Starting phenix.real_space_refine on Mon Nov 13 21:05:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/11_2023/7vgg_31968.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/11_2023/7vgg_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_31968/11_2023/7vgg_31968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/11_2023/7vgg_31968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/11_2023/7vgg_31968.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vgg_31968/11_2023/7vgg_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-1.21rc1-5144/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: 3.02, per 1000 atoms: 0.57 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: 1.58 Conformation dependent library (CDL) restraints added in 788.8 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: 0.62 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: 2.00 Time building geometry restraints manager: 1.74 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: 1.190 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: 4.830 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 17.770 Find NCS groups from input model: 0.130 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.640 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.597 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1960 time to fit residues: 18.7841 Evaluate side-chains 57 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8261 ------------------------------------------------------------------------------- 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: 0.7898 moved from start: 0.1081 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= 0.259 Angle : 0.531 5.186 7311 Z= 0.286 Chirality : 0.048 0.147 793 Planarity : 0.004 0.046 944 Dihedral : 4.369 15.617 733 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.92 % Allowed : 5.94 % Favored : 92.13 % 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: -0.58 (0.33), residues: 668 helix: -0.83 (1.80), residues: 13 sheet: -0.76 (0.30), residues: 249 loop : 0.02 (0.33), residues: 406 *********************** 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 76 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.534 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 68 average time/residue: 0.1776 time to fit residues: 16.1284 Evaluate side-chains 61 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.654 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0559 time to fit residues: 1.4884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5394 Z= 0.415 Angle : 0.597 6.693 7311 Z= 0.318 Chirality : 0.050 0.157 793 Planarity : 0.004 0.053 944 Dihedral : 4.636 17.300 733 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.22 % Allowed : 9.44 % Favored : 89.34 % 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: -0.68 (0.33), residues: 668 helix: -1.10 (1.67), residues: 13 sheet: -0.88 (0.31), residues: 238 loop : -0.04 (0.33), residues: 417 *********************** 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 65 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.615 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 62 average time/residue: 0.1977 time to fit residues: 15.9981 Evaluate side-chains 56 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.613 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0508 time to fit residues: 1.0216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5394 Z= 0.231 Angle : 0.492 4.687 7311 Z= 0.268 Chirality : 0.047 0.155 793 Planarity : 0.004 0.047 944 Dihedral : 4.313 15.657 733 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.57 % Allowed : 11.01 % Favored : 87.41 % 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: -0.66 (0.33), residues: 668 helix: -0.72 (1.76), residues: 13 sheet: -0.89 (0.30), residues: 243 loop : -0.01 (0.33), residues: 412 *********************** 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 71 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.544 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1694 time to fit residues: 15.2648 Evaluate side-chains 60 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0637 time to fit residues: 1.4251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5394 Z= 0.275 Angle : 0.507 5.364 7311 Z= 0.275 Chirality : 0.047 0.153 793 Planarity : 0.004 0.047 944 Dihedral : 4.316 16.128 733 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.92 % Allowed : 12.41 % Favored : 85.66 % 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: -0.58 (0.33), residues: 668 helix: 2.72 (2.58), residues: 7 sheet: -0.85 (0.31), residues: 238 loop : -0.04 (0.32), residues: 423 *********************** 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 70 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.620 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 0.1701 time to fit residues: 14.7147 Evaluate side-chains 61 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0931 time to fit residues: 1.9797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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: 0.7898 moved from start: 0.1918 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= 0.211 Angle : 0.472 4.554 7311 Z= 0.259 Chirality : 0.046 0.149 793 Planarity : 0.003 0.047 944 Dihedral : 4.194 15.312 733 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.22 % Allowed : 13.11 % Favored : 85.66 % 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: -0.51 (0.33), residues: 668 helix: 2.88 (2.49), residues: 7 sheet: -0.79 (0.30), residues: 243 loop : 0.00 (0.33), residues: 418 *********************** 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 66 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.643 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 62 average time/residue: 0.1679 time to fit residues: 14.2059 Evaluate side-chains 56 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.677 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0869 time to fit residues: 0.8693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 5394 Z= 0.442 Angle : 0.597 6.619 7311 Z= 0.323 Chirality : 0.051 0.162 793 Planarity : 0.004 0.052 944 Dihedral : 4.698 17.881 733 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.10 % Allowed : 12.76 % 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: -0.77 (0.32), residues: 668 helix: 2.61 (2.46), residues: 7 sheet: -1.01 (0.31), residues: 238 loop : -0.15 (0.32), residues: 423 *********************** 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 66 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.564 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 59 average time/residue: 0.1533 time to fit residues: 12.7096 Evaluate side-chains 59 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0599 time to fit residues: 1.6045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5394 Z= 0.287 Angle : 0.510 5.117 7311 Z= 0.276 Chirality : 0.048 0.157 793 Planarity : 0.004 0.048 944 Dihedral : 4.464 16.607 733 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.70 % Allowed : 14.16 % 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: -0.74 (0.33), residues: 668 helix: 2.90 (2.50), residues: 7 sheet: -1.04 (0.30), residues: 238 loop : -0.11 (0.32), residues: 423 *********************** 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 61 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.578 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 58 average time/residue: 0.1535 time to fit residues: 12.5693 Evaluate side-chains 56 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3963 time to fit residues: 1.2872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 63 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5394 Z= 0.170 Angle : 0.453 4.228 7311 Z= 0.252 Chirality : 0.046 0.149 793 Planarity : 0.004 0.048 944 Dihedral : 4.086 15.256 733 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.70 % Allowed : 14.51 % Favored : 84.79 % 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: 3.02 (2.42), residues: 7 sheet: -0.84 (0.31), residues: 244 loop : -0.01 (0.32), residues: 417 *********************** 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 64 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.616 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 63 average time/residue: 0.1511 time to fit residues: 13.5334 Evaluate side-chains 55 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.578 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0583 time to fit residues: 0.9038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.2137 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= 0.298 Angle : 0.518 5.539 7311 Z= 0.280 Chirality : 0.048 0.154 793 Planarity : 0.004 0.047 944 Dihedral : 4.293 15.112 733 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.52 % Allowed : 15.03 % 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: -0.62 (0.32), residues: 668 helix: 2.84 (2.43), residues: 7 sheet: -0.91 (0.31), residues: 238 loop : -0.05 (0.32), residues: 423 ********************** 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 55 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.575 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 54 average time/residue: 0.1463 time to fit residues: 11.3360 Evaluate side-chains 52 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0537 time to fit residues: 0.9241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.166574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141914 restraints weight = 6165.348| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.97 r_work: 0.3564 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5394 Z= 0.175 Angle : 0.478 10.337 7311 Z= 0.255 Chirality : 0.046 0.149 793 Planarity : 0.003 0.048 944 Dihedral : 4.045 15.304 733 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.17 % Allowed : 15.21 % Favored : 84.62 % 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 (0.32), residues: 668 helix: 2.87 (2.37), residues: 7 sheet: -0.76 (0.31), residues: 244 loop : 0.01 (0.32), residues: 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.12 seconds wall clock time: 27 minutes 42.88 seconds (1662.88 seconds total)