Starting phenix.real_space_refine on Sun Mar 10 21:33:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/03_2024/7vgg_31968.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/03_2024/7vgg_31968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/03_2024/7vgg_31968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/03_2024/7vgg_31968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/03_2024/7vgg_31968.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/03_2024/7vgg_31968.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3298 2.51 5 N 940 2.21 5 O 1010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 383": "OD1" <-> "OD2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 399": "OD1" <-> "OD2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 260": "OD1" <-> "OD2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B ASP 367": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5274 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2417 Classifications: {'peptide': 304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2857 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 12, 'TRANS': 363} Chain breaks: 1 Time building chain proxies: 3.26, per 1000 atoms: 0.62 Number of scatterers: 5274 At special positions: 0 Unit cell: (64.506, 66.16, 91.797, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1010 8.00 N 940 7.00 C 3298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 858.3 milliseconds 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 14 sheets defined 4.9% alpha, 38.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 99 removed outlier: 3.946A pdb=" N GLY B 98 " --> pdb=" O GLY B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 118 Processing helix chain 'B' and resid 167 through 170 Processing helix chain 'B' and resid 271 through 274 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.548A pdb=" N GLN B 328 " --> pdb=" O PRO B 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 362 removed outlier: 5.102A pdb=" N LEU A 356 " --> pdb=" O ALA A 674 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA A 674 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL A 358 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A 672 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 360 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 670 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N THR A 658 " --> pdb=" O TRP A 652 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TRP A 652 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 660 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 650 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA A 662 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 374 through 379 removed outlier: 4.458A pdb=" N GLY A 390 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N CYS A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 428 removed outlier: 3.689A pdb=" N CYS A 425 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP A 449 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER A 455 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 471 removed outlier: 3.866A pdb=" N LYS A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N CYS A 492 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N SER A 498 " --> pdb=" O CYS A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.306A pdb=" N TYR A 520 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 552 through 557 removed outlier: 4.060A pdb=" N THR A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG A 584 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP A 576 " --> pdb=" O PRO A 582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600 Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 22 removed outlier: 6.443A pdb=" N LEU B 30 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE B 20 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 28 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA B 22 " --> pdb=" O HIS B 26 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL B 36 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 59 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER B 38 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 57 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 74 Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 127 removed outlier: 6.480A pdb=" N VAL B 135 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 125 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 133 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N CYS B 127 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N HIS B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY B 145 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL B 162 " --> pdb=" O GLY B 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.132A pdb=" N GLY B 195 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 214 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 231 removed outlier: 6.208A pdb=" N THR B 247 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE B 266 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.738A pdb=" N LEU B 297 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY B 301 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N SER B 318 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 330 through 335 removed outlier: 6.703A pdb=" N VAL B 349 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS B 372 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ALA B 351 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B 370 " --> pdb=" O ALA B 351 " (cutoff:3.500A) 156 hydrogen bonds defined for protein. 402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1768 1.34 - 1.46: 1118 1.46 - 1.57: 2471 1.57 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 5394 Sorted by residual: bond pdb=" C SER B 282 " pdb=" N GLY B 283 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.46e-02 4.69e+03 8.69e-01 bond pdb=" C ARG B 55 " pdb=" O ARG B 55 " ideal model delta sigma weight residual 1.244 1.235 0.008 9.30e-03 1.16e+04 8.00e-01 bond pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta sigma weight residual 1.447 1.437 0.010 1.23e-02 6.61e+03 7.17e-01 bond pdb=" CB ASN B 203 " pdb=" CG ASN B 203 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.09e-01 bond pdb=" CG1 ILE B 174 " pdb=" CD1 ILE B 174 " ideal model delta sigma weight residual 1.513 1.486 0.027 3.90e-02 6.57e+02 4.88e-01 ... (remaining 5389 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.83: 145 106.83 - 113.65: 2978 113.65 - 120.46: 1927 120.46 - 127.27: 2178 127.27 - 134.09: 83 Bond angle restraints: 7311 Sorted by residual: angle pdb=" CA VAL B 214 " pdb=" C VAL B 214 " pdb=" N PRO B 215 " ideal model delta sigma weight residual 116.57 119.35 -2.78 9.80e-01 1.04e+00 8.07e+00 angle pdb=" N CYS A 651 " pdb=" CA CYS A 651 " pdb=" C CYS A 651 " ideal model delta sigma weight residual 107.93 112.41 -4.48 1.65e+00 3.67e-01 7.37e+00 angle pdb=" CA ARG A 623 " pdb=" C ARG A 623 " pdb=" N PRO A 624 " ideal model delta sigma weight residual 118.23 120.34 -2.11 9.20e-01 1.18e+00 5.26e+00 angle pdb=" N LYS A 512 " pdb=" CA LYS A 512 " pdb=" C LYS A 512 " ideal model delta sigma weight residual 108.48 112.31 -3.83 1.80e+00 3.09e-01 4.54e+00 angle pdb=" N SER A 539 " pdb=" CA SER A 539 " pdb=" C SER A 539 " ideal model delta sigma weight residual 112.12 109.45 2.67 1.34e+00 5.57e-01 3.98e+00 ... (remaining 7306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 2860 16.37 - 32.75: 207 32.75 - 49.12: 59 49.12 - 65.49: 17 65.49 - 81.86: 3 Dihedral angle restraints: 3146 sinusoidal: 1222 harmonic: 1924 Sorted by residual: dihedral pdb=" CA ASP B 211 " pdb=" CB ASP B 211 " pdb=" CG ASP B 211 " pdb=" OD1 ASP B 211 " ideal model delta sinusoidal sigma weight residual -30.00 -89.70 59.70 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA VAL A 600 " pdb=" C VAL A 600 " pdb=" N ASN A 601 " pdb=" CA ASN A 601 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CG ARG B 323 " pdb=" CD ARG B 323 " pdb=" NE ARG B 323 " pdb=" CZ ARG B 323 " ideal model delta sinusoidal sigma weight residual -90.00 -132.10 42.10 2 1.50e+01 4.44e-03 9.59e+00 ... (remaining 3143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 405 0.029 - 0.057: 266 0.057 - 0.086: 47 0.086 - 0.115: 52 0.115 - 0.143: 23 Chirality restraints: 793 Sorted by residual: chirality pdb=" CA ILE A 377 " pdb=" N ILE A 377 " pdb=" C ILE A 377 " pdb=" CB ILE A 377 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 395 " pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CB ILE A 395 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" CA VAL A 488 " pdb=" N VAL A 488 " pdb=" C VAL A 488 " pdb=" CB VAL A 488 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 790 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 214 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO B 215 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 441 " 0.011 2.00e-02 2.50e+03 7.12e-03 1.01e+00 pdb=" CG TYR A 441 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 441 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 441 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 441 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 441 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 441 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 441 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 367 " 0.004 2.00e-02 2.50e+03 8.79e-03 7.72e-01 pdb=" CG ASP B 367 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASP B 367 " 0.005 2.00e-02 2.50e+03 pdb=" OD2 ASP B 367 " 0.005 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 78 2.60 - 3.18: 4496 3.18 - 3.75: 8230 3.75 - 4.33: 12727 4.33 - 4.90: 21579 Nonbonded interactions: 47110 Sorted by model distance: nonbonded pdb=" O VAL A 374 " pdb=" OG SER A 648 " model vdw 2.025 2.440 nonbonded pdb=" O ARG A 465 " pdb=" OG SER A 483 " model vdw 2.165 2.440 nonbonded pdb=" NH1 ARG A 420 " pdb=" OD2 ASP B 129 " model vdw 2.234 2.520 nonbonded pdb=" NH1 ARG A 584 " pdb=" O LYS A 619 " model vdw 2.241 2.520 nonbonded pdb=" O THR A 585 " pdb=" OG1 THR A 622 " model vdw 2.250 2.440 ... (remaining 47105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.930 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.690 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 0.004 0.029 5394 Z= 0.245 Angle : 0.566 4.478 7311 Z= 0.336 Chirality : 0.046 0.143 793 Planarity : 0.003 0.035 944 Dihedral : 13.319 81.864 1918 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.33), residues: 668 helix: -1.15 (1.64), residues: 13 sheet: -1.07 (0.30), residues: 247 loop : -0.02 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 302 HIS 0.005 0.001 HIS B 102 PHE 0.013 0.002 PHE A 630 TYR 0.016 0.001 TYR A 441 ARG 0.002 0.000 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.555 Fit side-chains REVERT: A 422 LYS cc_start: 0.8433 (mtmm) cc_final: 0.8220 (mtmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1869 time to fit residues: 17.8694 Evaluate side-chains 58 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 HIS B 102 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5394 Z= 0.255 Angle : 0.533 5.405 7311 Z= 0.286 Chirality : 0.048 0.145 793 Planarity : 0.004 0.046 944 Dihedral : 4.377 15.505 733 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.10 % Allowed : 5.59 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.33), residues: 668 helix: -0.82 (1.80), residues: 13 sheet: -0.79 (0.30), residues: 250 loop : 0.03 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.005 0.001 HIS B 287 PHE 0.011 0.002 PHE A 398 TYR 0.020 0.002 TYR A 617 ARG 0.003 0.000 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.665 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1827 time to fit residues: 16.6057 Evaluate side-chains 62 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 50 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 665 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5394 Z= 0.236 Angle : 0.493 4.727 7311 Z= 0.267 Chirality : 0.047 0.153 793 Planarity : 0.004 0.045 944 Dihedral : 4.229 15.226 733 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.10 % Allowed : 8.74 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.33), residues: 668 helix: -0.92 (1.74), residues: 13 sheet: -0.77 (0.31), residues: 243 loop : 0.10 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.004 0.001 HIS B 287 PHE 0.012 0.002 PHE A 398 TYR 0.021 0.001 TYR A 617 ARG 0.003 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.597 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 66 average time/residue: 0.1811 time to fit residues: 15.8610 Evaluate side-chains 64 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 228 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5394 Z= 0.335 Angle : 0.541 5.958 7311 Z= 0.290 Chirality : 0.049 0.154 793 Planarity : 0.004 0.046 944 Dihedral : 4.416 16.900 733 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.80 % Allowed : 10.84 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.33), residues: 668 helix: 2.31 (2.64), residues: 7 sheet: -0.80 (0.31), residues: 238 loop : -0.04 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.005 0.001 HIS B 287 PHE 0.012 0.002 PHE A 398 TYR 0.021 0.002 TYR A 617 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 51 time to evaluate : 0.650 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.1551 time to fit residues: 12.9605 Evaluate side-chains 61 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7880 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5394 Z= 0.170 Angle : 0.451 4.309 7311 Z= 0.246 Chirality : 0.046 0.149 793 Planarity : 0.003 0.046 944 Dihedral : 4.078 15.259 733 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.27 % Allowed : 12.59 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.33), residues: 668 helix: 2.78 (2.56), residues: 7 sheet: -0.68 (0.31), residues: 243 loop : 0.05 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.003 0.001 HIS B 183 PHE 0.013 0.001 PHE A 398 TYR 0.020 0.001 TYR A 617 ARG 0.002 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.558 Fit side-chains REVERT: A 593 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7628 (pttp) REVERT: B 156 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6659 (p0) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.1753 time to fit residues: 15.2288 Evaluate side-chains 63 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 53 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 156 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 0.0020 chunk 47 optimal weight: 6.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5394 Z= 0.179 Angle : 0.446 4.349 7311 Z= 0.244 Chirality : 0.046 0.151 793 Planarity : 0.003 0.045 944 Dihedral : 4.015 15.109 733 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.62 % Allowed : 12.94 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.33), residues: 668 helix: 2.96 (2.46), residues: 7 sheet: -0.61 (0.31), residues: 243 loop : 0.05 (0.33), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.004 0.001 HIS A 528 PHE 0.011 0.001 PHE A 398 TYR 0.019 0.001 TYR A 617 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 57 time to evaluate : 0.838 Fit side-chains REVERT: A 593 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7594 (pttp) REVERT: B 156 ASP cc_start: 0.7113 (OUTLIER) cc_final: 0.6637 (p0) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 0.1962 time to fit residues: 18.1512 Evaluate side-chains 64 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 53 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 203 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5394 Z= 0.394 Angle : 0.559 6.257 7311 Z= 0.300 Chirality : 0.050 0.156 793 Planarity : 0.004 0.047 944 Dihedral : 4.460 14.725 733 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.62 % Allowed : 13.81 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.33), residues: 668 helix: 2.70 (2.49), residues: 7 sheet: -0.84 (0.31), residues: 238 loop : -0.04 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 233 HIS 0.006 0.002 HIS B 183 PHE 0.012 0.002 PHE A 386 TYR 0.021 0.002 TYR A 617 ARG 0.004 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.606 Fit side-chains REVERT: A 593 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7605 (pttp) REVERT: B 156 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6716 (p0) REVERT: B 228 MET cc_start: 0.8426 (ptm) cc_final: 0.8210 (ptp) outliers start: 15 outliers final: 9 residues processed: 60 average time/residue: 0.1492 time to fit residues: 12.6188 Evaluate side-chains 62 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 203 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5394 Z= 0.218 Angle : 0.470 4.749 7311 Z= 0.256 Chirality : 0.047 0.158 793 Planarity : 0.004 0.048 944 Dihedral : 4.178 15.192 733 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.80 % Allowed : 13.81 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.33), residues: 668 helix: 2.99 (2.53), residues: 7 sheet: -0.79 (0.31), residues: 238 loop : 0.00 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 198 HIS 0.004 0.001 HIS B 287 PHE 0.012 0.001 PHE A 398 TYR 0.019 0.001 TYR A 617 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 0.601 Fit side-chains REVERT: A 593 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7556 (pttp) REVERT: B 156 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6713 (p0) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.1565 time to fit residues: 14.6968 Evaluate side-chains 68 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 203 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5394 Z= 0.255 Angle : 0.490 5.183 7311 Z= 0.265 Chirality : 0.047 0.151 793 Planarity : 0.004 0.047 944 Dihedral : 4.175 15.021 733 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.45 % Allowed : 13.99 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.33), residues: 668 helix: 2.93 (2.49), residues: 7 sheet: -0.82 (0.31), residues: 238 loop : -0.02 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.008 0.001 HIS A 543 PHE 0.011 0.002 PHE A 398 TYR 0.020 0.002 TYR A 617 ARG 0.003 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 54 time to evaluate : 0.645 Fit side-chains REVERT: A 593 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7532 (pttp) REVERT: B 156 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6714 (p0) outliers start: 14 outliers final: 10 residues processed: 59 average time/residue: 0.1580 time to fit residues: 13.2460 Evaluate side-chains 66 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 203 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 overall best weight: 0.6902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5394 Z= 0.187 Angle : 0.456 4.518 7311 Z= 0.248 Chirality : 0.046 0.153 793 Planarity : 0.003 0.046 944 Dihedral : 4.011 15.137 733 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.80 % Allowed : 13.81 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.33), residues: 668 helix: 3.04 (2.42), residues: 7 sheet: -0.72 (0.31), residues: 244 loop : 0.06 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 198 HIS 0.007 0.001 HIS A 543 PHE 0.011 0.001 PHE A 398 TYR 0.018 0.001 TYR A 617 ARG 0.003 0.000 ARG B 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.587 Fit side-chains REVERT: B 156 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6701 (p0) outliers start: 16 outliers final: 9 residues processed: 65 average time/residue: 0.1459 time to fit residues: 13.3405 Evaluate side-chains 67 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 412 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 523 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 409 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.164388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.139160 restraints weight = 6168.701| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.05 r_work: 0.3558 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5394 Z= 0.251 Angle : 0.485 5.049 7311 Z= 0.262 Chirality : 0.047 0.150 793 Planarity : 0.004 0.047 944 Dihedral : 4.133 14.956 733 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.45 % Allowed : 13.99 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.33), residues: 668 helix: 2.91 (2.48), residues: 7 sheet: -0.77 (0.30), residues: 244 loop : 0.05 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 198 HIS 0.008 0.001 HIS A 543 PHE 0.010 0.001 PHE A 398 TYR 0.019 0.002 TYR A 617 ARG 0.003 0.000 ARG B 338 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.04 seconds wall clock time: 29 minutes 14.55 seconds (1754.55 seconds total)