Starting phenix.real_space_refine on Tue Mar 11 17:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6k_33642/03_2025/7y6k_33642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6k_33642/03_2025/7y6k_33642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6k_33642/03_2025/7y6k_33642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6k_33642/03_2025/7y6k_33642.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6k_33642/03_2025/7y6k_33642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6k_33642/03_2025/7y6k_33642.cif" } resolution = 3.34 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= -0.003 sd= 0.126 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 25 5.16 5 C 4010 2.51 5 N 1069 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6363 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1723 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Chain: "I" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1590 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "J" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1493 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.02, per 1000 atoms: 0.79 Number of scatterers: 6363 At special positions: 0 Unit cell: (82.0183, 68.4988, 126.182, 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 25 16.00 O 1259 8.00 N 1069 7.00 C 4010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 158 " - pdb=" SG CYS E 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS I 137 " - pdb=" SG CYS I 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 154 " - pdb=" SG CYS J 210 " 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 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 909.6 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 22 sheets defined 8.5% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.041A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.660A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.555A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP E 219 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 220 " --> pdb=" O SER E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 220' Processing helix chain 'I' and resid 124 through 131 removed outlier: 3.616A pdb=" N LEU I 128 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.222A pdb=" N GLU I 190 " --> pdb=" O LYS I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.678A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.849A pdb=" N ALA E 146 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 153 through 157 Processing sheet with id=AB1, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP E 172 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AB4, first strand: chain 'I' and resid 46 through 49 removed outlier: 6.306A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 46 through 49 removed outlier: 6.306A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 117 through 121 removed outlier: 3.529A pdb=" N VAL I 136 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR I 176 " --> pdb=" O ASN I 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER I 179 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 148 through 150 Processing sheet with id=AB8, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.526A pdb=" N TYR I 195 " --> pdb=" O PHE I 212 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 212 " --> pdb=" O TYR I 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.845A pdb=" N MET J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TRP J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 134 through 138 removed outlier: 4.309A pdb=" N GLY J 153 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU J 152 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 190 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 165 through 168 236 hydrogen bonds defined for protein. 573 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: 2.20 Time building geometry restraints manager: 1.75 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: 2034 1.34 - 1.45: 1188 1.45 - 1.57: 3263 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 6515 Sorted by residual: bond pdb=" N TYR B 453 " pdb=" CA TYR B 453 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.66e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" CA ASN I 53 " pdb=" CB ASN I 53 " ideal model delta sigma weight residual 1.537 1.568 -0.031 2.52e-02 1.57e+03 1.54e+00 bond pdb=" CB ASN E 77 " pdb=" CG ASN E 77 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.29e+00 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 6510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 8592 1.60 - 3.20: 217 3.20 - 4.80: 39 4.80 - 6.40: 11 6.40 - 8.00: 3 Bond angle restraints: 8862 Sorted by residual: angle pdb=" CB LYS J 223 " pdb=" CG LYS J 223 " pdb=" CD LYS J 223 " ideal model delta sigma weight residual 111.30 118.62 -7.32 2.30e+00 1.89e-01 1.01e+01 angle pdb=" CA TYR B 453 " pdb=" C TYR B 453 " pdb=" O TYR B 453 " ideal model delta sigma weight residual 121.33 118.26 3.07 1.08e+00 8.57e-01 8.09e+00 angle pdb=" C ASP E 187 " pdb=" N ASP E 188 " pdb=" CA ASP E 188 " ideal model delta sigma weight residual 121.54 126.91 -5.37 1.91e+00 2.74e-01 7.89e+00 angle pdb=" CA CYS E 22 " pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " ideal model delta sigma weight residual 114.40 120.48 -6.08 2.30e+00 1.89e-01 6.98e+00 angle pdb=" CB LYS B 356 " pdb=" CG LYS B 356 " pdb=" CD LYS B 356 " ideal model delta sigma weight residual 111.30 117.27 -5.97 2.30e+00 1.89e-01 6.75e+00 ... (remaining 8857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3446 17.29 - 34.59: 330 34.59 - 51.88: 60 51.88 - 69.18: 12 69.18 - 86.47: 10 Dihedral angle restraints: 3858 sinusoidal: 1469 harmonic: 2389 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -157.22 71.22 1 1.00e+01 1.00e-02 6.51e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -155.11 69.11 1 1.00e+01 1.00e-02 6.18e+01 dihedral pdb=" CA MET J 114 " pdb=" C MET J 114 " pdb=" N ASP J 115 " pdb=" CA ASP J 115 " ideal model delta harmonic sigma weight residual -180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 581 0.035 - 0.070: 289 0.070 - 0.105: 70 0.105 - 0.141: 30 0.141 - 0.176: 4 Chirality restraints: 974 Sorted by residual: chirality pdb=" CB THR J 91 " pdb=" CA THR J 91 " pdb=" OG1 THR J 91 " pdb=" CG2 THR J 91 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CA ASN E 77 " pdb=" N ASN E 77 " pdb=" C ASN E 77 " pdb=" CB ASN E 77 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CG LEU J 18 " pdb=" CB LEU J 18 " pdb=" CD1 LEU J 18 " pdb=" CD2 LEU J 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 971 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 103 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO E 104 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 104 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE J 160 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO J 161 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 161 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 161 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 143 " -0.029 5.00e-02 4.00e+02 4.52e-02 3.26e+00 pdb=" N PRO E 144 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 144 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 144 " -0.025 5.00e-02 4.00e+02 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 950 2.76 - 3.29: 6168 3.29 - 3.83: 10981 3.83 - 4.36: 13537 4.36 - 4.90: 23074 Nonbonded interactions: 54710 Sorted by model distance: nonbonded pdb=" OH TYR E 173 " pdb=" OH TYR E 235 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR I 37 " pdb=" OH TYR I 99 " model vdw 2.223 3.040 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.233 3.120 nonbonded pdb=" O PRO E 143 " pdb=" OG1 THR E 241 " model vdw 2.250 3.040 nonbonded pdb=" N VAL E 170 " pdb=" OD1 ASP E 188 " model vdw 2.253 3.120 ... (remaining 54705 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 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: 2.780 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.660 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 0.033 6515 Z= 0.249 Angle : 0.650 7.995 8862 Z= 0.335 Chirality : 0.045 0.176 974 Planarity : 0.005 0.049 1144 Dihedral : 14.232 86.469 2314 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.57 % Allowed : 9.27 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.02 (0.30), residues: 820 helix: -3.43 (0.54), residues: 41 sheet: -0.67 (0.30), residues: 264 loop : -0.36 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 47 HIS 0.003 0.001 HIS I 192 PHE 0.013 0.002 PHE E 102 TYR 0.017 0.001 TYR B 369 ARG 0.005 0.001 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.618 Fit side-chains REVERT: J 65 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8081 (mttt) outliers start: 4 outliers final: 3 residues processed: 103 average time/residue: 0.2393 time to fit residues: 31.2464 Evaluate side-chains 100 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain J residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 16 GLN I 28 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN I 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130060 restraints weight = 7072.470| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.53 r_work: 0.3123 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6515 Z= 0.374 Angle : 0.650 6.829 8862 Z= 0.339 Chirality : 0.046 0.178 974 Planarity : 0.005 0.045 1144 Dihedral : 5.081 35.421 933 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.00 % Allowed : 11.13 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -1.00 (0.30), residues: 820 helix: -3.30 (0.67), residues: 41 sheet: -0.57 (0.29), residues: 280 loop : -0.39 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 50 HIS 0.004 0.001 HIS I 192 PHE 0.015 0.002 PHE B 338 TYR 0.020 0.002 TYR B 453 ARG 0.003 0.001 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.718 Fit side-chains REVERT: E 164 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8149 (m110) REVERT: J 65 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8053 (mmtt) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.2154 time to fit residues: 33.3566 Evaluate side-chains 122 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 3 optimal weight: 0.0070 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.176619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132866 restraints weight = 7123.248| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.71 r_work: 0.3138 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6515 Z= 0.272 Angle : 0.588 6.133 8862 Z= 0.306 Chirality : 0.044 0.167 974 Planarity : 0.005 0.045 1144 Dihedral : 4.982 39.338 933 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.14 % Allowed : 15.41 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.88 (0.30), residues: 820 helix: -3.20 (0.67), residues: 41 sheet: -0.47 (0.30), residues: 281 loop : -0.33 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.002 0.001 HIS I 192 PHE 0.011 0.002 PHE E 29 TYR 0.016 0.001 TYR I 50 ARG 0.003 0.000 ARG J 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.644 Fit side-chains REVERT: B 405 ASP cc_start: 0.8158 (m-30) cc_final: 0.7958 (m-30) REVERT: J 38 ARG cc_start: 0.8558 (ttp-170) cc_final: 0.8311 (ttp-170) REVERT: J 65 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8047 (mmtt) outliers start: 22 outliers final: 20 residues processed: 115 average time/residue: 0.1897 time to fit residues: 28.4904 Evaluate side-chains 113 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.175328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.133005 restraints weight = 7078.712| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.40 r_work: 0.3134 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6515 Z= 0.310 Angle : 0.589 6.024 8862 Z= 0.308 Chirality : 0.045 0.170 974 Planarity : 0.005 0.046 1144 Dihedral : 5.051 41.400 933 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.85 % Allowed : 14.69 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.86 (0.31), residues: 820 helix: -3.16 (0.68), residues: 41 sheet: -0.45 (0.29), residues: 292 loop : -0.31 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.003 0.001 HIS I 192 PHE 0.011 0.002 PHE B 400 TYR 0.017 0.001 TYR B 369 ARG 0.003 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.719 Fit side-chains REVERT: B 405 ASP cc_start: 0.8412 (m-30) cc_final: 0.8166 (m-30) REVERT: J 65 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8060 (mttt) outliers start: 34 outliers final: 27 residues processed: 122 average time/residue: 0.2086 time to fit residues: 33.2569 Evaluate side-chains 125 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.0170 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 519 HIS I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.176181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.132983 restraints weight = 7030.709| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.39 r_work: 0.3142 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6515 Z= 0.259 Angle : 0.577 6.469 8862 Z= 0.302 Chirality : 0.044 0.175 974 Planarity : 0.005 0.048 1144 Dihedral : 5.038 43.586 933 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.28 % Allowed : 16.26 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.79 (0.31), residues: 820 helix: -2.99 (0.69), residues: 41 sheet: -0.39 (0.29), residues: 292 loop : -0.29 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.001 0.000 HIS J 178 PHE 0.017 0.002 PHE E 68 TYR 0.015 0.001 TYR I 50 ARG 0.004 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.865 Fit side-chains REVERT: B 405 ASP cc_start: 0.8379 (m-30) cc_final: 0.8165 (m-30) REVERT: J 65 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8121 (mmtt) REVERT: J 114 MET cc_start: 0.8997 (ttm) cc_final: 0.8542 (mtt) outliers start: 30 outliers final: 26 residues processed: 118 average time/residue: 0.2036 time to fit residues: 31.4555 Evaluate side-chains 125 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.175427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.130941 restraints weight = 6994.137| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.30 r_work: 0.3146 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6515 Z= 0.291 Angle : 0.583 6.507 8862 Z= 0.304 Chirality : 0.044 0.172 974 Planarity : 0.004 0.049 1144 Dihedral : 5.090 45.576 933 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.42 % Allowed : 16.98 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.79 (0.30), residues: 820 helix: -2.94 (0.70), residues: 41 sheet: -0.39 (0.29), residues: 290 loop : -0.29 (0.31), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 50 HIS 0.001 0.001 HIS J 178 PHE 0.011 0.002 PHE E 29 TYR 0.015 0.001 TYR I 50 ARG 0.004 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.674 Fit side-chains REVERT: B 405 ASP cc_start: 0.8361 (m-30) cc_final: 0.8121 (m-30) REVERT: J 60 TYR cc_start: 0.8561 (m-80) cc_final: 0.7847 (m-80) REVERT: J 65 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8169 (mmtt) REVERT: J 83 MET cc_start: 0.7766 (mtm) cc_final: 0.7563 (ptp) REVERT: J 114 MET cc_start: 0.9019 (ttm) cc_final: 0.8607 (mtt) outliers start: 31 outliers final: 29 residues processed: 116 average time/residue: 0.2164 time to fit residues: 32.3620 Evaluate side-chains 123 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.174807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.130915 restraints weight = 6970.628| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.48 r_work: 0.3139 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6515 Z= 0.304 Angle : 0.585 6.587 8862 Z= 0.306 Chirality : 0.044 0.160 974 Planarity : 0.005 0.050 1144 Dihedral : 5.110 46.537 932 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.56 % Allowed : 16.69 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.82 (0.30), residues: 820 helix: -2.98 (0.68), residues: 41 sheet: -0.42 (0.29), residues: 291 loop : -0.30 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 50 HIS 0.002 0.000 HIS B 519 PHE 0.012 0.002 PHE J 136 TYR 0.016 0.002 TYR B 369 ARG 0.005 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.721 Fit side-chains REVERT: B 405 ASP cc_start: 0.8389 (m-30) cc_final: 0.8140 (m-30) REVERT: J 65 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8094 (mttt) REVERT: J 114 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8553 (mtt) outliers start: 32 outliers final: 28 residues processed: 124 average time/residue: 0.1902 time to fit residues: 31.2596 Evaluate side-chains 126 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 74 optimal weight: 0.1980 chunk 53 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.184782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142431 restraints weight = 6948.887| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.24 r_work: 0.3289 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6515 Z= 0.230 Angle : 0.582 7.524 8862 Z= 0.303 Chirality : 0.043 0.157 974 Planarity : 0.004 0.051 1144 Dihedral : 4.976 40.813 932 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.14 % Allowed : 17.83 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.75 (0.30), residues: 820 helix: -2.87 (0.70), residues: 41 sheet: -0.39 (0.29), residues: 297 loop : -0.25 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.013 0.002 PHE E 68 TYR 0.015 0.001 TYR I 50 ARG 0.004 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.774 Fit side-chains REVERT: E 110 TYR cc_start: 0.8779 (m-80) cc_final: 0.8452 (m-80) REVERT: J 60 TYR cc_start: 0.8488 (m-80) cc_final: 0.7871 (m-80) REVERT: J 65 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8060 (mttt) REVERT: J 114 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8551 (mtt) outliers start: 29 outliers final: 27 residues processed: 116 average time/residue: 0.2093 time to fit residues: 32.4006 Evaluate side-chains 132 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140340 restraints weight = 7019.908| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.06 r_work: 0.3193 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6515 Z= 0.278 Angle : 0.599 7.466 8862 Z= 0.312 Chirality : 0.044 0.158 974 Planarity : 0.004 0.051 1144 Dihedral : 5.023 40.350 932 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.42 % Allowed : 17.97 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.75 (0.30), residues: 820 helix: -3.07 (0.61), residues: 41 sheet: -0.35 (0.29), residues: 297 loop : -0.25 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.014 0.002 PHE E 68 TYR 0.016 0.001 TYR I 50 ARG 0.005 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.717 Fit side-chains REVERT: E 110 TYR cc_start: 0.8810 (m-80) cc_final: 0.8460 (m-80) REVERT: J 65 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8032 (mttt) REVERT: J 114 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8577 (mtt) outliers start: 31 outliers final: 27 residues processed: 115 average time/residue: 0.1906 time to fit residues: 28.9111 Evaluate side-chains 121 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 60 optimal weight: 10.0000 chunk 40 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.184745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142158 restraints weight = 7011.577| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.04 r_work: 0.3198 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6515 Z= 0.255 Angle : 0.591 7.424 8862 Z= 0.306 Chirality : 0.044 0.152 974 Planarity : 0.004 0.051 1144 Dihedral : 5.004 40.688 932 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.99 % Allowed : 18.26 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.30), residues: 820 helix: -2.99 (0.62), residues: 41 sheet: -0.23 (0.29), residues: 291 loop : -0.27 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.013 0.002 PHE E 68 TYR 0.015 0.001 TYR I 50 ARG 0.005 0.000 ARG I 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.712 Fit side-chains REVERT: E 110 TYR cc_start: 0.8796 (m-80) cc_final: 0.8435 (m-80) REVERT: J 60 TYR cc_start: 0.8397 (m-80) cc_final: 0.7879 (m-80) REVERT: J 65 LYS cc_start: 0.8385 (mmtt) cc_final: 0.8047 (mttt) REVERT: J 114 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8578 (mtt) outliers start: 28 outliers final: 27 residues processed: 113 average time/residue: 0.1868 time to fit residues: 27.8609 Evaluate side-chains 128 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.183412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140162 restraints weight = 7157.134| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.12 r_work: 0.3196 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6515 Z= 0.257 Angle : 0.596 7.751 8862 Z= 0.306 Chirality : 0.044 0.179 974 Planarity : 0.004 0.051 1144 Dihedral : 5.011 41.504 932 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.99 % Allowed : 18.54 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.64 (0.30), residues: 820 helix: -2.86 (0.63), residues: 41 sheet: -0.25 (0.29), residues: 297 loop : -0.21 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 172 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.002 PHE J 136 TYR 0.015 0.001 TYR I 50 ARG 0.003 0.000 ARG I 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.18 seconds wall clock time: 69 minutes 55.12 seconds (4195.12 seconds total)