Starting phenix.real_space_refine on Sat Dec 9 07:51:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/12_2023/7pmy_13544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/12_2023/7pmy_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_13544/12_2023/7pmy_13544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/12_2023/7pmy_13544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/12_2023/7pmy_13544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmy_13544/12_2023/7pmy_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-1.21rc1-5172/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: 5.06, 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: 8.29 Conformation dependent library (CDL) restraints added in 1.1 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: 0.99 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: 4.07 Time building geometry restraints manager: 8.41 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: 4627 15.36 - 30.72: 201 30.72 - 46.09: 59 46.09 - 61.45: 17 61.45 - 76.81: 4 Dihedral angle restraints: 4908 sinusoidal: 2539 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 4905 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: 0.730 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: 4.040 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 37.620 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- 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 : 0.862 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 outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 0.3855 time to fit residues: 45.4234 Evaluate side-chains 66 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3901 time to fit residues: 3.3484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.8045 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5355 Z= 0.278 Angle : 0.572 4.786 7278 Z= 0.324 Chirality : 0.041 0.142 832 Planarity : 0.005 0.065 906 Dihedral : 4.284 17.259 706 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.75 % Favored : 96.95 % Rotamer: Outliers : 1.05 % Allowed : 8.42 % Favored : 90.53 % 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: 0.34 (0.32), residues: 655 helix: 0.93 (0.27), residues: 353 sheet: -0.03 (0.51), residues: 91 loop : -0.73 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 596 HIS 0.004 0.001 HIS A 479 PHE 0.011 0.001 PHE A 466 TYR 0.023 0.001 TYR A 121 ARG 0.006 0.001 ARG A 518 *********************** 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 67 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.791 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 outliers start: 6 outliers final: 5 residues processed: 65 average time/residue: 0.3434 time to fit residues: 30.3469 Evaluate side-chains 60 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.809 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1230 time to fit residues: 2.0912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.0060 chunk 18 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5355 Z= 0.197 Angle : 0.505 4.688 7278 Z= 0.279 Chirality : 0.039 0.140 832 Planarity : 0.004 0.055 906 Dihedral : 4.251 18.736 706 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.35 % Allowed : 8.95 % 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: 0.44 (0.32), residues: 655 helix: 1.08 (0.27), residues: 351 sheet: 0.04 (0.52), residues: 91 loop : -0.81 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 596 HIS 0.002 0.001 HIS A 479 PHE 0.016 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.002 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 66 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.788 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 outliers start: 2 outliers final: 2 residues processed: 66 average time/residue: 0.3481 time to fit residues: 30.9290 Evaluate side-chains 59 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.986 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1232 time to fit residues: 1.4788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2802 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= 0.205 Angle : 0.502 5.970 7278 Z= 0.274 Chirality : 0.039 0.163 832 Planarity : 0.004 0.049 906 Dihedral : 4.218 19.160 706 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.88 % Allowed : 9.12 % 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: 0.43 (0.32), residues: 655 helix: 1.27 (0.28), residues: 342 sheet: 0.01 (0.50), 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 0.002 0.001 HIS A 479 PHE 0.014 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.003 0.000 ARG A 180 *********************** 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 62 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.907 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 outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.3404 time to fit residues: 28.4577 Evaluate side-chains 60 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.967 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1363 time to fit residues: 2.0381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 32 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3002 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= 0.256 Angle : 0.511 5.633 7278 Z= 0.279 Chirality : 0.038 0.141 832 Planarity : 0.004 0.046 906 Dihedral : 4.226 19.204 706 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.88 % Allowed : 9.47 % Favored : 89.65 % 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: 0.41 (0.32), residues: 655 helix: 1.18 (0.28), residues: 345 sheet: -0.21 (0.48), residues: 98 loop : -0.91 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.004 0.001 HIS A 125 PHE 0.013 0.001 PHE A 261 TYR 0.022 0.001 TYR A 121 ARG 0.002 0.000 ARG A 180 *********************** 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 63 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 0.3624 time to fit residues: 30.1950 Evaluate side-chains 56 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.821 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1376 time to fit residues: 1.7740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5355 Z= 0.161 Angle : 0.496 7.097 7278 Z= 0.265 Chirality : 0.038 0.142 832 Planarity : 0.004 0.044 906 Dihedral : 4.116 18.586 706 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.23 % Allowed : 9.82 % Favored : 88.95 % 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: 0.54 (0.32), residues: 655 helix: 1.36 (0.28), residues: 342 sheet: -0.07 (0.48), residues: 98 loop : -1.01 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.003 0.000 HIS A 87 PHE 0.013 0.001 PHE A 261 TYR 0.018 0.001 TYR A 121 ARG 0.006 0.001 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 61 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.849 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: 7 outliers final: 6 residues processed: 59 average time/residue: 0.2915 time to fit residues: 24.4191 Evaluate side-chains 57 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.762 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1306 time to fit residues: 2.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3415 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= 0.235 Angle : 0.504 5.946 7278 Z= 0.272 Chirality : 0.038 0.159 832 Planarity : 0.004 0.043 906 Dihedral : 4.133 18.487 706 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.18 % Allowed : 10.53 % Favored : 89.30 % 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: 0.54 (0.32), residues: 655 helix: 1.32 (0.28), residues: 342 sheet: 0.09 (0.46), residues: 104 loop : -1.05 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.002 0.001 HIS A 467 PHE 0.012 0.001 PHE A 261 TYR 0.020 0.001 TYR A 121 ARG 0.002 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 55 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 55 average time/residue: 0.3221 time to fit residues: 25.4137 Evaluate side-chains 51 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 1.094 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1284 time to fit residues: 1.3179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 42 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- 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: 0.3552 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= 0.152 Angle : 0.480 6.169 7278 Z= 0.255 Chirality : 0.038 0.147 832 Planarity : 0.004 0.042 906 Dihedral : 4.010 17.928 706 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.53 % Allowed : 11.40 % 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: 0.76 (0.32), residues: 655 helix: 1.49 (0.28), residues: 344 sheet: 0.22 (0.46), residues: 104 loop : -0.98 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.003 0.001 HIS A 87 PHE 0.013 0.001 PHE A 261 TYR 0.018 0.001 TYR A 121 ARG 0.002 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 60 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.904 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 outliers start: 3 outliers final: 3 residues processed: 58 average time/residue: 0.3399 time to fit residues: 26.8764 Evaluate side-chains 58 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.854 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1302 time to fit residues: 1.7279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5355 Z= 0.296 Angle : 0.520 5.986 7278 Z= 0.283 Chirality : 0.039 0.146 832 Planarity : 0.004 0.042 906 Dihedral : 4.120 18.705 706 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.70 % Allowed : 10.88 % 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: 0.63 (0.32), residues: 655 helix: 1.34 (0.28), residues: 347 sheet: 0.16 (0.45), residues: 104 loop : -0.98 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.003 0.001 HIS A 467 PHE 0.011 0.001 PHE A 261 TYR 0.024 0.001 TYR A 121 ARG 0.002 0.000 ARG A 180 *********************** 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 59 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.938 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: 4 outliers final: 3 residues processed: 59 average time/residue: 0.3363 time to fit residues: 27.6604 Evaluate side-chains 56 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.759 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1256 time to fit residues: 1.6336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 51 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7998 moved from start: 0.3715 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= 0.161 Angle : 0.503 9.909 7278 Z= 0.265 Chirality : 0.038 0.183 832 Planarity : 0.004 0.042 906 Dihedral : 4.026 17.972 706 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.53 % Allowed : 12.11 % 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: 0.68 (0.32), residues: 655 helix: 1.42 (0.28), residues: 345 sheet: 0.18 (0.45), residues: 104 loop : -1.02 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 596 HIS 0.003 0.001 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 58 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.796 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: 3 outliers final: 3 residues processed: 58 average time/residue: 0.3406 time to fit residues: 27.0572 Evaluate side-chains 57 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.856 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1291 time to fit residues: 1.7243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.139201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.102618 restraints weight = 33405.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101662 restraints weight = 24420.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103387 restraints weight = 21067.061| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5355 Z= 0.227 Angle : 0.507 9.325 7278 Z= 0.271 Chirality : 0.038 0.171 832 Planarity : 0.004 0.042 906 Dihedral : 4.050 18.092 706 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.18 % Allowed : 12.28 % 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: 0.59 (0.32), residues: 655 helix: 1.38 (0.28), residues: 344 sheet: 0.15 (0.44), residues: 104 loop : -1.10 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 596 HIS 0.002 0.000 HIS A 467 PHE 0.012 0.001 PHE A 261 TYR 0.021 0.001 TYR A 121 ARG 0.002 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2676.87 seconds wall clock time: 48 minutes 17.75 seconds (2897.75 seconds total)