Starting phenix.real_space_refine on Fri Jul 25 15:30:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fx8_50843/07_2025/9fx8_50843.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fx8_50843/07_2025/9fx8_50843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fx8_50843/07_2025/9fx8_50843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fx8_50843/07_2025/9fx8_50843.map" model { file = "/net/cci-nas-00/data/ceres_data/9fx8_50843/07_2025/9fx8_50843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fx8_50843/07_2025/9fx8_50843.cif" } resolution = 3.6 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= 0.001 sd= 0.020 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 23 5.16 5 C 4860 2.51 5 N 1369 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7738 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1541 Classifications: {'peptide': 198} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 5170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5170 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 24, 'TRANS': 640} Chain breaks: 7 Chain: "I" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1027 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain breaks: 4 Time building chain proxies: 5.26, per 1000 atoms: 0.68 Number of scatterers: 7738 At special positions: 0 Unit cell: (93.84, 78.54, 128.52, 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 23 16.00 O 1486 8.00 N 1369 7.00 C 4860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 810 " - pdb=" SG CYS D 832 " distance=2.03 Simple disulfide: pdb=" SG CYS I 24 " - pdb=" SG CYS I 64 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 15 sheets defined 4.7% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 242 through 245 Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 387 through 389 No H-bonds generated for 'chain 'D' and resid 387 through 389' Processing helix chain 'D' and resid 558 through 560 No H-bonds generated for 'chain 'D' and resid 558 through 560' Processing helix chain 'D' and resid 567 through 571 removed outlier: 3.598A pdb=" N HIS D 571 " --> pdb=" O GLN D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 720 Processing helix chain 'D' and resid 817 through 822 Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 65 through 71 removed outlier: 3.767A pdb=" N ARG I 71 " --> pdb=" O VAL I 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 8 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 8 through 12 current: chain 'C' and resid 54 through 58 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 54 through 58 current: chain 'C' and resid 102 through 116 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 34 through 36 current: chain 'I' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.575A pdb=" N SER C 173 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 171 " --> pdb=" O ASN C 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 157 removed outlier: 3.925A pdb=" N ARG C 160 " --> pdb=" O ALA C 157 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 160 through 161 current: chain 'C' and resid 200 through 201 Processing sheet with id=AA5, first strand: chain 'D' and resid 139 through 151 removed outlier: 3.532A pdb=" N ALA D 139 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 147 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP D 179 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG D 176 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU D 205 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG D 178 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR D 203 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN D 180 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 184 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 197 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 16.192A pdb=" N ILE D 201 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 10.529A pdb=" N TYR D 222 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR D 203 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 218 " --> pdb=" O LEU D 205 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 232 through 234 current: chain 'D' and resid 332 through 334 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 332 through 334 current: chain 'D' and resid 364 through 372 removed outlier: 4.011A pdb=" N ALA D 377 " --> pdb=" O GLN D 370 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR D 375 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN D 398 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 407 through 409 current: chain 'D' and resid 430 through 437 removed outlier: 5.366A pdb=" N ARG D 481 " --> pdb=" O SER D 437 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 496 " --> pdb=" O LEU D 492 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 496 through 500 current: chain 'D' and resid 531 through 537 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 586 through 589 current: chain 'D' and resid 603 through 604 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 603 through 604 current: chain 'D' and resid 635 through 636 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 649 through 652 current: chain 'D' and resid 662 through 666 Processing sheet with id=AA6, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.702A pdb=" N ALA D 260 " --> pdb=" O GLY D 283 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 283 " --> pdb=" O ALA D 260 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 273 through 280 removed outlier: 5.325A pdb=" N ASP D 274 " --> pdb=" O GLN D 270 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN D 270 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR D 276 " --> pdb=" O ILE D 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 622 through 624 Processing sheet with id=AA9, first strand: chain 'D' and resid 699 through 702 removed outlier: 3.761A pdb=" N VAL D 674 " --> pdb=" O LEU D 702 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 713 through 714 Processing sheet with id=AB2, first strand: chain 'D' and resid 724 through 726 Processing sheet with id=AB3, first strand: chain 'D' and resid 751 through 756 removed outlier: 5.358A pdb=" N ILE D 751 " --> pdb=" O GLY D 791 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 791 " --> pdb=" O ILE D 751 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 758 through 759 Processing sheet with id=AB5, first strand: chain 'D' and resid 778 through 780 Processing sheet with id=AB6, first strand: chain 'I' and resid 25 through 28 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 55 through 62 current: chain 'I' and resid 98 through 106 removed outlier: 5.833A pdb=" N ASN I 99 " --> pdb=" O THR I 140 " (cutoff:3.500A) 173 hydrogen bonds defined for protein. 450 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: 2.55 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2592 1.34 - 1.46: 1506 1.46 - 1.57: 3758 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 7898 Sorted by residual: bond pdb=" N VAL I 55 " pdb=" CA VAL I 55 " ideal model delta sigma weight residual 1.454 1.462 -0.007 7.70e-03 1.69e+04 8.54e-01 bond pdb=" C VAL D 280 " pdb=" O VAL D 280 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 7.84e-01 bond pdb=" CG PRO C 52 " pdb=" CD PRO C 52 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.70e-02 1.37e+03 5.64e-01 bond pdb=" CA LEU D 359 " pdb=" C LEU D 359 " ideal model delta sigma weight residual 1.517 1.524 -0.007 1.02e-02 9.61e+03 4.88e-01 bond pdb=" CB ASN D 171 " pdb=" CG ASN D 171 " ideal model delta sigma weight residual 1.516 1.499 0.017 2.50e-02 1.60e+03 4.78e-01 ... (remaining 7893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 10144 0.86 - 1.72: 486 1.72 - 2.59: 54 2.59 - 3.45: 41 3.45 - 4.31: 5 Bond angle restraints: 10730 Sorted by residual: angle pdb=" N VAL D 280 " pdb=" CA VAL D 280 " pdb=" C VAL D 280 " ideal model delta sigma weight residual 107.61 110.50 -2.89 1.19e+00 7.06e-01 5.89e+00 angle pdb=" C ASN D 760 " pdb=" N ASN D 761 " pdb=" CA ASN D 761 " ideal model delta sigma weight residual 121.54 125.49 -3.95 1.91e+00 2.74e-01 4.28e+00 angle pdb=" C THR D 279 " pdb=" N VAL D 280 " pdb=" CA VAL D 280 " ideal model delta sigma weight residual 123.33 121.78 1.55 8.70e-01 1.32e+00 3.15e+00 angle pdb=" N VAL D 280 " pdb=" CA VAL D 280 " pdb=" CB VAL D 280 " ideal model delta sigma weight residual 112.37 110.62 1.75 1.06e+00 8.90e-01 2.72e+00 angle pdb=" N ILE D 201 " pdb=" CA ILE D 201 " pdb=" C ILE D 201 " ideal model delta sigma weight residual 109.34 112.45 -3.11 2.08e+00 2.31e-01 2.23e+00 ... (remaining 10725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4295 17.62 - 35.24: 311 35.24 - 52.86: 30 52.86 - 70.49: 17 70.49 - 88.11: 3 Dihedral angle restraints: 4656 sinusoidal: 1810 harmonic: 2846 Sorted by residual: dihedral pdb=" CB CYS D 810 " pdb=" SG CYS D 810 " pdb=" SG CYS D 832 " pdb=" CB CYS D 832 " ideal model delta sinusoidal sigma weight residual -86.00 -146.36 60.36 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CG ARG I 138 " pdb=" CD ARG I 138 " pdb=" NE ARG I 138 " pdb=" CZ ARG I 138 " ideal model delta sinusoidal sigma weight residual 90.00 133.94 -43.94 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG D 742 " pdb=" CD ARG D 742 " pdb=" NE ARG D 742 " pdb=" CZ ARG D 742 " ideal model delta sinusoidal sigma weight residual 90.00 131.00 -41.00 2 1.50e+01 4.44e-03 9.18e+00 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 700 0.027 - 0.055: 302 0.055 - 0.082: 87 0.082 - 0.110: 75 0.110 - 0.137: 20 Chirality restraints: 1184 Sorted by residual: chirality pdb=" CA VAL D 320 " pdb=" N VAL D 320 " pdb=" C VAL D 320 " pdb=" CB VAL D 320 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA ILE D 128 " pdb=" N ILE D 128 " pdb=" C ILE D 128 " pdb=" CB ILE D 128 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE D 637 " pdb=" N ILE D 637 " pdb=" C ILE D 637 " pdb=" CB ILE D 637 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1181 not shown) Planarity restraints: 1405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 320 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO D 321 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 359 " 0.020 5.00e-02 4.00e+02 2.96e-02 1.40e+00 pdb=" N PRO D 360 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO D 360 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 360 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 197 " 0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO C 198 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 198 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 198 " 0.016 5.00e-02 4.00e+02 ... (remaining 1402 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1971 2.80 - 3.33: 6398 3.33 - 3.85: 11956 3.85 - 4.38: 13399 4.38 - 4.90: 24492 Nonbonded interactions: 58216 Sorted by model distance: nonbonded pdb=" OG1 THR D 672 " pdb=" O ALA D 705 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASN D 186 " pdb=" OG SER D 188 " model vdw 2.308 3.040 nonbonded pdb=" OD2 ASP D 395 " pdb=" NH2 ARG D 415 " model vdw 2.311 3.120 nonbonded pdb=" OG SER D 575 " pdb=" O GLY D 591 " model vdw 2.330 3.040 nonbonded pdb=" OG SER C 136 " pdb=" OG SER C 139 " model vdw 2.341 3.040 ... (remaining 58211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.790 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.003 0.027 7900 Z= 0.146 Angle : 0.449 4.309 10734 Z= 0.238 Chirality : 0.041 0.137 1184 Planarity : 0.003 0.034 1405 Dihedral : 12.092 88.107 2838 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.27), residues: 970 helix: -1.68 (2.00), residues: 6 sheet: -1.39 (0.23), residues: 505 loop : -0.39 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 530 HIS 0.003 0.001 HIS I 77 PHE 0.012 0.002 PHE D 416 TYR 0.011 0.001 TYR D 366 ARG 0.006 0.001 ARG D 339 Details of bonding type rmsd hydrogen bonds : bond 0.25771 ( 173) hydrogen bonds : angle 11.83367 ( 450) SS BOND : bond 0.00215 ( 2) SS BOND : angle 0.53276 ( 4) covalent geometry : bond 0.00337 ( 7898) covalent geometry : angle 0.44868 (10730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 ASN cc_start: 0.7860 (m-40) cc_final: 0.7541 (t0) REVERT: C 130 LYS cc_start: 0.8490 (mttm) cc_final: 0.8166 (mptt) REVERT: C 154 GLU cc_start: 0.8896 (tt0) cc_final: 0.8688 (tt0) REVERT: D 300 GLN cc_start: 0.7478 (tt0) cc_final: 0.7113 (tm-30) REVERT: D 382 ILE cc_start: 0.8685 (tt) cc_final: 0.8262 (pt) REVERT: D 529 ASN cc_start: 0.7779 (t0) cc_final: 0.7463 (t0) REVERT: D 546 ASP cc_start: 0.8065 (t0) cc_final: 0.7674 (t70) REVERT: D 687 GLU cc_start: 0.7845 (tp30) cc_final: 0.7632 (tp30) REVERT: D 728 ASN cc_start: 0.8325 (m-40) cc_final: 0.7786 (p0) REVERT: D 730 VAL cc_start: 0.9566 (t) cc_final: 0.9274 (m) REVERT: D 821 GLN cc_start: 0.7818 (mt0) cc_final: 0.7538 (tm-30) REVERT: I 22 GLU cc_start: 0.8405 (pt0) cc_final: 0.8106 (pt0) REVERT: I 33 MET cc_start: 0.8192 (mmt) cc_final: 0.7154 (mtt) REVERT: I 121 TRP cc_start: 0.6210 (m-90) cc_final: 0.5853 (m100) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2020 time to fit residues: 34.6384 Evaluate side-chains 90 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0270 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.135473 restraints weight = 8263.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133954 restraints weight = 11510.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.135115 restraints weight = 10457.622| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7900 Z= 0.147 Angle : 0.500 5.821 10734 Z= 0.266 Chirality : 0.043 0.145 1184 Planarity : 0.004 0.041 1405 Dihedral : 3.677 30.456 1085 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.97 % Allowed : 8.12 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.27), residues: 970 helix: -2.82 (1.36), residues: 6 sheet: -1.30 (0.23), residues: 510 loop : -0.31 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 530 HIS 0.003 0.001 HIS I 77 PHE 0.011 0.002 PHE D 313 TYR 0.018 0.001 TYR I 159 ARG 0.005 0.000 ARG D 494 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 173) hydrogen bonds : angle 7.63402 ( 450) SS BOND : bond 0.00295 ( 2) SS BOND : angle 0.62102 ( 4) covalent geometry : bond 0.00338 ( 7898) covalent geometry : angle 0.49947 (10730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7820 (t0) cc_final: 0.7533 (m-30) REVERT: D 546 ASP cc_start: 0.7914 (t0) cc_final: 0.7654 (t70) REVERT: D 578 MET cc_start: 0.6607 (tpt) cc_final: 0.6177 (tpt) REVERT: D 728 ASN cc_start: 0.8104 (m-40) cc_final: 0.7685 (p0) REVERT: D 730 VAL cc_start: 0.9411 (t) cc_final: 0.9065 (m) REVERT: I 33 MET cc_start: 0.8232 (mmt) cc_final: 0.7539 (mtt) outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 0.1980 time to fit residues: 26.9349 Evaluate side-chains 82 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 637 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN D 196 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.165737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.144046 restraints weight = 8343.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142556 restraints weight = 14282.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143233 restraints weight = 12905.334| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7900 Z= 0.118 Angle : 0.471 6.049 10734 Z= 0.250 Chirality : 0.042 0.145 1184 Planarity : 0.004 0.044 1405 Dihedral : 3.583 27.547 1085 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.45 % Allowed : 10.30 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 970 helix: -3.38 (1.21), residues: 6 sheet: -1.16 (0.23), residues: 510 loop : -0.24 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 204 HIS 0.002 0.001 HIS I 77 PHE 0.009 0.001 PHE D 416 TYR 0.017 0.001 TYR I 159 ARG 0.004 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.03190 ( 173) hydrogen bonds : angle 6.77545 ( 450) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.49153 ( 4) covalent geometry : bond 0.00271 ( 7898) covalent geometry : angle 0.47099 (10730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 ASN cc_start: 0.8681 (p0) cc_final: 0.8463 (p0) REVERT: C 45 ASP cc_start: 0.7731 (t0) cc_final: 0.7490 (m-30) REVERT: D 529 ASN cc_start: 0.7401 (t0) cc_final: 0.7148 (t0) REVERT: D 728 ASN cc_start: 0.7893 (m-40) cc_final: 0.7578 (p0) REVERT: D 730 VAL cc_start: 0.9369 (t) cc_final: 0.9029 (m) REVERT: I 33 MET cc_start: 0.8175 (mmt) cc_final: 0.7583 (mtt) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.1821 time to fit residues: 24.5182 Evaluate side-chains 90 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 196 ASN Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain I residue 22 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN D 196 ASN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.146317 restraints weight = 8338.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140277 restraints weight = 13583.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137105 restraints weight = 9100.916| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7900 Z= 0.118 Angle : 0.464 5.486 10734 Z= 0.245 Chirality : 0.042 0.145 1184 Planarity : 0.004 0.043 1405 Dihedral : 3.509 24.833 1085 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.82 % Allowed : 10.91 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 970 helix: -3.55 (1.18), residues: 6 sheet: -1.16 (0.23), residues: 513 loop : -0.23 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 204 HIS 0.002 0.001 HIS I 77 PHE 0.008 0.001 PHE D 416 TYR 0.015 0.001 TYR I 159 ARG 0.003 0.000 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 173) hydrogen bonds : angle 6.41612 ( 450) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.49314 ( 4) covalent geometry : bond 0.00272 ( 7898) covalent geometry : angle 0.46416 (10730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7711 (t0) cc_final: 0.7506 (m-30) REVERT: C 172 GLU cc_start: 0.8309 (pm20) cc_final: 0.7841 (pt0) REVERT: D 728 ASN cc_start: 0.7830 (m-40) cc_final: 0.7554 (p0) REVERT: D 730 VAL cc_start: 0.9322 (t) cc_final: 0.8994 (m) REVERT: I 33 MET cc_start: 0.8284 (mmt) cc_final: 0.7598 (mtt) outliers start: 15 outliers final: 8 residues processed: 95 average time/residue: 0.2067 time to fit residues: 27.7436 Evaluate side-chains 90 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 73 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.164733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146496 restraints weight = 8344.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139788 restraints weight = 14485.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.136439 restraints weight = 10438.919| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7900 Z= 0.130 Angle : 0.464 5.102 10734 Z= 0.246 Chirality : 0.042 0.144 1184 Planarity : 0.004 0.044 1405 Dihedral : 3.491 23.037 1085 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.82 % Allowed : 11.15 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.27), residues: 970 helix: -3.92 (0.97), residues: 6 sheet: -1.18 (0.23), residues: 516 loop : -0.22 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 204 HIS 0.003 0.001 HIS I 77 PHE 0.008 0.001 PHE D 416 TYR 0.011 0.001 TYR I 159 ARG 0.006 0.000 ARG I 138 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 173) hydrogen bonds : angle 6.19660 ( 450) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.50537 ( 4) covalent geometry : bond 0.00302 ( 7898) covalent geometry : angle 0.46427 (10730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7744 (t0) cc_final: 0.7480 (m-30) REVERT: D 728 ASN cc_start: 0.7790 (m-40) cc_final: 0.7505 (p0) REVERT: D 730 VAL cc_start: 0.9314 (t) cc_final: 0.8978 (m) REVERT: I 33 MET cc_start: 0.8310 (mmt) cc_final: 0.7615 (mtt) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.2846 time to fit residues: 36.5731 Evaluate side-chains 89 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.160791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.137485 restraints weight = 8398.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134778 restraints weight = 12764.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.136262 restraints weight = 12832.066| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7900 Z= 0.187 Angle : 0.505 5.390 10734 Z= 0.270 Chirality : 0.043 0.149 1184 Planarity : 0.004 0.045 1405 Dihedral : 3.716 23.605 1085 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.42 % Allowed : 11.39 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.27), residues: 970 helix: -4.38 (0.69), residues: 6 sheet: -1.26 (0.23), residues: 512 loop : -0.30 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 204 HIS 0.004 0.001 HIS I 77 PHE 0.012 0.002 PHE D 350 TYR 0.013 0.001 TYR I 159 ARG 0.005 0.000 ARG D 215 Details of bonding type rmsd hydrogen bonds : bond 0.02850 ( 173) hydrogen bonds : angle 6.24558 ( 450) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.68831 ( 4) covalent geometry : bond 0.00433 ( 7898) covalent geometry : angle 0.50463 (10730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7802 (t0) cc_final: 0.7506 (m-30) REVERT: D 687 GLU cc_start: 0.7732 (tp30) cc_final: 0.7480 (tp30) REVERT: D 728 ASN cc_start: 0.7862 (m-40) cc_final: 0.7499 (p0) REVERT: D 730 VAL cc_start: 0.9394 (t) cc_final: 0.9033 (m) REVERT: D 744 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6872 (pt0) REVERT: I 33 MET cc_start: 0.8312 (mmt) cc_final: 0.7647 (mtt) REVERT: I 121 TRP cc_start: 0.7177 (OUTLIER) cc_final: 0.6430 (m-90) outliers start: 20 outliers final: 11 residues processed: 99 average time/residue: 0.2867 time to fit residues: 40.7708 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 121 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.145770 restraints weight = 8385.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143719 restraints weight = 13627.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143411 restraints weight = 13494.132| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7900 Z= 0.110 Angle : 0.467 6.423 10734 Z= 0.247 Chirality : 0.042 0.145 1184 Planarity : 0.004 0.045 1405 Dihedral : 3.547 21.443 1085 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.18 % Allowed : 12.36 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.27), residues: 970 helix: -4.42 (0.64), residues: 6 sheet: -1.18 (0.23), residues: 517 loop : -0.26 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 204 HIS 0.002 0.001 HIS D 328 PHE 0.008 0.001 PHE D 416 TYR 0.010 0.001 TYR D 366 ARG 0.005 0.000 ARG D 494 Details of bonding type rmsd hydrogen bonds : bond 0.02615 ( 173) hydrogen bonds : angle 5.99088 ( 450) SS BOND : bond 0.00149 ( 2) SS BOND : angle 0.53334 ( 4) covalent geometry : bond 0.00253 ( 7898) covalent geometry : angle 0.46684 (10730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.069 Fit side-chains REVERT: C 45 ASP cc_start: 0.7734 (t0) cc_final: 0.7470 (m-30) REVERT: D 687 GLU cc_start: 0.7662 (tp30) cc_final: 0.7419 (mm-30) REVERT: D 728 ASN cc_start: 0.7869 (m-40) cc_final: 0.7518 (p0) REVERT: D 730 VAL cc_start: 0.9362 (t) cc_final: 0.9010 (m) REVERT: D 744 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6828 (pt0) REVERT: I 33 MET cc_start: 0.8215 (mmt) cc_final: 0.7608 (mtt) REVERT: I 121 TRP cc_start: 0.7212 (OUTLIER) cc_final: 0.6558 (m-90) outliers start: 18 outliers final: 12 residues processed: 94 average time/residue: 0.2305 time to fit residues: 31.0480 Evaluate side-chains 91 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 121 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 559 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144571 restraints weight = 8406.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142807 restraints weight = 12929.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142451 restraints weight = 12369.694| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7900 Z= 0.103 Angle : 0.458 6.120 10734 Z= 0.243 Chirality : 0.042 0.141 1184 Planarity : 0.004 0.044 1405 Dihedral : 3.411 18.930 1085 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.30 % Allowed : 12.61 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 970 helix: None (None), residues: 0 sheet: -1.11 (0.23), residues: 518 loop : -0.15 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 204 HIS 0.002 0.001 HIS D 328 PHE 0.007 0.001 PHE D 525 TYR 0.009 0.001 TYR D 366 ARG 0.006 0.000 ARG D 494 Details of bonding type rmsd hydrogen bonds : bond 0.02529 ( 173) hydrogen bonds : angle 5.75338 ( 450) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.43896 ( 4) covalent geometry : bond 0.00238 ( 7898) covalent geometry : angle 0.45822 (10730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: C 45 ASP cc_start: 0.7776 (t0) cc_final: 0.7514 (m-30) REVERT: D 728 ASN cc_start: 0.7897 (m-40) cc_final: 0.7545 (p0) REVERT: D 730 VAL cc_start: 0.9394 (t) cc_final: 0.9036 (m) REVERT: D 744 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6883 (pt0) REVERT: I 33 MET cc_start: 0.8243 (mmt) cc_final: 0.7662 (mtt) REVERT: I 121 TRP cc_start: 0.7196 (OUTLIER) cc_final: 0.6456 (m-90) outliers start: 19 outliers final: 12 residues processed: 95 average time/residue: 0.1703 time to fit residues: 23.2300 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 121 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.162711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141439 restraints weight = 8509.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139315 restraints weight = 13914.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139085 restraints weight = 13249.310| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7900 Z= 0.167 Angle : 0.505 5.622 10734 Z= 0.269 Chirality : 0.043 0.145 1184 Planarity : 0.004 0.044 1405 Dihedral : 3.605 20.050 1085 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.18 % Allowed : 13.21 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.26), residues: 970 helix: -4.56 (0.55), residues: 6 sheet: -1.23 (0.23), residues: 520 loop : -0.33 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 204 HIS 0.003 0.001 HIS D 328 PHE 0.012 0.002 PHE D 350 TYR 0.011 0.001 TYR D 650 ARG 0.006 0.000 ARG D 494 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 173) hydrogen bonds : angle 5.93182 ( 450) SS BOND : bond 0.00183 ( 2) SS BOND : angle 0.65894 ( 4) covalent geometry : bond 0.00390 ( 7898) covalent geometry : angle 0.50459 (10730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.822 Fit side-chains REVERT: C 45 ASP cc_start: 0.7798 (t0) cc_final: 0.7497 (m-30) REVERT: D 728 ASN cc_start: 0.7937 (m-40) cc_final: 0.7559 (p0) REVERT: D 730 VAL cc_start: 0.9419 (t) cc_final: 0.9030 (m) REVERT: D 744 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: I 33 MET cc_start: 0.8300 (mmt) cc_final: 0.7673 (mtt) REVERT: I 121 TRP cc_start: 0.7213 (OUTLIER) cc_final: 0.6448 (m-90) outliers start: 18 outliers final: 15 residues processed: 94 average time/residue: 0.1739 time to fit residues: 23.6519 Evaluate side-chains 97 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 121 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.161737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136453 restraints weight = 8405.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133072 restraints weight = 12836.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.134743 restraints weight = 12279.797| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7900 Z= 0.142 Angle : 0.502 6.142 10734 Z= 0.269 Chirality : 0.043 0.145 1184 Planarity : 0.004 0.044 1405 Dihedral : 3.599 19.658 1085 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.18 % Allowed : 13.58 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.26), residues: 970 helix: -4.51 (0.57), residues: 6 sheet: -1.22 (0.23), residues: 518 loop : -0.32 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 204 HIS 0.003 0.001 HIS I 77 PHE 0.008 0.001 PHE D 416 TYR 0.010 0.001 TYR D 366 ARG 0.007 0.000 ARG D 494 Details of bonding type rmsd hydrogen bonds : bond 0.02624 ( 173) hydrogen bonds : angle 5.86982 ( 450) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.58580 ( 4) covalent geometry : bond 0.00328 ( 7898) covalent geometry : angle 0.50186 (10730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1940 Ramachandran restraints generated. 970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.062 Fit side-chains REVERT: C 45 ASP cc_start: 0.7778 (t0) cc_final: 0.7482 (m-30) REVERT: C 172 GLU cc_start: 0.8346 (pm20) cc_final: 0.7678 (pt0) REVERT: D 728 ASN cc_start: 0.7925 (m-40) cc_final: 0.7571 (p0) REVERT: D 730 VAL cc_start: 0.9402 (t) cc_final: 0.9013 (m) REVERT: D 744 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: I 33 MET cc_start: 0.8336 (mmt) cc_final: 0.7732 (mtt) REVERT: I 121 TRP cc_start: 0.7267 (OUTLIER) cc_final: 0.6486 (m-90) outliers start: 18 outliers final: 15 residues processed: 94 average time/residue: 0.2022 time to fit residues: 27.5065 Evaluate side-chains 96 residues out of total 825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 578 MET Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 672 THR Chi-restraints excluded: chain D residue 716 ASP Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 757 LEU Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 121 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 83 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 583 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.162509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140721 restraints weight = 8417.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.138214 restraints weight = 13712.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138280 restraints weight = 13525.965| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7900 Z= 0.169 Angle : 0.515 5.656 10734 Z= 0.276 Chirality : 0.043 0.148 1184 Planarity : 0.004 0.045 1405 Dihedral : 3.657 19.517 1085 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.30 % Allowed : 13.58 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.26), residues: 970 helix: -4.58 (0.53), residues: 6 sheet: -1.29 (0.23), residues: 518 loop : -0.38 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 204 HIS 0.003 0.001 HIS D 328 PHE 0.011 0.002 PHE D 350 TYR 0.011 0.001 TYR D 366 ARG 0.011 0.000 ARG D 562 Details of bonding type rmsd hydrogen bonds : bond 0.02680 ( 173) hydrogen bonds : angle 5.94662 ( 450) SS BOND : bond 0.00173 ( 2) SS BOND : angle 0.66672 ( 4) covalent geometry : bond 0.00392 ( 7898) covalent geometry : angle 0.51527 (10730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.45 seconds wall clock time: 60 minutes 8.48 seconds (3608.48 seconds total)