Starting phenix.real_space_refine on Fri Mar 15 03:14:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/03_2024/7pmy_13544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/03_2024/7pmy_13544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/03_2024/7pmy_13544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/03_2024/7pmy_13544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/03_2024/7pmy_13544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/03_2024/7pmy_13544.pdb" } resolution = 3.8 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= 1.000 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3425 2.51 5 N 845 2.21 5 O 924 1.98 5 H 5276 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10499 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10466 Classifications: {'peptide': 657} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 632} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 5.09, per 1000 atoms: 0.48 Number of scatterers: 10499 At special positions: 0 Unit cell: (85.85, 82.45, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 924 8.00 N 845 7.00 C 3425 6.00 H 5276 1.00 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: 9.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1238 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 62.5% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 41 through 46 removed outlier: 4.142A pdb=" N ILE A 46 " --> pdb=" O TYR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.630A pdb=" N VAL A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 78 through 95 Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.073A pdb=" N TRP A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.706A pdb=" N GLY A 137 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 171 removed outlier: 3.988A pdb=" N VAL A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.627A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 208 Proline residue: A 203 - end of helix removed outlier: 3.828A pdb=" N GLY A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 4.082A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.750A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 249 through 270 removed outlier: 4.671A pdb=" N ALA A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.734A pdb=" N TRP A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 304 removed outlier: 3.629A pdb=" N VAL A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 Proline residue: A 308 - end of helix No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.754A pdb=" N TRP A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 315 " --> pdb=" O MET A 311 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 removed outlier: 4.706A pdb=" N THR A 324 " --> pdb=" O GLY A 320 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.521A pdb=" N ILE A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Proline residue: A 357 - end of helix removed outlier: 7.533A pdb=" N ASP A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 372 through 376 removed outlier: 4.149A pdb=" N SER A 376 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 405 removed outlier: 3.631A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 Processing helix chain 'A' and resid 611 through 637 removed outlier: 3.762A pdb=" N TYR A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR A 628 " --> pdb=" O MET A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 667 removed outlier: 3.763A pdb=" N LEU A 645 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 650 " --> pdb=" O GLN A 646 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 660 " --> pdb=" O GLY A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 removed outlier: 3.617A pdb=" N ILE A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA2, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443 removed outlier: 3.605A pdb=" N LEU A 439 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 removed outlier: 6.558A pdb=" N THR A 516 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE A 583 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 518 " --> pdb=" O PHE A 583 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 585 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 520 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ASN A 587 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 580 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 537 through 539 removed outlier: 4.031A pdb=" N HIS A 560 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 333 hydrogen bonds defined for protein. 936 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: 3.80 Time building geometry restraints manager: 9.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5265 1.03 - 1.23: 11 1.23 - 1.42: 2276 1.42 - 1.61: 3032 1.61 - 1.81: 47 Bond restraints: 10631 Sorted by residual: bond pdb=" N ASN A 41 " pdb=" CA ASN A 41 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ASN A 41 " pdb=" H ASN A 41 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" CA VAL A 430 " pdb=" CB VAL A 430 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 1.02e+00 bond pdb=" CA HIS A 176 " pdb=" C HIS A 176 " ideal model delta sigma weight residual 1.531 1.522 0.009 1.12e-02 7.97e+03 7.14e-01 bond pdb=" CA ILE A 307 " pdb=" CB ILE A 307 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.08e-01 ... (remaining 10626 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.32: 283 107.32 - 113.97: 12541 113.97 - 120.63: 3732 120.63 - 127.28: 2605 127.28 - 133.93: 60 Bond angle restraints: 19221 Sorted by residual: angle pdb=" N ILE A 354 " pdb=" CA ILE A 354 " pdb=" C ILE A 354 " ideal model delta sigma weight residual 112.96 109.35 3.61 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N HIS A 524 " pdb=" CA HIS A 524 " pdb=" C HIS A 524 " ideal model delta sigma weight residual 112.93 110.07 2.86 1.12e+00 7.97e-01 6.54e+00 angle pdb=" N SER A 640 " pdb=" CA SER A 640 " pdb=" CB SER A 640 " ideal model delta sigma weight residual 113.65 110.20 3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" N ARG A 509 " pdb=" CA ARG A 509 " pdb=" C ARG A 509 " ideal model delta sigma weight residual 114.56 111.70 2.86 1.27e+00 6.20e-01 5.06e+00 angle pdb=" C PHE A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta sigma weight residual 122.97 120.99 1.98 9.80e-01 1.04e+00 4.10e+00 ... (remaining 19216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.36: 4663 15.36 - 30.72: 212 30.72 - 46.09: 73 46.09 - 61.45: 63 61.45 - 76.81: 4 Dihedral angle restraints: 5015 sinusoidal: 2646 harmonic: 2369 Sorted by residual: dihedral pdb=" CA LYS A 244 " pdb=" CB LYS A 244 " pdb=" CG LYS A 244 " pdb=" CD LYS A 244 " ideal model delta sinusoidal sigma weight residual 180.00 -120.50 -59.50 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LEU A 309 " pdb=" C LEU A 309 " pdb=" N PRO A 310 " pdb=" CA PRO A 310 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" N HIS A 125 " pdb=" CA HIS A 125 " pdb=" CB HIS A 125 " pdb=" CG HIS A 125 " ideal model delta sinusoidal sigma weight residual -180.00 -127.17 -52.83 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 5012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 578 0.029 - 0.058: 159 0.058 - 0.088: 59 0.088 - 0.117: 32 0.117 - 0.146: 4 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ILE A 356 " pdb=" N ILE A 356 " pdb=" C ILE A 356 " pdb=" CB ILE A 356 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA ILE A 598 " pdb=" N ILE A 598 " pdb=" C ILE A 598 " pdb=" CB ILE A 598 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 829 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 601 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 602 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 307 " 0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 308 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 309 " -0.016 5.00e-02 4.00e+02 2.37e-02 8.95e-01 pdb=" N PRO A 310 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.013 5.00e-02 4.00e+02 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 885 2.23 - 2.82: 23188 2.82 - 3.41: 28626 3.41 - 4.01: 37576 4.01 - 4.60: 57865 Nonbonded interactions: 148140 Sorted by model distance: nonbonded pdb=" OE2 GLU A 507 " pdb=" H THR A 510 " model vdw 1.631 1.850 nonbonded pdb=" H GLN A 412 " pdb=" OE1 GLU A 483 " model vdw 1.640 1.850 nonbonded pdb=" HE ARG A 266 " pdb=" OE1 GLN A 278 " model vdw 1.654 1.850 nonbonded pdb=" OD2 ASP A 317 " pdb="HD22 ASN A 657 " model vdw 1.655 1.850 nonbonded pdb="HH22 ARG A 277 " pdb=" OE2 GLU A 286 " model vdw 1.659 1.850 ... (remaining 148135 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: 1.380 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: 0.150 Extract box with map and model: 4.010 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 38.040 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.002 0.033 5355 Z= 0.147 Angle : 0.460 4.606 7278 Z= 0.276 Chirality : 0.036 0.146 832 Planarity : 0.003 0.031 906 Dihedral : 9.150 67.769 1896 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.98 % Favored : 97.86 % Rotamer: Outliers : 1.40 % Allowed : 3.51 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.55 (0.33), residues: 655 helix: 0.76 (0.29), residues: 336 sheet: 0.40 (0.51), residues: 104 loop : -0.08 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 313 HIS 0.001 0.000 HIS A 467 PHE 0.007 0.001 PHE A 172 TYR 0.010 0.001 TYR A 121 ARG 0.002 0.000 ARG A 562 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 85 time to evaluate : 0.893 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9282 (tp) cc_final: 0.8998 (tt) outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.3791 time to fit residues: 44.4398 Evaluate side-chains 67 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5355 Z= 0.295 Angle : 0.583 4.939 7278 Z= 0.327 Chirality : 0.040 0.140 832 Planarity : 0.005 0.065 906 Dihedral : 6.134 58.252 718 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.75 % Favored : 96.95 % Rotamer: Outliers : 2.11 % Allowed : 7.19 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.25 (0.32), residues: 655 helix: 0.85 (0.27), residues: 353 sheet: -0.06 (0.52), residues: 91 loop : -0.74 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 596 HIS 0.003 0.001 HIS A 479 PHE 0.014 0.002 PHE A 391 TYR 0.025 0.001 TYR A 121 ARG 0.007 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 63 time to evaluate : 0.967 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9171 (tp) cc_final: 0.8923 (tt) outliers start: 12 outliers final: 10 residues processed: 72 average time/residue: 0.3638 time to fit residues: 35.1652 Evaluate side-chains 65 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 55 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5355 Z= 0.168 Angle : 0.502 4.844 7278 Z= 0.274 Chirality : 0.039 0.139 832 Planarity : 0.004 0.054 906 Dihedral : 6.016 59.386 718 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.58 % Allowed : 8.42 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.37 (0.32), residues: 655 helix: 1.17 (0.27), residues: 342 sheet: 0.02 (0.51), residues: 91 loop : -1.05 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 PHE 0.017 0.001 PHE A 261 TYR 0.018 0.001 TYR A 121 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.768 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9143 (tp) cc_final: 0.8928 (tt) outliers start: 9 outliers final: 9 residues processed: 70 average time/residue: 0.3558 time to fit residues: 32.9070 Evaluate side-chains 65 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5355 Z= 0.202 Angle : 0.501 5.860 7278 Z= 0.272 Chirality : 0.039 0.146 832 Planarity : 0.004 0.048 906 Dihedral : 5.948 59.120 718 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.93 % Allowed : 10.00 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.45 (0.32), residues: 655 helix: 1.27 (0.27), residues: 342 sheet: 0.04 (0.50), residues: 91 loop : -1.08 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.002 0.001 HIS A 87 PHE 0.014 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.857 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9132 (tp) cc_final: 0.8908 (tt) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.3706 time to fit residues: 31.9197 Evaluate side-chains 64 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 20.0000 chunk 32 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5355 Z= 0.210 Angle : 0.490 5.701 7278 Z= 0.267 Chirality : 0.038 0.140 832 Planarity : 0.004 0.046 906 Dihedral : 5.802 59.056 717 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 9.65 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.47 (0.32), residues: 655 helix: 1.30 (0.28), residues: 342 sheet: 0.10 (0.49), residues: 91 loop : -1.12 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.002 0.001 HIS A 87 PHE 0.013 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.001 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.802 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: symmetry clash REVERT: A 582 LEU cc_start: 0.9123 (tp) cc_final: 0.8889 (tt) REVERT: A 692 MET cc_start: 0.7655 (ttm) cc_final: 0.7450 (ttt) outliers start: 11 outliers final: 11 residues processed: 67 average time/residue: 0.3661 time to fit residues: 32.6227 Evaluate side-chains 63 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5355 Z= 0.156 Angle : 0.485 6.338 7278 Z= 0.260 Chirality : 0.038 0.162 832 Planarity : 0.004 0.044 906 Dihedral : 5.743 59.517 717 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.28 % Allowed : 10.35 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.66 (0.32), residues: 655 helix: 1.47 (0.28), residues: 342 sheet: 0.24 (0.48), residues: 91 loop : -1.09 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.013 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.006 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.684 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9110 (tp) cc_final: 0.8877 (tt) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 0.3215 time to fit residues: 29.7058 Evaluate side-chains 65 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5355 Z= 0.227 Angle : 0.496 5.895 7278 Z= 0.269 Chirality : 0.038 0.163 832 Planarity : 0.004 0.043 906 Dihedral : 5.757 58.871 717 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.11 % Allowed : 10.35 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.57 (0.32), residues: 655 helix: 1.37 (0.28), residues: 342 sheet: 0.26 (0.47), residues: 91 loop : -1.12 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.002 0.001 HIS A 467 PHE 0.012 0.001 PHE A 261 TYR 0.022 0.001 TYR A 121 ARG 0.004 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.918 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 180 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7623 (tpp-160) REVERT: A 416 LEU cc_start: 0.8757 (tp) cc_final: 0.8431 (tt) REVERT: A 582 LEU cc_start: 0.9115 (tp) cc_final: 0.8892 (tt) outliers start: 12 outliers final: 11 residues processed: 63 average time/residue: 0.3201 time to fit residues: 27.7050 Evaluate side-chains 63 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5355 Z= 0.196 Angle : 0.485 6.680 7278 Z= 0.262 Chirality : 0.038 0.167 832 Planarity : 0.004 0.043 906 Dihedral : 5.737 59.074 717 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.28 % Allowed : 10.35 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.66 (0.32), residues: 655 helix: 1.43 (0.28), residues: 344 sheet: 0.10 (0.45), residues: 104 loop : -1.00 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.002 0.001 HIS A 87 PHE 0.012 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.003 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 52 time to evaluate : 0.935 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: symmetry clash REVERT: A 180 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7661 (tpp-160) outliers start: 13 outliers final: 11 residues processed: 63 average time/residue: 0.3511 time to fit residues: 29.5788 Evaluate side-chains 65 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5355 Z= 0.243 Angle : 0.498 6.060 7278 Z= 0.271 Chirality : 0.039 0.160 832 Planarity : 0.004 0.042 906 Dihedral : 5.741 58.527 717 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.11 % Allowed : 10.35 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.65 (0.32), residues: 655 helix: 1.36 (0.28), residues: 347 sheet: 0.12 (0.45), residues: 104 loop : -0.94 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.002 0.001 HIS A 467 PHE 0.012 0.001 PHE A 261 TYR 0.022 0.001 TYR A 121 ARG 0.002 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 2.357 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 180 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7656 (tpp-160) outliers start: 12 outliers final: 11 residues processed: 62 average time/residue: 0.3484 time to fit residues: 29.3940 Evaluate side-chains 62 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5355 Z= 0.160 Angle : 0.492 10.419 7278 Z= 0.258 Chirality : 0.038 0.185 832 Planarity : 0.004 0.042 906 Dihedral : 5.697 59.226 717 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.11 % Allowed : 10.88 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.73 (0.32), residues: 655 helix: 1.48 (0.28), residues: 345 sheet: 0.16 (0.44), residues: 104 loop : -1.00 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.013 0.001 PHE A 261 TYR 0.019 0.001 TYR A 121 ARG 0.002 0.000 ARG A 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1310 Ramachandran restraints generated. 655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.820 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: symmetry clash outliers start: 12 outliers final: 12 residues processed: 65 average time/residue: 0.3389 time to fit residues: 29.4830 Evaluate side-chains 62 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 488 SER Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.139878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104356 restraints weight = 33347.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103570 restraints weight = 24138.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105364 restraints weight = 20355.358| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5355 Z= 0.189 Angle : 0.495 9.511 7278 Z= 0.261 Chirality : 0.038 0.172 832 Planarity : 0.004 0.041 906 Dihedral : 5.675 59.215 717 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.11 % Allowed : 11.58 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.74 (0.32), residues: 655 helix: 1.47 (0.28), residues: 346 sheet: 0.24 (0.45), residues: 104 loop : -1.02 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 596 HIS 0.002 0.000 HIS A 87 PHE 0.012 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.002 0.000 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2755.45 seconds wall clock time: 49 minutes 0.10 seconds (2940.10 seconds total)