Starting phenix.real_space_refine on Mon Mar 11 00:43:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6k_33642/03_2024/7y6k_33642.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6k_33642/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6k_33642/03_2024/7y6k_33642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6k_33642/03_2024/7y6k_33642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6k_33642/03_2024/7y6k_33642.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y6k_33642/03_2024/7y6k_33642.pdb" } 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 Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 3.92, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 343 " Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.81 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: 1.97 Time building geometry restraints manager: 2.42 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: 99.45 - 106.36: 186 106.36 - 113.27: 3442 113.27 - 120.19: 2185 120.19 - 127.10: 2979 127.10 - 134.01: 70 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 2.440 nonbonded pdb=" OH TYR I 37 " pdb=" OH TYR I 99 " model vdw 2.223 2.440 nonbonded pdb=" O PHE E 29 " pdb=" NH2 ARG E 72 " model vdw 2.233 2.520 nonbonded pdb=" O PRO E 143 " pdb=" OG1 THR E 241 " model vdw 2.250 2.440 nonbonded pdb=" N VAL E 170 " pdb=" OD1 ASP E 188 " model vdw 2.253 2.520 ... (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 ========== 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: 3.340 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: 13.350 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.690 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.460 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.739 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: 0.2395 time to fit residues: 31.3395 Evaluate side-chains 100 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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: 0.5980 chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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: 0.7789 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6515 Z= 0.289 Angle : 0.595 6.266 8862 Z= 0.308 Chirality : 0.044 0.173 974 Planarity : 0.005 0.043 1144 Dihedral : 4.824 33.227 933 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.00 % Allowed : 10.27 % Favored : 86.73 % 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: -0.96 (0.30), residues: 820 helix: -3.33 (0.58), residues: 47 sheet: -0.51 (0.30), residues: 270 loop : -0.34 (0.30), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.004 0.001 HIS I 192 PHE 0.012 0.002 PHE B 338 TYR 0.019 0.002 TYR B 453 ARG 0.011 0.001 ARG I 214 *********************** 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 127 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.681 Fit side-chains REVERT: J 65 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8051 (mmtt) outliers start: 21 outliers final: 20 residues processed: 118 average time/residue: 0.2034 time to fit residues: 31.0281 Evaluate side-chains 113 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 398 ASP 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 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 135 VAL 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 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: 0.8980 chunk 22 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6515 Z= 0.233 Angle : 0.552 5.869 8862 Z= 0.287 Chirality : 0.043 0.165 974 Planarity : 0.004 0.043 1144 Dihedral : 4.727 37.916 933 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.57 % Allowed : 13.27 % Favored : 83.17 % 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: -0.81 (0.30), residues: 820 helix: -3.16 (0.69), residues: 41 sheet: -0.41 (0.30), residues: 270 loop : -0.30 (0.30), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 50 HIS 0.003 0.001 HIS I 192 PHE 0.009 0.002 PHE I 142 TYR 0.015 0.001 TYR I 50 ARG 0.004 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 128 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.714 Fit side-chains REVERT: E 164 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7910 (m110) REVERT: J 65 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8020 (mttt) outliers start: 25 outliers final: 20 residues processed: 113 average time/residue: 0.2009 time to fit residues: 29.5043 Evaluate side-chains 117 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 48 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 3 GLN Chi-restraints excluded: chain J residue 30 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 78 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 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 E 74 ASN 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: 0.7816 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6515 Z= 0.298 Angle : 0.569 6.082 8862 Z= 0.297 Chirality : 0.044 0.165 974 Planarity : 0.004 0.042 1144 Dihedral : 4.841 41.193 933 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.71 % Allowed : 13.12 % Favored : 82.17 % 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: -0.79 (0.30), residues: 820 helix: -3.26 (0.67), residues: 41 sheet: -0.37 (0.30), residues: 271 loop : -0.29 (0.30), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 50 HIS 0.003 0.001 HIS I 192 PHE 0.013 0.002 PHE E 68 TYR 0.016 0.001 TYR I 50 ARG 0.004 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 fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 0.691 Fit side-chains REVERT: B 405 ASP cc_start: 0.8127 (m-30) cc_final: 0.7907 (m-30) REVERT: E 164 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8211 (m110) REVERT: J 65 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8056 (mttt) outliers start: 33 outliers final: 26 residues processed: 120 average time/residue: 0.2016 time to fit residues: 31.7844 Evaluate side-chains 127 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP 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 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 70 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.3980 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 overall best weight: 0.5320 ------------------------------------------------------------------------------- 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 519 HIS 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: 0.7795 moved from start: 0.1461 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= 0.242 Angle : 0.551 5.764 8862 Z= 0.286 Chirality : 0.043 0.167 974 Planarity : 0.004 0.044 1144 Dihedral : 4.834 43.988 933 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.28 % Allowed : 15.26 % 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: -0.72 (0.31), residues: 820 helix: -3.27 (0.65), residues: 41 sheet: -0.33 (0.30), residues: 272 loop : -0.22 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 50 HIS 0.001 0.000 HIS I 201 PHE 0.009 0.002 PHE I 142 TYR 0.015 0.001 TYR E 32 ARG 0.003 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 fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.723 Fit side-chains REVERT: E 164 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8136 (m110) REVERT: J 65 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8063 (mttt) outliers start: 30 outliers final: 26 residues processed: 117 average time/residue: 0.1834 time to fit residues: 28.6753 Evaluate side-chains 122 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP 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 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 70 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 6515 Z= 0.316 Angle : 0.573 6.086 8862 Z= 0.299 Chirality : 0.044 0.162 974 Planarity : 0.004 0.046 1144 Dihedral : 4.973 46.022 933 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.71 % Allowed : 15.83 % 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: -0.80 (0.31), residues: 820 helix: -3.30 (0.64), residues: 41 sheet: -0.35 (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 B 519 PHE 0.011 0.002 PHE B 400 TYR 0.016 0.001 TYR I 50 ARG 0.003 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 133 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 0.819 Fit side-chains REVERT: J 60 TYR cc_start: 0.8419 (m-80) cc_final: 0.7469 (m-80) REVERT: J 65 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8146 (mttt) outliers start: 33 outliers final: 28 residues processed: 120 average time/residue: 0.2207 time to fit residues: 35.1538 Evaluate side-chains 124 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP 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 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 70 THR Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 171 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 0.0570 chunk 78 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.0050 chunk 23 optimal weight: 0.0870 overall best weight: 0.3692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 I 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1714 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= 0.198 Angle : 0.530 5.402 8862 Z= 0.276 Chirality : 0.042 0.151 974 Planarity : 0.004 0.046 1144 Dihedral : 4.821 48.311 933 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.28 % Allowed : 16.98 % 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: -0.67 (0.30), residues: 820 helix: -3.23 (0.62), residues: 41 sheet: -0.26 (0.30), residues: 280 loop : -0.21 (0.31), residues: 499 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 0.009 0.001 PHE E 29 TYR 0.013 0.001 TYR I 50 ARG 0.002 0.000 ARG E 72 *********************** 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 129 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.797 Fit side-chains REVERT: J 60 TYR cc_start: 0.8329 (m-80) cc_final: 0.7440 (m-80) REVERT: J 65 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8122 (mttt) outliers start: 30 outliers final: 25 residues processed: 116 average time/residue: 0.1944 time to fit residues: 29.6691 Evaluate side-chains 124 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 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 498 GLN 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 70 THR Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 171 SER 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 125 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 61 optimal weight: 0.0010 chunk 71 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6515 Z= 0.193 Angle : 0.538 5.426 8862 Z= 0.279 Chirality : 0.043 0.154 974 Planarity : 0.004 0.046 1144 Dihedral : 4.450 32.661 931 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.99 % Allowed : 17.97 % 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: -0.52 (0.31), residues: 820 helix: -3.15 (0.62), residues: 41 sheet: -0.08 (0.30), residues: 290 loop : -0.16 (0.31), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.009 0.001 PHE I 142 TYR 0.014 0.001 TYR E 32 ARG 0.002 0.000 ARG E 72 *********************** 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 121 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.735 Fit side-chains REVERT: E 43 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7768 (ttmm) REVERT: J 65 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8013 (mttm) REVERT: J 114 MET cc_start: 0.8972 (ttm) cc_final: 0.8582 (mtt) outliers start: 28 outliers final: 26 residues processed: 109 average time/residue: 0.2039 time to fit residues: 29.0203 Evaluate side-chains 119 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP 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 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 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 70 THR Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 171 SER 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 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6515 Z= 0.330 Angle : 0.587 7.272 8862 Z= 0.304 Chirality : 0.044 0.157 974 Planarity : 0.004 0.046 1144 Dihedral : 4.708 34.513 931 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.28 % Allowed : 17.55 % Favored : 78.17 % 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: -0.60 (0.31), residues: 820 helix: -3.26 (0.62), residues: 41 sheet: -0.17 (0.30), residues: 287 loop : -0.18 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 172 HIS 0.002 0.001 HIS B 519 PHE 0.013 0.002 PHE E 102 TYR 0.017 0.002 TYR E 32 ARG 0.002 0.000 ARG B 403 *********************** 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 129 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 99 time to evaluate : 0.813 Fit side-chains REVERT: E 43 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7791 (ttmm) REVERT: I 70 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7107 (p) REVERT: I 83 ASP cc_start: 0.8081 (m-30) cc_final: 0.7797 (t0) REVERT: J 65 LYS cc_start: 0.8493 (mmtt) cc_final: 0.7990 (mttm) REVERT: J 114 MET cc_start: 0.9012 (ttm) cc_final: 0.8636 (mtt) outliers start: 30 outliers final: 27 residues processed: 117 average time/residue: 0.2017 time to fit residues: 31.7690 Evaluate side-chains 123 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP 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 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 70 THR Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 171 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 9.9990 chunk 74 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1925 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= 0.231 Angle : 0.556 6.037 8862 Z= 0.289 Chirality : 0.043 0.179 974 Planarity : 0.004 0.046 1144 Dihedral : 4.597 33.643 931 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.99 % Allowed : 17.83 % Favored : 78.17 % 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: -0.56 (0.31), residues: 820 helix: -3.19 (0.62), residues: 41 sheet: -0.08 (0.30), residues: 286 loop : -0.20 (0.31), residues: 493 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 0.009 0.001 PHE I 142 TYR 0.017 0.001 TYR E 32 ARG 0.002 0.000 ARG B 403 ********************** 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 126 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 0.737 Fit side-chains REVERT: E 43 LYS cc_start: 0.7984 (ttpt) cc_final: 0.7728 (ttmm) REVERT: J 60 TYR cc_start: 0.8352 (m-80) cc_final: 0.7360 (m-80) REVERT: J 65 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8029 (mttm) REVERT: J 114 MET cc_start: 0.8989 (ttm) cc_final: 0.8604 (mtt) outliers start: 28 outliers final: 27 residues processed: 114 average time/residue: 0.2083 time to fit residues: 31.5223 Evaluate side-chains 123 residues out of total 703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP 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 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 70 THR Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 171 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3960 r_free = 0.3960 target = 0.179811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137976 restraints weight = 6960.588| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.14 r_work: 0.3188 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6515 Z= 0.282 Angle : 0.578 7.550 8862 Z= 0.298 Chirality : 0.044 0.177 974 Planarity : 0.004 0.047 1144 Dihedral : 4.817 34.803 931 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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 : 0.13 % 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: -0.60 (0.31), residues: 820 helix: -3.14 (0.63), residues: 41 sheet: -0.07 (0.30), residues: 296 loop : -0.27 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.002 PHE B 400 TYR 0.018 0.001 TYR E 32 ARG 0.002 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.48 seconds wall clock time: 38 minutes 25.59 seconds (2305.59 seconds total)