 (p) REVERT: B 461 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 469 SER cc_start: 0.9268 (t) cc_final: 0.9021 (p) REVERT: B 474 GLN cc_start: 0.7677 (tt0) cc_final: 0.7217 (tp40) REVERT: B 501 ASN cc_start: 0.8704 (m110) cc_final: 0.8226 (m110) REVERT: C 13 GLN cc_start: 0.8380 (mp10) cc_final: 0.7900 (mp10) REVERT: C 27 PHE cc_start: 0.8949 (m-80) cc_final: 0.8665 (m-80) REVERT: C 68 PHE cc_start: 0.9175 (m-10) cc_final: 0.8822 (m-10) REVERT: C 73 ASP cc_start: 0.8356 (m-30) cc_final: 0.7161 (m-30) REVERT: C 76 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8018 (mtmm) REVERT: C 80 TYR cc_start: 0.7612 (m-80) cc_final: 0.7173 (m-80) REVERT: C 87 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7754 (mmmt) REVERT: C 91 THR cc_start: 0.8709 (p) cc_final: 0.8450 (p) REVERT: C 125 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 3 GLN cc_start: 0.8397 (pt0) cc_final: 0.7823 (pm20) REVERT: A 5 GLN cc_start: 0.7875 (mp10) cc_final: 0.7511 (mp10) REVERT: A 19 ARG cc_start: 0.8147 (mpp80) cc_final: 0.7864 (mpp80) REVERT: A 100 MET cc_start: 0.8256 (mmm) cc_final: 0.7239 (mtm) outliers start: 23 outliers final: 19 residues processed: 131 average time/residue: 0.2049 time to fit residues: 31.1111 Evaluate side-chains 136 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3575 Z= 0.162 Angle : 0.560 6.948 4848 Z= 0.289 Chirality : 0.043 0.146 501 Planarity : 0.003 0.025 633 Dihedral : 3.612 13.549 500 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.20 % Allowed : 18.60 % Favored : 75.20 % 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: 0.11 (0.39), residues: 442 helix: -3.03 (1.07), residues: 21 sheet: 1.53 (0.43), residues: 137 loop : -0.43 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.000 0.000 HIS C 114 PHE 0.006 0.001 PHE B 486 TYR 0.011 0.001 TYR C 32 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8012 (mp0) REVERT: B 357 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7383 (tmm160) REVERT: B 466 ARG cc_start: 0.7794 (ptm160) cc_final: 0.7359 (ptm160) REVERT: B 469 SER cc_start: 0.9234 (t) cc_final: 0.8978 (p) REVERT: B 474 GLN cc_start: 0.7734 (tt0) cc_final: 0.7264 (tp40) REVERT: B 501 ASN cc_start: 0.8677 (m110) cc_final: 0.8150 (m110) REVERT: C 2 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7529 (m) REVERT: C 13 GLN cc_start: 0.8379 (mp10) cc_final: 0.7993 (mp10) REVERT: C 27 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: C 67 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8316 (mtm-85) REVERT: C 68 PHE cc_start: 0.9145 (m-10) cc_final: 0.8906 (m-10) REVERT: C 73 ASP cc_start: 0.8283 (m-30) cc_final: 0.7333 (m-30) REVERT: C 76 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8009 (mtmm) REVERT: C 87 LYS cc_start: 0.7999 (mmtp) cc_final: 0.7754 (mmmt) REVERT: C 91 THR cc_start: 0.8694 (p) cc_final: 0.8451 (p) REVERT: A 3 GLN cc_start: 0.8417 (pt0) cc_final: 0.7837 (pm20) REVERT: A 5 GLN cc_start: 0.7872 (mp10) cc_final: 0.7513 (mp10) REVERT: A 19 ARG cc_start: 0.8101 (mpp80) cc_final: 0.7858 (mpp80) REVERT: A 89 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7773 (t0) REVERT: A 100 MET cc_start: 0.8143 (mmm) cc_final: 0.7174 (mtm) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.1974 time to fit residues: 29.7460 Evaluate side-chains 135 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3575 Z= 0.157 Angle : 0.542 6.939 4848 Z= 0.279 Chirality : 0.042 0.147 501 Planarity : 0.003 0.026 633 Dihedral : 3.483 14.252 500 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.93 % Allowed : 18.33 % Favored : 75.74 % 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: 0.22 (0.39), residues: 442 helix: -2.97 (1.09), residues: 21 sheet: 1.93 (0.45), residues: 126 loop : -0.45 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS C 114 PHE 0.006 0.001 PHE B 486 TYR 0.011 0.001 TYR C 32 ARG 0.006 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8555 (mm-30) cc_final: 0.7999 (mp0) REVERT: B 357 ARG cc_start: 0.7727 (ttp80) cc_final: 0.7391 (tmm160) REVERT: B 420 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: B 466 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7368 (ptm160) REVERT: B 469 SER cc_start: 0.9194 (t) cc_final: 0.8970 (p) REVERT: B 474 GLN cc_start: 0.7731 (tt0) cc_final: 0.7258 (tp40) REVERT: B 501 ASN cc_start: 0.8669 (m110) cc_final: 0.8151 (m110) REVERT: C 2 VAL cc_start: 0.7822 (OUTLIER) cc_final: 0.7532 (m) REVERT: C 13 GLN cc_start: 0.8384 (mp10) cc_final: 0.7992 (mp10) REVERT: C 27 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: C 65 LYS cc_start: 0.6759 (mtmt) cc_final: 0.6527 (mtmt) REVERT: C 67 ARG cc_start: 0.8558 (mtm-85) cc_final: 0.8320 (mtm-85) REVERT: C 68 PHE cc_start: 0.9137 (m-10) cc_final: 0.8913 (m-10) REVERT: C 73 ASP cc_start: 0.8269 (m-30) cc_final: 0.7708 (m-30) REVERT: C 87 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7742 (mmmt) REVERT: C 91 THR cc_start: 0.8702 (p) cc_final: 0.8476 (p) REVERT: A 3 GLN cc_start: 0.8468 (pt0) cc_final: 0.7865 (pm20) REVERT: A 5 GLN cc_start: 0.7909 (mp10) cc_final: 0.7562 (mp10) REVERT: A 19 ARG cc_start: 0.8084 (mpp80) cc_final: 0.7832 (mpp80) REVERT: A 89 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 100 MET cc_start: 0.8106 (mmm) cc_final: 0.7133 (mtm) outliers start: 22 outliers final: 17 residues processed: 125 average time/residue: 0.1957 time to fit residues: 28.6744 Evaluate side-chains 134 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.0670 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3575 Z= 0.298 Angle : 0.619 8.229 4848 Z= 0.324 Chirality : 0.044 0.148 501 Planarity : 0.003 0.027 633 Dihedral : 4.007 14.446 500 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 6.20 % Allowed : 19.68 % Favored : 74.12 % 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: 0.05 (0.39), residues: 442 helix: -3.18 (1.06), residues: 21 sheet: 1.56 (0.43), residues: 137 loop : -0.50 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 353 HIS 0.000 0.000 HIS C 114 PHE 0.008 0.001 PHE B 486 TYR 0.014 0.001 TYR C 32 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8048 (mp0) REVERT: B 357 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7395 (tmm160) REVERT: B 406 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8037 (mt-10) REVERT: B 420 ASP cc_start: 0.7184 (OUTLIER) cc_final: 0.6686 (m-30) REVERT: B 466 ARG cc_start: 0.7888 (ptm160) cc_final: 0.7433 (ptm160) REVERT: B 469 SER cc_start: 0.9231 (t) cc_final: 0.9001 (p) REVERT: B 474 GLN cc_start: 0.7645 (tt0) cc_final: 0.7133 (tp40) REVERT: B 501 ASN cc_start: 0.8764 (m110) cc_final: 0.8302 (m110) REVERT: C 2 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7662 (m) REVERT: C 5 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 27 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: C 59 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7540 (mtpt) REVERT: C 67 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8346 (mtm-85) REVERT: C 73 ASP cc_start: 0.8273 (m-30) cc_final: 0.7392 (m-30) REVERT: C 76 LYS cc_start: 0.8362 (mmmt) cc_final: 0.8058 (mtmm) REVERT: C 87 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7781 (mmmt) REVERT: C 91 THR cc_start: 0.8784 (p) cc_final: 0.8555 (p) REVERT: A 100 MET cc_start: 0.8249 (mmm) cc_final: 0.7198 (mtm) REVERT: A 121 VAL cc_start: 0.8773 (t) cc_final: 0.8463 (m) outliers start: 23 outliers final: 20 residues processed: 123 average time/residue: 0.2075 time to fit residues: 29.9768 Evaluate side-chains 135 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 1 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3575 Z= 0.170 Angle : 0.563 6.697 4848 Z= 0.290 Chirality : 0.042 0.148 501 Planarity : 0.003 0.029 633 Dihedral : 3.604 12.685 500 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.58 % Allowed : 22.37 % Favored : 73.05 % 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: 0.08 (0.39), residues: 442 helix: -3.14 (1.05), residues: 21 sheet: 1.53 (0.43), residues: 136 loop : -0.45 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 105 HIS 0.001 0.000 HIS B 519 PHE 0.008 0.001 PHE B 486 TYR 0.011 0.001 TYR C 32 ARG 0.006 0.000 ARG A 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 884 Ramachandran restraints generated. 442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8017 (mp0) REVERT: B 357 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7426 (tmm160) REVERT: B 406 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 466 ARG cc_start: 0.7768 (ptm160) cc_final: 0.7329 (ptm160) REVERT: B 469 SER cc_start: 0.9210 (t) cc_final: 0.8965 (p) REVERT: B 474 GLN cc_start: 0.7765 (tt0) cc_final: 0.7289 (tp40) REVERT: B 501 ASN cc_start: 0.8677 (m110) cc_final: 0.8142 (m110) REVERT: C 2 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7589 (m) REVERT: C 5 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 27 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8701 (m-80) REVERT: C 67 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8280 (mtm-85) REVERT: C 73 ASP cc_start: 0.8170 (m-30) cc_final: 0.7643 (m-30) REVERT: C 87 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7797 (mmmt) REVERT: C 91 THR cc_start: 0.8739 (p) cc_final: 0.8521 (p) REVERT: A 5 GLN cc_start: 0.7945 (mp10) cc_final: 0.7622 (mp10) REVERT: A 19 ARG cc_start: 0.8064 (mpp80) cc_final: 0.7797 (mpp80) REVERT: A 75 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8243 (mtpt) REVERT: A 89 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7783 (t0) REVERT: A 100 MET cc_start: 0.8146 (mmm) cc_final: 0.7233 (mtm) outliers start: 17 outliers final: 13 residues processed: 120 average time/residue: 0.2035 time to fit residues: 28.5518 Evaluate side-chains 128 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.121691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103150 restraints weight = 5797.587| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.59 r_work: 0.3085 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3575 Z= 0.183 Angle : 0.584 7.412 4848 Z= 0.301 Chirality : 0.043 0.146 501 Planarity : 0.003 0.030 633 Dihedral : 3.652 17.424 500 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 6.47 % Allowed : 21.29 % Favored : 72.24 % 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: 0.09 (0.39), residues: 442 helix: -3.22 (1.03), residues: 21 sheet: 1.51 (0.43), residues: 137 loop : -0.43 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 105 HIS 0.001 0.000 HIS C 114 PHE 0.026 0.001 PHE C 68 TYR 0.011 0.001 TYR C 32 ARG 0.008 0.001 ARG A 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.55 seconds wall clock time: 25 minutes 1.15 seconds (1501.15 seconds total)