Starting phenix.real_space_refine on Fri Dec 27 18:50:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6k_33642/12_2024/7y6k_33642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6k_33642/12_2024/7y6k_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_33642/12_2024/7y6k_33642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6k_33642/12_2024/7y6k_33642.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6k_33642/12_2024/7y6k_33642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6k_33642/12_2024/7y6k_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-5532/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: 4.88, per 1000 atoms: 0.77 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: 1.53 Conformation dependent library (CDL) restraints added in 928.5 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: 1.17 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: 2.58 Time building geometry restraints manager: 1.79 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: 7.460 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.260 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.100 ------------------------------------------------------------------------------- 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 : 0.691 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: 0.2268 time to fit residues: 29.7354 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 : 0.658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1100 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 35.418 933 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 : 0.752 Fit side-chains REVERT: B 406 GLU cc_start: 0.8211 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 164 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7958 (m110) REVERT: J 65 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8052 (mmtt) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.2124 time to fit residues: 32.7748 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 : 0.743 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6515 Z= 0.331 Angle : 0.610 6.312 8862 Z= 0.317 Chirality : 0.045 0.171 974 Planarity : 0.005 0.045 1144 Dihedral : 5.079 39.689 933 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.57 % Allowed : 15.26 % Favored : 81.17 % 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: -0.94 (0.30), residues: 820 helix: -3.27 (0.66), residues: 41 sheet: -0.52 (0.29), residues: 291 loop : -0.35 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 50 HIS 0.002 0.001 HIS I 192 PHE 0.012 0.002 PHE E 29 TYR 0.017 0.002 TYR I 50 ARG 0.003 0.000 ARG I 62 *********************** 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 131 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.748 Fit side-chains REVERT: B 405 ASP cc_start: 0.8108 (m-30) cc_final: 0.7861 (m-30) REVERT: B 406 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8014 (mt-10) REVERT: E 164 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7945 (m110) REVERT: J 38 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.8325 (ttp-170) REVERT: J 65 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8079 (mmtt) outliers start: 25 outliers final: 22 residues processed: 116 average time/residue: 0.2015 time to fit residues: 30.5725 Evaluate side-chains 119 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 164 ASN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 78 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1548 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= 0.275 Angle : 0.578 6.220 8862 Z= 0.302 Chirality : 0.044 0.178 974 Planarity : 0.005 0.046 1144 Dihedral : 5.043 41.906 933 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.85 % Allowed : 14.98 % Favored : 80.17 % 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: -3.18 (0.67), residues: 41 sheet: -0.45 (0.29), residues: 292 loop : -0.30 (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 0.012 0.002 PHE E 29 TYR 0.016 0.001 TYR I 50 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 134 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.838 Fit side-chains REVERT: B 405 ASP cc_start: 0.8085 (m-30) cc_final: 0.7858 (m-30) REVERT: B 406 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7954 (mt-10) REVERT: J 38 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8315 (ttp-170) REVERT: J 60 TYR cc_start: 0.8368 (m-80) cc_final: 0.7876 (m-80) REVERT: J 65 LYS cc_start: 0.8483 (mmtt) cc_final: 0.8071 (mttt) outliers start: 34 outliers final: 28 residues processed: 120 average time/residue: 0.2137 time to fit residues: 33.1804 Evaluate side-chains 133 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU 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 1 optimal weight: 0.5980 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6515 Z= 0.277 Angle : 0.583 6.303 8862 Z= 0.305 Chirality : 0.044 0.171 974 Planarity : 0.005 0.048 1144 Dihedral : 5.054 43.532 933 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.56 % Allowed : 15.69 % Favored : 79.74 % 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: -0.81 (0.31), residues: 820 helix: -3.13 (0.66), 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 0.002 0.001 HIS J 178 PHE 0.016 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 134 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.643 Fit side-chains REVERT: B 405 ASP cc_start: 0.8103 (m-30) cc_final: 0.7899 (m-30) REVERT: B 406 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7842 (mt-10) REVERT: J 60 TYR cc_start: 0.8372 (m-80) cc_final: 0.7789 (m-80) REVERT: J 65 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8109 (mttt) outliers start: 32 outliers final: 28 residues processed: 120 average time/residue: 0.2008 time to fit residues: 31.4382 Evaluate side-chains 124 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 93 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 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 45 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.0030 chunk 41 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6515 Z= 0.217 Angle : 0.558 6.434 8862 Z= 0.290 Chirality : 0.043 0.161 974 Planarity : 0.004 0.049 1144 Dihedral : 4.999 45.907 933 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.42 % Allowed : 16.83 % 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: -0.74 (0.30), residues: 820 helix: -3.07 (0.66), residues: 41 sheet: -0.29 (0.30), residues: 279 loop : -0.29 (0.31), residues: 500 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 0.011 0.002 PHE E 29 TYR 0.014 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 131 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.767 Fit side-chains REVERT: B 406 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7814 (mt-10) REVERT: J 60 TYR cc_start: 0.8327 (m-80) cc_final: 0.7588 (m-80) REVERT: J 65 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8171 (mmtt) REVERT: J 114 MET cc_start: 0.8978 (ttm) cc_final: 0.8563 (mtt) outliers start: 31 outliers final: 29 residues processed: 116 average time/residue: 0.1948 time to fit residues: 29.8329 Evaluate side-chains 130 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 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 93 VAL Chi-restraints excluded: chain E residue 156 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 chunk 31 optimal weight: 0.0670 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.4322 ------------------------------------------------------------------------------- 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** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6515 Z= 0.217 Angle : 0.554 6.603 8862 Z= 0.288 Chirality : 0.043 0.169 974 Planarity : 0.004 0.050 1144 Dihedral : 4.959 47.432 933 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.99 % Allowed : 17.69 % Favored : 78.32 % 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: -0.71 (0.30), residues: 820 helix: -2.91 (0.69), residues: 41 sheet: -0.26 (0.30), residues: 280 loop : -0.29 (0.31), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE E 68 TYR 0.014 0.001 TYR B 369 ARG 0.004 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 123 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 1.083 Fit side-chains REVERT: E 110 TYR cc_start: 0.8616 (m-80) cc_final: 0.8388 (m-80) REVERT: E 209 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8538 (m) REVERT: J 60 TYR cc_start: 0.8300 (m-80) cc_final: 0.7553 (m-80) REVERT: J 65 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8180 (mmtt) REVERT: J 114 MET cc_start: 0.8974 (ttm) cc_final: 0.8604 (mtt) outliers start: 28 outliers final: 25 residues processed: 110 average time/residue: 0.2041 time to fit residues: 29.8597 Evaluate side-chains 118 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 156 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6515 Z= 0.334 Angle : 0.587 6.600 8862 Z= 0.306 Chirality : 0.044 0.165 974 Planarity : 0.004 0.051 1144 Dihedral : 4.831 34.866 932 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.42 % Allowed : 17.26 % Favored : 78.32 % 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: -3.02 (0.66), residues: 41 sheet: -0.30 (0.29), residues: 292 loop : -0.29 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 172 HIS 0.002 0.001 HIS B 519 PHE 0.012 0.002 PHE B 400 TYR 0.016 0.002 TYR B 369 ARG 0.005 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 130 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.663 Fit side-chains REVERT: E 110 TYR cc_start: 0.8747 (m-80) cc_final: 0.8535 (m-80) REVERT: J 60 TYR cc_start: 0.8359 (m-80) cc_final: 0.7559 (m-80) REVERT: J 65 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8202 (mmtt) REVERT: J 114 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8644 (mtt) outliers start: 31 outliers final: 28 residues processed: 116 average time/residue: 0.2061 time to fit residues: 31.0954 Evaluate side-chains 125 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 156 LEU 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 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 31 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2022 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= 0.279 Angle : 0.590 6.619 8862 Z= 0.308 Chirality : 0.044 0.166 974 Planarity : 0.004 0.052 1144 Dihedral : 4.819 35.071 931 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.28 % Allowed : 17.69 % 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: -0.76 (0.30), residues: 820 helix: -3.10 (0.63), residues: 41 sheet: -0.33 (0.29), residues: 299 loop : -0.27 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.012 0.002 PHE E 29 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 124 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.756 Fit side-chains REVERT: I 57 SER cc_start: 0.8385 (m) cc_final: 0.8140 (p) REVERT: J 60 TYR cc_start: 0.8351 (m-80) cc_final: 0.7507 (m-80) REVERT: J 65 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8205 (mmtt) REVERT: J 114 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8618 (mtt) outliers start: 30 outliers final: 28 residues processed: 110 average time/residue: 0.2077 time to fit residues: 30.0503 Evaluate side-chains 124 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 10.0000 chunk 74 optimal weight: 0.0040 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6515 Z= 0.274 Angle : 0.588 7.883 8862 Z= 0.306 Chirality : 0.044 0.160 974 Planarity : 0.005 0.052 1144 Dihedral : 4.816 35.167 931 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.99 % Allowed : 17.69 % Favored : 78.32 % 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: -0.73 (0.30), residues: 820 helix: -3.07 (0.63), residues: 41 sheet: -0.31 (0.29), residues: 299 loop : -0.25 (0.31), residues: 480 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 0.012 0.002 PHE E 29 TYR 0.016 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 122 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.822 Fit side-chains REVERT: I 57 SER cc_start: 0.8344 (m) cc_final: 0.8128 (p) REVERT: J 60 TYR cc_start: 0.8343 (m-80) cc_final: 0.7516 (m-80) REVERT: J 65 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8166 (mmtt) REVERT: J 114 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8628 (mtt) outliers start: 28 outliers final: 27 residues processed: 110 average time/residue: 0.2433 time to fit residues: 34.8250 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 : 0.801 ------------------------------------------------------------------------------- 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 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 0.0870 chunk 66 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 overall best weight: 0.1936 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.188153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.143480 restraints weight = 6861.335| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.19 r_work: 0.3280 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6515 Z= 0.175 Angle : 0.556 6.903 8862 Z= 0.288 Chirality : 0.043 0.162 974 Planarity : 0.004 0.051 1144 Dihedral : 4.659 33.661 931 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.14 % Allowed : 18.97 % Favored : 77.89 % 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: -0.61 (0.30), residues: 820 helix: -2.83 (0.65), residues: 41 sheet: -0.21 (0.29), residues: 287 loop : -0.21 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.014 0.002 PHE E 29 TYR 0.013 0.001 TYR B 369 ARG 0.005 0.000 ARG I 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2002.35 seconds wall clock time: 37 minutes 9.76 seconds (2229.76 seconds total)