Starting phenix.real_space_refine on Sun Mar 10 20:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hru_34980/03_2024/8hru_34980.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hru_34980/03_2024/8hru_34980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hru_34980/03_2024/8hru_34980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hru_34980/03_2024/8hru_34980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hru_34980/03_2024/8hru_34980.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hru_34980/03_2024/8hru_34980.pdb" } resolution = 3.9 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= 0.007 sd= 0.066 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 29 5.16 5 C 3115 2.51 5 N 806 2.21 5 O 920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Time building chain proxies: 3.13, per 1000 atoms: 0.64 Number of scatterers: 4870 At special positions: 0 Unit cell: (85.324, 85.324, 71.96, 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 29 16.00 O 920 8.00 N 806 7.00 C 3115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 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: 2.01 Conformation dependent library (CDL) restraints added in 876.8 milliseconds 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 3 sheets defined 64.5% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 5.108A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.730A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.891A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.848A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.578A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.567A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.585A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.752A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 172' Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.563A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.952A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.863A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.606A pdb=" N LEU A 278 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 removed outlier: 4.057A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.569A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.895A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.607A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.838A pdb=" N HIS A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.709A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 removed outlier: 3.643A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 474 through 482 removed outlier: 4.260A pdb=" N MET A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.955A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.679A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.750A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.154A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.793A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.631A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.361A pdb=" N VAL A 132 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 142 " --> pdb=" O VAL A 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.845A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.838A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 639 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: 1.28 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1578 1.35 - 1.47: 1270 1.47 - 1.59: 2107 1.59 - 1.71: 2 1.71 - 1.83: 50 Bond restraints: 5007 Sorted by residual: bond pdb=" CG PRO A 289 " pdb=" CD PRO A 289 " ideal model delta sigma weight residual 1.503 1.272 0.231 3.40e-02 8.65e+02 4.61e+01 bond pdb=" N PRO A 289 " pdb=" CD PRO A 289 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" CB PRO A 289 " pdb=" CG PRO A 289 " ideal model delta sigma weight residual 1.492 1.686 -0.194 5.00e-02 4.00e+02 1.51e+01 bond pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.69e+00 bond pdb=" N PRO A 289 " pdb=" CA PRO A 289 " ideal model delta sigma weight residual 1.469 1.444 0.024 1.28e-02 6.10e+03 3.62e+00 ... (remaining 5002 not shown) Histogram of bond angle deviations from ideal: 88.77 - 98.02: 3 98.02 - 107.27: 204 107.27 - 116.51: 3028 116.51 - 125.76: 3441 125.76 - 135.01: 127 Bond angle restraints: 6803 Sorted by residual: angle pdb=" CA PRO A 289 " pdb=" N PRO A 289 " pdb=" CD PRO A 289 " ideal model delta sigma weight residual 112.00 94.31 17.69 1.40e+00 5.10e-01 1.60e+02 angle pdb=" N PRO A 289 " pdb=" CD PRO A 289 " pdb=" CG PRO A 289 " ideal model delta sigma weight residual 103.20 88.77 14.43 1.50e+00 4.44e-01 9.25e+01 angle pdb=" CA PRO A 289 " pdb=" CB PRO A 289 " pdb=" CG PRO A 289 " ideal model delta sigma weight residual 104.50 92.34 12.16 1.90e+00 2.77e-01 4.09e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 105.47 6.53 1.40e+00 5.10e-01 2.18e+01 angle pdb=" CA LYS A 353 " pdb=" CB LYS A 353 " pdb=" CG LYS A 353 " ideal model delta sigma weight residual 114.10 121.64 -7.54 2.00e+00 2.50e-01 1.42e+01 ... (remaining 6798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 2461 16.24 - 32.48: 363 32.48 - 48.71: 101 48.71 - 64.95: 18 64.95 - 81.19: 16 Dihedral angle restraints: 2959 sinusoidal: 1205 harmonic: 1754 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 133.57 -40.57 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" CA CYS A 530 " pdb=" C CYS A 530 " pdb=" N GLN A 531 " pdb=" CA GLN A 531 " ideal model delta harmonic sigma weight residual 180.00 158.21 21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA MET A 579 " pdb=" C MET A 579 " pdb=" N ASN A 580 " pdb=" CA ASN A 580 " ideal model delta harmonic sigma weight residual -180.00 -162.91 -17.09 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 2956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 538 0.053 - 0.106: 144 0.106 - 0.159: 23 0.159 - 0.212: 3 0.212 - 0.265: 2 Chirality restraints: 710 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB THR A 118 " pdb=" CA THR A 118 " pdb=" OG1 THR A 118 " pdb=" CG2 THR A 118 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU A 391 " pdb=" CB LEU A 391 " pdb=" CD1 LEU A 391 " pdb=" CD2 LEU A 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.35e-01 ... (remaining 707 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 288 " -0.079 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO A 289 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.055 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 500 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.042 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO A 258 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.034 5.00e-02 4.00e+02 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 62 2.58 - 3.16: 4222 3.16 - 3.74: 8348 3.74 - 4.32: 10856 4.32 - 4.90: 17365 Nonbonded interactions: 40853 Sorted by model distance: nonbonded pdb=" O ARG A 482 " pdb=" NH1 ARG A 482 " model vdw 2.000 2.520 nonbonded pdb=" O THR A 92 " pdb=" NE2 GLN A 96 " model vdw 2.165 2.520 nonbonded pdb=" O ALA A 403 " pdb=" NE2 GLN A 522 " model vdw 2.196 2.520 nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.204 2.440 nonbonded pdb=" NH2 ARG A 245 " pdb=" O PHE A 603 " model vdw 2.226 2.520 ... (remaining 40848 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.010 Find NCS groups from input model: 0.130 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 : 0.006 0.231 5007 Z= 0.395 Angle : 0.980 17.687 6803 Z= 0.547 Chirality : 0.050 0.265 710 Planarity : 0.007 0.106 881 Dihedral : 17.398 81.191 1820 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.38 % Allowed : 26.57 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.35), residues: 595 helix: -0.65 (0.28), residues: 334 sheet: -2.31 (1.19), residues: 10 loop : -0.87 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 302 HIS 0.006 0.001 HIS A 265 PHE 0.024 0.002 PHE A 588 TYR 0.034 0.002 TYR A 521 ARG 0.011 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7125 (mmp) cc_final: 0.6647 (mmp) REVERT: A 350 ASP cc_start: 0.8261 (t0) cc_final: 0.6468 (t0) outliers start: 2 outliers final: 0 residues processed: 97 average time/residue: 0.1678 time to fit residues: 21.0366 Evaluate side-chains 87 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5007 Z= 0.238 Angle : 0.689 9.975 6803 Z= 0.342 Chirality : 0.044 0.154 710 Planarity : 0.005 0.058 881 Dihedral : 4.848 20.170 642 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.80 % Allowed : 23.53 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.99 (0.35), residues: 595 helix: -0.36 (0.28), residues: 347 sheet: -1.72 (1.37), residues: 12 loop : -0.85 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 477 HIS 0.005 0.001 HIS A 265 PHE 0.018 0.002 PHE A 525 TYR 0.021 0.002 TYR A 521 ARG 0.003 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8143 (mmp) cc_final: 0.7906 (mmt) REVERT: A 481 LYS cc_start: 0.5837 (mttt) cc_final: 0.5195 (mttt) outliers start: 20 outliers final: 11 residues processed: 106 average time/residue: 0.1420 time to fit residues: 20.3267 Evaluate side-chains 90 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 606 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5007 Z= 0.170 Angle : 0.642 13.033 6803 Z= 0.310 Chirality : 0.043 0.158 710 Planarity : 0.004 0.046 881 Dihedral : 4.600 19.984 642 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.98 % Allowed : 22.39 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.63 (0.35), residues: 595 helix: -0.02 (0.28), residues: 343 sheet: -1.91 (1.37), residues: 12 loop : -0.76 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 594 HIS 0.003 0.001 HIS A 417 PHE 0.013 0.001 PHE A 525 TYR 0.039 0.002 TYR A 521 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8685 (m-30) cc_final: 0.8081 (p0) REVERT: A 123 MET cc_start: 0.8161 (mmp) cc_final: 0.7852 (mmt) REVERT: A 168 TRP cc_start: 0.7605 (t-100) cc_final: 0.6331 (t-100) REVERT: A 237 TYR cc_start: 0.6744 (t80) cc_final: 0.6074 (t80) REVERT: A 601 ASN cc_start: 0.8929 (p0) cc_final: 0.8616 (m-40) outliers start: 21 outliers final: 11 residues processed: 114 average time/residue: 0.1523 time to fit residues: 23.0886 Evaluate side-chains 99 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 606 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.0670 chunk 32 optimal weight: 7.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5007 Z= 0.222 Angle : 0.677 12.689 6803 Z= 0.331 Chirality : 0.044 0.169 710 Planarity : 0.004 0.038 881 Dihedral : 4.760 20.969 642 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.61 % Allowed : 23.53 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.52 (0.36), residues: 595 helix: 0.06 (0.29), residues: 342 sheet: -2.00 (1.36), residues: 12 loop : -0.69 (0.43), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 594 HIS 0.005 0.001 HIS A 239 PHE 0.013 0.002 PHE A 512 TYR 0.026 0.002 TYR A 521 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8718 (m-30) cc_final: 0.8139 (p0) REVERT: A 123 MET cc_start: 0.8263 (mmp) cc_final: 0.7977 (mmt) REVERT: A 168 TRP cc_start: 0.8063 (t-100) cc_final: 0.7350 (t-100) REVERT: A 237 TYR cc_start: 0.6886 (t80) cc_final: 0.6227 (t80) REVERT: A 271 TRP cc_start: 0.6707 (m100) cc_final: 0.6355 (m100) REVERT: A 471 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8378 (p0) REVERT: A 521 TYR cc_start: 0.6569 (m-80) cc_final: 0.5895 (m-10) REVERT: A 525 PHE cc_start: 0.7679 (m-80) cc_final: 0.6955 (m-80) REVERT: A 579 MET cc_start: 0.6989 (ppp) cc_final: 0.6778 (ppp) REVERT: A 601 ASN cc_start: 0.8944 (p0) cc_final: 0.8585 (m-40) outliers start: 19 outliers final: 15 residues processed: 106 average time/residue: 0.1367 time to fit residues: 19.5088 Evaluate side-chains 105 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.002 0.028 5007 Z= 0.145 Angle : 0.634 11.445 6803 Z= 0.302 Chirality : 0.043 0.165 710 Planarity : 0.003 0.036 881 Dihedral : 4.407 18.540 642 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.85 % Allowed : 25.05 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.23 (0.36), residues: 595 helix: 0.20 (0.28), residues: 345 sheet: -1.67 (1.54), residues: 10 loop : -0.43 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 594 HIS 0.007 0.001 HIS A 239 PHE 0.010 0.001 PHE A 523 TYR 0.026 0.001 TYR A 521 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8665 (m-30) cc_final: 0.8132 (p0) REVERT: A 168 TRP cc_start: 0.7655 (t-100) cc_final: 0.6796 (t-100) REVERT: A 237 TYR cc_start: 0.6982 (t80) cc_final: 0.6505 (t80) REVERT: A 297 MET cc_start: 0.8488 (mpp) cc_final: 0.8124 (mpp) REVERT: A 541 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7611 (ptpt) REVERT: A 572 ASN cc_start: 0.8698 (m110) cc_final: 0.8444 (m-40) REVERT: A 601 ASN cc_start: 0.8981 (p0) cc_final: 0.8657 (m-40) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.1489 time to fit residues: 21.3464 Evaluate side-chains 101 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5007 Z= 0.252 Angle : 0.727 10.995 6803 Z= 0.351 Chirality : 0.045 0.147 710 Planarity : 0.004 0.037 881 Dihedral : 4.823 19.499 642 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.36 % Allowed : 25.24 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.30 (0.36), residues: 595 helix: 0.14 (0.29), residues: 344 sheet: -1.93 (1.33), residues: 12 loop : -0.41 (0.44), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 477 HIS 0.006 0.001 HIS A 239 PHE 0.012 0.002 PHE A 390 TYR 0.031 0.002 TYR A 521 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8744 (m-30) cc_final: 0.8157 (p0) REVERT: A 168 TRP cc_start: 0.8148 (t-100) cc_final: 0.7897 (t-100) REVERT: A 237 TYR cc_start: 0.7208 (t80) cc_final: 0.6627 (t80) REVERT: A 481 LYS cc_start: 0.6284 (pttt) cc_final: 0.5206 (ptpp) REVERT: A 525 PHE cc_start: 0.7626 (m-10) cc_final: 0.7117 (m-80) REVERT: A 572 ASN cc_start: 0.8824 (m110) cc_final: 0.8514 (m-40) outliers start: 23 outliers final: 19 residues processed: 102 average time/residue: 0.1426 time to fit residues: 19.4438 Evaluate side-chains 105 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5007 Z= 0.280 Angle : 0.752 10.934 6803 Z= 0.370 Chirality : 0.046 0.147 710 Planarity : 0.004 0.035 881 Dihedral : 5.083 20.288 642 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.55 % Allowed : 26.57 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.35 (0.36), residues: 595 helix: 0.08 (0.29), residues: 338 sheet: -2.04 (1.32), residues: 12 loop : -0.39 (0.44), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 271 HIS 0.010 0.001 HIS A 239 PHE 0.012 0.002 PHE A 452 TYR 0.028 0.002 TYR A 521 ARG 0.002 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9306 (mttt) cc_final: 0.8942 (mmtt) REVERT: A 67 ASP cc_start: 0.8782 (m-30) cc_final: 0.8170 (p0) REVERT: A 168 TRP cc_start: 0.8185 (t-100) cc_final: 0.7979 (t-100) REVERT: A 237 TYR cc_start: 0.7358 (t80) cc_final: 0.6718 (t80) REVERT: A 481 LYS cc_start: 0.6567 (pttt) cc_final: 0.4972 (pttt) REVERT: A 525 PHE cc_start: 0.7686 (m-10) cc_final: 0.7168 (m-80) REVERT: A 572 ASN cc_start: 0.8855 (m110) cc_final: 0.8471 (m-40) outliers start: 24 outliers final: 20 residues processed: 108 average time/residue: 0.1464 time to fit residues: 21.0458 Evaluate side-chains 106 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 381 TYR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.0000 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 20.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5007 Z= 0.175 Angle : 0.695 11.533 6803 Z= 0.335 Chirality : 0.044 0.176 710 Planarity : 0.003 0.032 881 Dihedral : 4.808 18.452 642 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.85 % Allowed : 27.89 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.19 (0.37), residues: 595 helix: 0.20 (0.29), residues: 345 sheet: -1.73 (1.34), residues: 12 loop : -0.32 (0.45), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 271 HIS 0.007 0.001 HIS A 239 PHE 0.010 0.001 PHE A 390 TYR 0.038 0.002 TYR A 521 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8711 (m-30) cc_final: 0.8128 (p0) REVERT: A 152 MET cc_start: 0.7695 (mmm) cc_final: 0.7233 (mmp) REVERT: A 228 HIS cc_start: 0.8817 (t70) cc_final: 0.7944 (t70) REVERT: A 237 TYR cc_start: 0.7432 (t80) cc_final: 0.6784 (t80) REVERT: A 481 LYS cc_start: 0.6282 (pttt) cc_final: 0.5578 (pttm) REVERT: A 525 PHE cc_start: 0.7616 (m-10) cc_final: 0.7105 (m-80) REVERT: A 541 LYS cc_start: 0.8077 (mttt) cc_final: 0.7677 (ptpt) REVERT: A 568 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 572 ASN cc_start: 0.8739 (m110) cc_final: 0.8170 (m-40) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.1488 time to fit residues: 20.2210 Evaluate side-chains 99 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5007 Z= 0.197 Angle : 0.697 10.891 6803 Z= 0.340 Chirality : 0.045 0.152 710 Planarity : 0.004 0.033 881 Dihedral : 4.792 18.210 642 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.66 % Allowed : 29.03 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.21 (0.36), residues: 595 helix: 0.21 (0.29), residues: 340 sheet: -1.61 (1.36), residues: 12 loop : -0.38 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 271 HIS 0.011 0.001 HIS A 239 PHE 0.009 0.001 PHE A 390 TYR 0.035 0.002 TYR A 521 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9295 (mttt) cc_final: 0.8936 (mmtt) REVERT: A 62 MET cc_start: 0.8729 (ptm) cc_final: 0.8385 (ptt) REVERT: A 67 ASP cc_start: 0.8708 (m-30) cc_final: 0.8120 (p0) REVERT: A 168 TRP cc_start: 0.7825 (t-100) cc_final: 0.7493 (t-100) REVERT: A 228 HIS cc_start: 0.8815 (t70) cc_final: 0.7933 (t70) REVERT: A 237 TYR cc_start: 0.7433 (t80) cc_final: 0.6674 (t80) REVERT: A 271 TRP cc_start: 0.6729 (m100) cc_final: 0.6375 (m100) REVERT: A 481 LYS cc_start: 0.6432 (pttt) cc_final: 0.4882 (pttt) REVERT: A 525 PHE cc_start: 0.7675 (m-10) cc_final: 0.7109 (m-80) REVERT: A 541 LYS cc_start: 0.8127 (mttt) cc_final: 0.7710 (ptpt) REVERT: A 568 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7666 (tt) REVERT: A 572 ASN cc_start: 0.8758 (m110) cc_final: 0.8153 (m-40) REVERT: A 595 LEU cc_start: 0.8390 (mm) cc_final: 0.7979 (mm) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.1566 time to fit residues: 20.6289 Evaluate side-chains 99 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5007 Z= 0.176 Angle : 0.708 11.282 6803 Z= 0.342 Chirality : 0.046 0.341 710 Planarity : 0.003 0.030 881 Dihedral : 4.676 17.817 642 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.85 % Allowed : 28.46 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.14 (0.36), residues: 595 helix: 0.21 (0.29), residues: 337 sheet: -1.49 (1.38), residues: 12 loop : -0.26 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 271 HIS 0.010 0.001 HIS A 239 PHE 0.011 0.001 PHE A 390 TYR 0.038 0.002 TYR A 521 ARG 0.002 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1190 Ramachandran restraints generated. 595 Oldfield, 0 Emsley, 595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9295 (mttt) cc_final: 0.8938 (mmtt) REVERT: A 62 MET cc_start: 0.8706 (ptm) cc_final: 0.8363 (ptt) REVERT: A 67 ASP cc_start: 0.8648 (m-30) cc_final: 0.8266 (m-30) REVERT: A 152 MET cc_start: 0.7895 (mmp) cc_final: 0.7194 (mmp) REVERT: A 168 TRP cc_start: 0.7843 (t-100) cc_final: 0.7296 (t-100) REVERT: A 228 HIS cc_start: 0.8805 (t70) cc_final: 0.7931 (t70) REVERT: A 237 TYR cc_start: 0.7380 (t80) cc_final: 0.6697 (t80) REVERT: A 271 TRP cc_start: 0.6613 (m100) cc_final: 0.6403 (m100) REVERT: A 476 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8059 (mmmt) REVERT: A 481 LYS cc_start: 0.6410 (pttt) cc_final: 0.5749 (pttm) REVERT: A 525 PHE cc_start: 0.7661 (m-10) cc_final: 0.7131 (m-80) REVERT: A 541 LYS cc_start: 0.8077 (mttt) cc_final: 0.7669 (ptpt) REVERT: A 568 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7656 (tt) REVERT: A 572 ASN cc_start: 0.8720 (m110) cc_final: 0.8141 (m-40) REVERT: A 584 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7273 (tp) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.1629 time to fit residues: 21.0005 Evaluate side-chains 100 residues out of total 527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 477 TRP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 0.0070 overall best weight: 1.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.132487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.113833 restraints weight = 15959.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.116926 restraints weight = 10343.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.118820 restraints weight = 7456.254| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5007 Z= 0.184 Angle : 0.709 11.047 6803 Z= 0.345 Chirality : 0.046 0.257 710 Planarity : 0.003 0.029 881 Dihedral : 4.669 19.886 642 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.47 % Allowed : 29.03 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.13 (0.36), residues: 595 helix: 0.19 (0.29), residues: 342 sheet: -1.44 (1.38), residues: 12 loop : -0.21 (0.45), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 271 HIS 0.013 0.002 HIS A 417 PHE 0.011 0.001 PHE A 390 TYR 0.036 0.002 TYR A 521 ARG 0.003 0.000 ARG A 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.76 seconds wall clock time: 23 minutes 16.44 seconds (1396.44 seconds total)