Starting phenix.real_space_refine on Wed Feb 14 08:36:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/02_2024/8fy3_29551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/02_2024/8fy3_29551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/02_2024/8fy3_29551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/02_2024/8fy3_29551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/02_2024/8fy3_29551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy3_29551/02_2024/8fy3_29551.pdb" } resolution = 2.88 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= 0.058 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 55 5.16 5 C 5739 2.51 5 N 1537 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4520 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 25, 'TRANS': 535} Chain breaks: 6 Chain: "B" Number of atoms: 4114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4114 Classifications: {'peptide': 524} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 504} Chain breaks: 6 Chain: "C" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 7, 'TRANS': 30} Time building chain proxies: 5.14, per 1000 atoms: 0.57 Number of scatterers: 8948 At special positions: 0 Unit cell: (69.3, 107.415, 178.101, 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 55 16.00 O 1617 8.00 N 1537 7.00 C 5739 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 71.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.669A pdb=" N HIS A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 82 removed outlier: 3.760A pdb=" N ILE A 82 " --> pdb=" O CYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.188A pdb=" N VAL A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 163 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.525A pdb=" N PHE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.705A pdb=" N VAL A 293 " --> pdb=" O GLN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 removed outlier: 3.986A pdb=" N LEU A 341 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 360 removed outlier: 3.517A pdb=" N VAL A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 386 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 442 through 448 removed outlier: 4.045A pdb=" N TRP A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.761A pdb=" N ILE A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.925A pdb=" N PHE A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.641A pdb=" N HIS A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 Processing helix chain 'A' and resid 496 through 511 Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.789A pdb=" N ILE A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 removed outlier: 3.786A pdb=" N MET A 542 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 557 through 567 Processing helix chain 'A' and resid 579 through 592 removed outlier: 4.615A pdb=" N ILE A 583 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 585 " --> pdb=" O PHE A 581 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 608 removed outlier: 3.767A pdb=" N TRP A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 602 " --> pdb=" O ASP A 598 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 45 through 57 Processing helix chain 'B' and resid 60 through 75 removed outlier: 4.018A pdb=" N ILE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 144 through 162 Processing helix chain 'B' and resid 164 through 181 Processing helix chain 'B' and resid 208 through 230 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 265 through 276 removed outlier: 3.509A pdb=" N SER B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 290 through 306 Processing helix chain 'B' and resid 308 through 331 Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 353 through 369 Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.757A pdb=" N GLU B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 403 removed outlier: 3.686A pdb=" N ASN B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 removed outlier: 3.633A pdb=" N ILE B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 547 Processing helix chain 'B' and resid 548 through 561 Processing helix chain 'B' and resid 566 through 584 Processing helix chain 'B' and resid 586 through 594 removed outlier: 3.595A pdb=" N THR B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 637 through 656 removed outlier: 3.670A pdb=" N ALA B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 672 removed outlier: 3.518A pdb=" N LYS B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 692 removed outlier: 3.551A pdb=" N ILE B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) 533 hydrogen bonds defined for protein. 1575 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: 2.39 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2912 1.34 - 1.46: 1860 1.46 - 1.58: 4286 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 9137 Sorted by residual: bond pdb=" CA PRO B 679 " pdb=" C PRO B 679 " ideal model delta sigma weight residual 1.514 1.520 -0.005 5.50e-03 3.31e+04 9.83e-01 bond pdb=" N TYR B 634 " pdb=" CA TYR B 634 " ideal model delta sigma weight residual 1.463 1.457 0.006 6.90e-03 2.10e+04 7.80e-01 bond pdb=" C TYR B 634 " pdb=" N PRO B 635 " ideal model delta sigma weight residual 1.340 1.364 -0.023 2.76e-02 1.31e+03 7.25e-01 bond pdb=" CB PRO B 635 " pdb=" CG PRO B 635 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.13e-01 bond pdb=" CG GLU A 261 " pdb=" CD GLU A 261 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.65e-01 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.13: 284 107.13 - 113.84: 5169 113.84 - 120.54: 3665 120.54 - 127.24: 3129 127.24 - 133.95: 110 Bond angle restraints: 12357 Sorted by residual: angle pdb=" CA TRP C 312 " pdb=" CB TRP C 312 " pdb=" CG TRP C 312 " ideal model delta sigma weight residual 113.60 118.72 -5.12 1.90e+00 2.77e-01 7.27e+00 angle pdb=" C LYS A 23 " pdb=" N ASN A 24 " pdb=" CA ASN A 24 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.87e+00 angle pdb=" C ILE C 310 " pdb=" N GLN C 311 " pdb=" CA GLN C 311 " ideal model delta sigma weight residual 122.39 119.18 3.21 1.64e+00 3.72e-01 3.83e+00 angle pdb=" CA LEU A 240 " pdb=" CB LEU A 240 " pdb=" CG LEU A 240 " ideal model delta sigma weight residual 116.30 122.89 -6.59 3.50e+00 8.16e-02 3.54e+00 angle pdb=" CA ARG B 84 " pdb=" CB ARG B 84 " pdb=" CG ARG B 84 " ideal model delta sigma weight residual 114.10 117.86 -3.76 2.00e+00 2.50e-01 3.53e+00 ... (remaining 12352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5187 17.23 - 34.45: 272 34.45 - 51.68: 62 51.68 - 68.91: 13 68.91 - 86.13: 3 Dihedral angle restraints: 5537 sinusoidal: 2236 harmonic: 3301 Sorted by residual: dihedral pdb=" CA SER B 241 " pdb=" C SER B 241 " pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA GLN C 311 " pdb=" C GLN C 311 " pdb=" N TRP C 312 " pdb=" CA TRP C 312 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB ARG A 211 " pdb=" CG ARG A 211 " pdb=" CD ARG A 211 " pdb=" NE ARG A 211 " ideal model delta sinusoidal sigma weight residual -180.00 -121.12 -58.88 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 797 0.027 - 0.053: 401 0.053 - 0.080: 141 0.080 - 0.107: 50 0.107 - 0.133: 4 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ILE C 310 " pdb=" N ILE C 310 " pdb=" C ILE C 310 " pdb=" CB ILE C 310 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE B 453 " pdb=" N ILE B 453 " pdb=" C ILE B 453 " pdb=" CB ILE B 453 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA PRO A 154 " pdb=" N PRO A 154 " pdb=" C PRO A 154 " pdb=" CB PRO A 154 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.36e-01 ... (remaining 1390 not shown) Planarity restraints: 1577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 475 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 476 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 240 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 241 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 312 " -0.013 2.00e-02 2.50e+03 8.38e-03 1.75e+00 pdb=" CG TRP C 312 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 312 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP C 312 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 312 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 312 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 312 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 312 " -0.001 2.00e-02 2.50e+03 ... (remaining 1574 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 400 2.73 - 3.27: 9333 3.27 - 3.81: 15008 3.81 - 4.36: 17488 4.36 - 4.90: 30067 Nonbonded interactions: 72296 Sorted by model distance: nonbonded pdb=" O ILE A 368 " pdb=" OG SER A 407 " model vdw 2.186 2.440 nonbonded pdb=" O SER B 75 " pdb=" OG1 THR B 78 " model vdw 2.187 2.440 nonbonded pdb=" NE2 GLN A 102 " pdb=" OG SER A 104 " model vdw 2.222 2.520 nonbonded pdb=" O LEU B 158 " pdb=" OG1 THR B 162 " model vdw 2.225 2.440 nonbonded pdb=" OG SER A 138 " pdb=" OD1 ASP A 140 " model vdw 2.229 2.440 ... (remaining 72291 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 13.120 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.970 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9137 Z= 0.202 Angle : 0.492 10.243 12357 Z= 0.255 Chirality : 0.036 0.133 1393 Planarity : 0.004 0.041 1577 Dihedral : 11.506 86.133 3383 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.96 % Allowed : 6.33 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.07 (0.26), residues: 1093 helix: 1.55 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -1.31 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 312 HIS 0.003 0.001 HIS B 303 PHE 0.012 0.002 PHE B 571 TYR 0.013 0.001 TYR B 261 ARG 0.003 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 0.908 Fit side-chains REVERT: A 73 PHE cc_start: 0.7729 (t80) cc_final: 0.7143 (t80) REVERT: A 360 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6534 (tm-30) REVERT: A 547 MET cc_start: 0.2744 (mmt) cc_final: 0.2518 (mmt) REVERT: A 617 MET cc_start: 0.4735 (pmm) cc_final: 0.2549 (ttm) REVERT: B 73 PHE cc_start: 0.7544 (m-10) cc_final: 0.7328 (m-10) REVERT: B 135 LYS cc_start: 0.6496 (mtmt) cc_final: 0.5714 (ttpp) REVERT: B 292 ARG cc_start: 0.7206 (mtt90) cc_final: 0.6476 (mtp85) REVERT: B 322 GLU cc_start: 0.7040 (tp30) cc_final: 0.6713 (tp30) REVERT: B 331 SER cc_start: 0.7306 (t) cc_final: 0.7079 (p) REVERT: B 344 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7933 (ttm170) REVERT: B 347 CYS cc_start: 0.8111 (m) cc_final: 0.7678 (p) REVERT: B 370 ARG cc_start: 0.7529 (mtm-85) cc_final: 0.7264 (mtt-85) REVERT: B 525 LYS cc_start: 0.7238 (tttp) cc_final: 0.6417 (pmtt) REVERT: B 575 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7534 (mp) outliers start: 29 outliers final: 6 residues processed: 192 average time/residue: 1.0723 time to fit residues: 220.7145 Evaluate side-chains 114 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.0000 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 410 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9137 Z= 0.204 Angle : 0.535 10.572 12357 Z= 0.262 Chirality : 0.037 0.134 1393 Planarity : 0.004 0.060 1577 Dihedral : 5.045 55.608 1207 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.49 % Allowed : 10.52 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.28 (0.26), residues: 1093 helix: 1.65 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -1.15 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 312 HIS 0.003 0.001 HIS A 39 PHE 0.017 0.002 PHE A 68 TYR 0.011 0.001 TYR B 163 ARG 0.003 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 112 time to evaluate : 0.972 Fit side-chains REVERT: A 37 ASN cc_start: 0.7174 (m-40) cc_final: 0.6939 (m110) REVERT: A 42 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: A 48 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 77 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7307 (mm-30) REVERT: A 360 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6457 (tm-30) REVERT: A 362 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.5696 (p0) REVERT: A 547 MET cc_start: 0.2741 (mmt) cc_final: 0.2536 (mmt) REVERT: B 135 LYS cc_start: 0.6527 (mtmt) cc_final: 0.5885 (ttpp) REVERT: B 344 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7853 (ttm170) REVERT: B 347 CYS cc_start: 0.8152 (m) cc_final: 0.7767 (p) REVERT: B 525 LYS cc_start: 0.7203 (tttp) cc_final: 0.6349 (pmtt) REVERT: B 558 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7160 (ttpt) REVERT: C 293 ILE cc_start: 0.7907 (OUTLIER) cc_final: 0.7530 (mp) REVERT: C 297 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7492 (tt0) outliers start: 44 outliers final: 17 residues processed: 141 average time/residue: 0.9756 time to fit residues: 149.7181 Evaluate side-chains 122 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 297 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 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 33 GLN A 37 ASN A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 HIS ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9137 Z= 0.191 Angle : 0.507 10.345 12357 Z= 0.244 Chirality : 0.036 0.133 1393 Planarity : 0.004 0.054 1577 Dihedral : 4.770 54.172 1204 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.19 % Allowed : 12.05 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.42 (0.26), residues: 1093 helix: 1.76 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -1.12 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 312 HIS 0.003 0.001 HIS C 292 PHE 0.012 0.002 PHE A 196 TYR 0.012 0.001 TYR B 163 ARG 0.004 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 1.072 Fit side-chains REVERT: A 33 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7750 (tp-100) REVERT: A 42 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6898 (tp30) REVERT: A 77 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 360 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6441 (tm-30) REVERT: A 362 ASP cc_start: 0.6537 (m-30) cc_final: 0.5529 (p0) REVERT: A 417 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: B 135 LYS cc_start: 0.6534 (mtmt) cc_final: 0.5875 (ttpp) REVERT: B 344 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7798 (ttm170) REVERT: B 347 CYS cc_start: 0.8132 (m) cc_final: 0.7800 (p) REVERT: B 525 LYS cc_start: 0.7280 (tttp) cc_final: 0.6405 (pmtt) REVERT: B 558 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7126 (ttpm) REVERT: C 293 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7501 (mp) outliers start: 41 outliers final: 17 residues processed: 133 average time/residue: 0.9707 time to fit residues: 140.1962 Evaluate side-chains 120 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 54 HIS Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9137 Z= 0.212 Angle : 0.506 10.501 12357 Z= 0.245 Chirality : 0.036 0.134 1393 Planarity : 0.004 0.056 1577 Dihedral : 4.797 56.678 1204 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.68 % Allowed : 13.89 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.44 (0.26), residues: 1093 helix: 1.78 (0.19), residues: 772 sheet: None (None), residues: 0 loop : -1.09 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.005 0.001 HIS B 303 PHE 0.012 0.001 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7350 (mt0) REVERT: A 42 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6924 (tp30) REVERT: A 77 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 360 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6510 (tm-30) REVERT: A 362 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.5611 (p0) REVERT: A 414 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7816 (pt) REVERT: B 135 LYS cc_start: 0.6568 (mtmt) cc_final: 0.5907 (ttpp) REVERT: B 344 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7794 (ttm170) REVERT: B 347 CYS cc_start: 0.8130 (m) cc_final: 0.7801 (p) REVERT: B 525 LYS cc_start: 0.7240 (tttp) cc_final: 0.6331 (pmtt) REVERT: B 558 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7209 (ttpt) REVERT: B 575 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7557 (mp) REVERT: C 293 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7502 (mp) outliers start: 36 outliers final: 20 residues processed: 127 average time/residue: 0.9321 time to fit residues: 129.1284 Evaluate side-chains 123 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.0040 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9137 Z= 0.189 Angle : 0.494 9.920 12357 Z= 0.241 Chirality : 0.036 0.131 1393 Planarity : 0.004 0.054 1577 Dihedral : 4.380 55.668 1202 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.09 % Allowed : 13.89 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.56 (0.26), residues: 1093 helix: 1.85 (0.19), residues: 771 sheet: None (None), residues: 0 loop : -0.98 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.015 0.001 PHE A 196 TYR 0.010 0.001 TYR B 355 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 0.970 Fit side-chains REVERT: A 42 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6941 (tp30) REVERT: A 77 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 360 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6543 (tm-30) REVERT: A 362 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.5608 (p0) REVERT: B 135 LYS cc_start: 0.6615 (mtmt) cc_final: 0.5914 (ttpp) REVERT: B 344 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7832 (ttm170) REVERT: B 347 CYS cc_start: 0.8104 (m) cc_final: 0.7792 (p) REVERT: B 525 LYS cc_start: 0.7258 (tttp) cc_final: 0.6317 (pmtt) REVERT: B 558 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7192 (ttpt) REVERT: B 575 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7516 (mp) REVERT: C 293 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7487 (mp) outliers start: 40 outliers final: 21 residues processed: 128 average time/residue: 0.9230 time to fit residues: 128.9093 Evaluate side-chains 124 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLN Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9137 Z= 0.205 Angle : 0.498 7.283 12357 Z= 0.243 Chirality : 0.036 0.133 1393 Planarity : 0.004 0.055 1577 Dihedral : 4.348 56.582 1202 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.98 % Allowed : 14.71 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.58 (0.26), residues: 1093 helix: 1.84 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.007 0.001 HIS B 219 PHE 0.013 0.001 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 108 time to evaluate : 1.035 Fit side-chains REVERT: A 42 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6960 (tp30) REVERT: A 77 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7322 (mm-30) REVERT: A 360 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6560 (tm-30) REVERT: A 362 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.5728 (p0) REVERT: A 459 ARG cc_start: 0.6929 (tpm170) cc_final: 0.6673 (tpm170) REVERT: B 135 LYS cc_start: 0.6655 (mtmt) cc_final: 0.5993 (ttpp) REVERT: B 344 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7859 (ttm170) REVERT: B 347 CYS cc_start: 0.8122 (m) cc_final: 0.7797 (p) REVERT: B 525 LYS cc_start: 0.7213 (tttp) cc_final: 0.6220 (pmtt) REVERT: B 558 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7225 (ttpt) REVERT: C 293 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7488 (mp) outliers start: 39 outliers final: 23 residues processed: 135 average time/residue: 0.9257 time to fit residues: 136.1687 Evaluate side-chains 131 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 90 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 42 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 349 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9137 Z= 0.218 Angle : 0.514 7.533 12357 Z= 0.252 Chirality : 0.036 0.132 1393 Planarity : 0.004 0.056 1577 Dihedral : 4.359 57.597 1202 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.78 % Allowed : 14.81 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.58 (0.26), residues: 1093 helix: 1.83 (0.19), residues: 773 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.013 0.002 PHE A 196 TYR 0.011 0.001 TYR B 355 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 102 time to evaluate : 1.005 Fit side-chains REVERT: A 42 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: A 77 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 360 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6563 (tm-30) REVERT: A 362 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6407 (t0) REVERT: A 414 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7746 (pt) REVERT: A 459 ARG cc_start: 0.6963 (tpm170) cc_final: 0.6721 (tpm170) REVERT: B 63 ILE cc_start: 0.8274 (mm) cc_final: 0.8018 (mt) REVERT: B 135 LYS cc_start: 0.6684 (mtmt) cc_final: 0.5972 (ttpp) REVERT: B 344 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7855 (ttm170) REVERT: B 347 CYS cc_start: 0.8122 (m) cc_final: 0.7799 (p) REVERT: B 525 LYS cc_start: 0.7225 (tttp) cc_final: 0.6223 (pmtt) REVERT: B 531 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7051 (tt) REVERT: B 558 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7258 (ttpt) REVERT: C 293 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7524 (mp) outliers start: 37 outliers final: 23 residues processed: 125 average time/residue: 0.9875 time to fit residues: 135.0689 Evaluate side-chains 132 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain C residue 293 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 chunk 9 optimal weight: 0.1980 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9137 Z= 0.168 Angle : 0.494 7.195 12357 Z= 0.245 Chirality : 0.036 0.128 1393 Planarity : 0.003 0.053 1577 Dihedral : 3.933 37.418 1200 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.47 % Allowed : 15.63 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.68 (0.26), residues: 1093 helix: 1.91 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS A 34 PHE 0.012 0.001 PHE A 196 TYR 0.009 0.001 TYR B 355 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 0.973 Fit side-chains REVERT: A 42 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6945 (tp30) REVERT: A 73 PHE cc_start: 0.7916 (t80) cc_final: 0.7582 (t80) REVERT: A 77 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 360 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6560 (tm-30) REVERT: A 362 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6350 (t0) REVERT: A 459 ARG cc_start: 0.6961 (tpm170) cc_final: 0.6736 (tpm170) REVERT: B 63 ILE cc_start: 0.8246 (mm) cc_final: 0.7972 (mt) REVERT: B 135 LYS cc_start: 0.6618 (mtmt) cc_final: 0.5957 (ttpp) REVERT: B 344 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7803 (ttm170) REVERT: B 347 CYS cc_start: 0.8096 (m) cc_final: 0.7783 (p) REVERT: B 525 LYS cc_start: 0.7248 (tttp) cc_final: 0.6252 (pmtt) outliers start: 34 outliers final: 19 residues processed: 127 average time/residue: 0.9290 time to fit residues: 128.4197 Evaluate side-chains 123 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9137 Z= 0.167 Angle : 0.494 7.180 12357 Z= 0.244 Chirality : 0.036 0.127 1393 Planarity : 0.003 0.054 1577 Dihedral : 3.874 34.488 1200 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.96 % Allowed : 16.34 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.73 (0.26), residues: 1093 helix: 1.96 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 312 HIS 0.004 0.001 HIS B 303 PHE 0.011 0.001 PHE A 196 TYR 0.026 0.001 TYR A 359 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 1.095 Fit side-chains REVERT: A 42 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6917 (tp30) REVERT: A 77 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 360 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6552 (tm-30) REVERT: A 362 ASP cc_start: 0.6860 (OUTLIER) cc_final: 0.6415 (t0) REVERT: A 414 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7743 (pt) REVERT: A 459 ARG cc_start: 0.6993 (tpm170) cc_final: 0.6779 (tpm170) REVERT: B 135 LYS cc_start: 0.6630 (mtmt) cc_final: 0.5957 (ttpp) REVERT: B 344 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7796 (ttm170) REVERT: B 347 CYS cc_start: 0.8037 (m) cc_final: 0.7735 (p) REVERT: B 575 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7354 (mp) outliers start: 29 outliers final: 18 residues processed: 121 average time/residue: 0.9693 time to fit residues: 127.7297 Evaluate side-chains 122 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 100 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 chunk 53 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 HIS ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9137 Z= 0.250 Angle : 0.546 7.956 12357 Z= 0.268 Chirality : 0.037 0.132 1393 Planarity : 0.004 0.060 1577 Dihedral : 4.051 35.882 1200 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.96 % Allowed : 16.55 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.55 (0.26), residues: 1093 helix: 1.80 (0.19), residues: 774 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.005 0.001 HIS B 303 PHE 0.016 0.002 PHE B 304 TYR 0.013 0.001 TYR B 355 ARG 0.003 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.889 Fit side-chains REVERT: A 34 HIS cc_start: 0.6699 (OUTLIER) cc_final: 0.6414 (t-90) REVERT: A 77 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 360 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6573 (tm-30) REVERT: B 63 ILE cc_start: 0.8293 (mm) cc_final: 0.8051 (mt) REVERT: B 347 CYS cc_start: 0.8147 (m) cc_final: 0.7803 (p) outliers start: 29 outliers final: 19 residues processed: 116 average time/residue: 0.8734 time to fit residues: 111.1617 Evaluate side-chains 114 residues out of total 979 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 352 ASN ** 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 = 0.4815 r_free = 0.4815 target = 0.264854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.203249 restraints weight = 8549.378| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.21 r_work: 0.4027 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 9137 Z= 0.241 Angle : 0.832 48.084 12357 Z= 0.540 Chirality : 0.039 0.302 1393 Planarity : 0.004 0.059 1577 Dihedral : 4.068 35.344 1200 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.45 % Allowed : 17.47 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: 1.50 (0.26), residues: 1093 helix: 1.76 (0.19), residues: 775 sheet: None (None), residues: 0 loop : -0.91 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 312 HIS 0.058 0.002 HIS A 34 PHE 0.014 0.002 PHE A 196 TYR 0.019 0.001 TYR A 359 ARG 0.002 0.000 ARG A 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3666.60 seconds wall clock time: 65 minutes 43.86 seconds (3943.86 seconds total)