Starting phenix.real_space_refine on Sat May 10 14:35:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6k_33642/05_2025/7y6k_33642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6k_33642/05_2025/7y6k_33642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y6k_33642/05_2025/7y6k_33642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6k_33642/05_2025/7y6k_33642.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6k_33642/05_2025/7y6k_33642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6k_33642/05_2025/7y6k_33642.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.126 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4010 2.51 5 N 1069 2.21 5 O 1259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.21, per 1000 atoms: 0.50 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: 1.47 Conformation dependent library (CDL) restraints added in 956.3 milliseconds 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 22 sheets defined 8.5% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 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: 2.50 Time building geometry restraints manager: 1.77 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: 13.480 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 16.090 Find NCS groups from input model: 0.130 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- 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 6526 Z= 0.165 Angle : 0.653 7.995 8885 Z= 0.336 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 1) link_NAG-ASN : angle 1.76082 ( 3) hydrogen bonds : bond 0.12631 ( 211) hydrogen bonds : angle 7.94435 ( 573) SS BOND : bond 0.00291 ( 10) SS BOND : angle 1.30407 ( 20) covalent geometry : bond 0.00374 ( 6515) covalent geometry : angle 0.65032 ( 8862) *********************** 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 : 0.720 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: 0.2392 time to fit residues: 31.7883 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 : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain J residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 16 GLN I 28 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN I 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130057 restraints weight = 7072.484| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.53 r_work: 0.3122 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 6526 Z= 0.244 Angle : 0.652 6.829 8885 Z= 0.340 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.95397 ( 3) hydrogen bonds : bond 0.03147 ( 211) hydrogen bonds : angle 6.69399 ( 573) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.23581 ( 20) covalent geometry : bond 0.00562 ( 6515) covalent geometry : angle 0.64954 ( 8862) *********************** 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 : 0.811 Fit side-chains REVERT: E 164 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8148 (m110) REVERT: J 65 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8052 (mmtt) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.2235 time to fit residues: 34.7058 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 : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.175693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.131263 restraints weight = 7103.106| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.65 r_work: 0.3126 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6526 Z= 0.195 Angle : 0.599 6.275 8885 Z= 0.312 Chirality : 0.044 0.168 974 Planarity : 0.005 0.045 1144 Dihedral : 5.028 39.248 933 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.57 % Allowed : 15.12 % Favored : 81.31 % 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: -0.92 (0.31), residues: 820 helix: -3.23 (0.67), residues: 41 sheet: -0.50 (0.29), residues: 291 loop : -0.34 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.003 0.001 HIS I 192 PHE 0.011 0.002 PHE E 29 TYR 0.016 0.001 TYR I 50 ARG 0.003 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 1) link_NAG-ASN : angle 1.74309 ( 3) hydrogen bonds : bond 0.03005 ( 211) hydrogen bonds : angle 6.49677 ( 573) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.98563 ( 20) covalent geometry : bond 0.00450 ( 6515) covalent geometry : angle 0.59701 ( 8862) *********************** 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 : 0.724 Fit side-chains REVERT: B 405 ASP cc_start: 0.8205 (m-30) cc_final: 0.7953 (m-30) REVERT: E 164 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7937 (m110) REVERT: J 38 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8380 (ttp-170) REVERT: J 65 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8062 (mmtt) outliers start: 25 outliers final: 22 residues processed: 116 average time/residue: 0.2074 time to fit residues: 31.3705 Evaluate side-chains 120 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 498 GLN 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 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 8 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.174115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.129994 restraints weight = 7092.144| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.74 r_work: 0.3093 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6526 Z= 0.230 Angle : 0.611 6.185 8885 Z= 0.319 Chirality : 0.045 0.169 974 Planarity : 0.005 0.046 1144 Dihedral : 5.140 41.520 933 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.71 % Allowed : 14.98 % Favored : 80.31 % 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: -0.91 (0.31), residues: 820 helix: -3.21 (0.67), residues: 41 sheet: -0.49 (0.29), residues: 292 loop : -0.34 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 50 HIS 0.003 0.001 HIS I 192 PHE 0.012 0.002 PHE B 400 TYR 0.017 0.002 TYR I 50 ARG 0.003 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 1) link_NAG-ASN : angle 1.79026 ( 3) hydrogen bonds : bond 0.03032 ( 211) hydrogen bonds : angle 6.50243 ( 573) SS BOND : bond 0.00267 ( 10) SS BOND : angle 1.01255 ( 20) covalent geometry : bond 0.00533 ( 6515) covalent geometry : angle 0.60856 ( 8862) *********************** 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 133 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.709 Fit side-chains REVERT: B 405 ASP cc_start: 0.8201 (m-30) cc_final: 0.7920 (m-30) REVERT: J 65 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8046 (mttt) outliers start: 33 outliers final: 26 residues processed: 119 average time/residue: 0.2046 time to fit residues: 31.4722 Evaluate side-chains 124 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR 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 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 31 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 519 HIS I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.175896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.132711 restraints weight = 7035.570| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.39 r_work: 0.3129 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6526 Z= 0.168 Angle : 0.582 6.348 8885 Z= 0.305 Chirality : 0.044 0.174 974 Planarity : 0.005 0.048 1144 Dihedral : 5.074 43.200 933 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.14 % Allowed : 16.83 % Favored : 79.03 % 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: -0.83 (0.31), residues: 820 helix: -3.06 (0.68), residues: 41 sheet: -0.44 (0.29), residues: 292 loop : -0.30 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 50 HIS 0.001 0.000 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 1) link_NAG-ASN : angle 1.67402 ( 3) hydrogen bonds : bond 0.02783 ( 211) hydrogen bonds : angle 6.30477 ( 573) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.87388 ( 20) covalent geometry : bond 0.00387 ( 6515) covalent geometry : angle 0.58043 ( 8862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1640 Ramachandran restraints generated. 820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.650 Fit side-chains REVERT: B 405 ASP cc_start: 0.8155 (m-30) cc_final: 0.7909 (m-30) REVERT: J 60 TYR cc_start: 0.8454 (m-80) cc_final: 0.7769 (m-80) REVERT: J 65 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8138 (mmtt) outliers start: 29 outliers final: 25 residues processed: 117 average time/residue: 0.1852 time to fit residues: 28.6011 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 : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 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 93 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** 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 = 0.3889 r_free = 0.3889 target = 0.174180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130801 restraints weight = 7008.340| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.40 r_work: 0.3105 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6526 Z= 0.214 Angle : 0.600 6.407 8885 Z= 0.314 Chirality : 0.044 0.167 974 Planarity : 0.005 0.049 1144 Dihedral : 5.175 44.961 933 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -0.84 (0.31), residues: 820 helix: -3.12 (0.66), residues: 41 sheet: -0.42 (0.29), residues: 292 loop : -0.32 (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 B 519 PHE 0.012 0.002 PHE E 29 TYR 0.015 0.001 TYR I 50 ARG 0.004 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00267 ( 1) link_NAG-ASN : angle 1.76055 ( 3) hydrogen bonds : bond 0.02893 ( 211) hydrogen bonds : angle 6.32588 ( 573) SS BOND : bond 0.00270 ( 10) SS BOND : angle 0.95269 ( 20) covalent geometry : bond 0.00498 ( 6515) covalent geometry : angle 0.59775 ( 8862) *********************** 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 134 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.722 Fit side-chains REVERT: B 405 ASP cc_start: 0.8181 (m-30) cc_final: 0.7915 (m-30) REVERT: I 106 LYS cc_start: 0.8534 (tptp) cc_final: 0.8274 (tptp) REVERT: J 60 TYR cc_start: 0.8469 (m-80) cc_final: 0.7717 (m-80) REVERT: J 65 LYS cc_start: 0.8427 (mmtt) cc_final: 0.8148 (mmtt) REVERT: J 114 MET cc_start: 0.8918 (ttm) cc_final: 0.8493 (mtt) outliers start: 31 outliers final: 25 residues processed: 120 average time/residue: 0.2050 time to fit residues: 31.7712 Evaluate side-chains 124 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 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 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.181346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.138994 restraints weight = 6948.380| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.04 r_work: 0.3302 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6526 Z= 0.207 Angle : 0.596 6.485 8885 Z= 0.313 Chirality : 0.044 0.158 974 Planarity : 0.005 0.049 1144 Dihedral : 5.162 45.955 932 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.85 % Allowed : 17.83 % 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: -0.90 (0.30), residues: 820 helix: -3.09 (0.64), residues: 41 sheet: -0.47 (0.29), residues: 293 loop : -0.35 (0.31), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.002 0.000 HIS B 519 PHE 0.012 0.002 PHE E 29 TYR 0.016 0.002 TYR I 50 ARG 0.005 0.000 ARG J 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 1) link_NAG-ASN : angle 1.75074 ( 3) hydrogen bonds : bond 0.02844 ( 211) hydrogen bonds : angle 6.28765 ( 573) SS BOND : bond 0.00237 ( 10) SS BOND : angle 0.93286 ( 20) covalent geometry : bond 0.00481 ( 6515) covalent geometry : angle 0.59384 ( 8862) *********************** 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 130 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.684 Fit side-chains REVERT: B 405 ASP cc_start: 0.8339 (m-30) cc_final: 0.8103 (m-30) REVERT: I 106 LYS cc_start: 0.8610 (tptp) cc_final: 0.8319 (tptp) REVERT: J 60 TYR cc_start: 0.8519 (m-80) cc_final: 0.7749 (m-80) REVERT: J 65 LYS cc_start: 0.8454 (mmtt) cc_final: 0.8119 (mttt) REVERT: J 114 MET cc_start: 0.8978 (ttm) cc_final: 0.8561 (mtt) outliers start: 27 outliers final: 26 residues processed: 120 average time/residue: 0.1876 time to fit residues: 29.6170 Evaluate side-chains 127 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 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 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.182564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140102 restraints weight = 6999.771| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.98 r_work: 0.3308 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6526 Z= 0.204 Angle : 0.604 6.500 8885 Z= 0.318 Chirality : 0.044 0.157 974 Planarity : 0.005 0.051 1144 Dihedral : 5.123 39.229 932 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.85 % Allowed : 17.83 % 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: -0.91 (0.30), residues: 820 helix: -2.96 (0.66), residues: 41 sheet: -0.52 (0.29), residues: 299 loop : -0.33 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.002 0.001 HIS B 519 PHE 0.016 0.002 PHE E 68 TYR 0.017 0.002 TYR I 50 ARG 0.004 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 1.75230 ( 3) hydrogen bonds : bond 0.02866 ( 211) hydrogen bonds : angle 6.26625 ( 573) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.90476 ( 20) covalent geometry : bond 0.00473 ( 6515) covalent geometry : angle 0.60204 ( 8862) *********************** 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 127 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.689 Fit side-chains REVERT: B 405 ASP cc_start: 0.8263 (m-30) cc_final: 0.8033 (m-30) REVERT: I 57 SER cc_start: 0.8426 (m) cc_final: 0.8178 (p) REVERT: I 106 LYS cc_start: 0.8626 (tptp) cc_final: 0.8338 (tptp) REVERT: J 60 TYR cc_start: 0.8517 (m-80) cc_final: 0.7803 (m-80) REVERT: J 65 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8114 (mttt) REVERT: J 114 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8581 (mtt) outliers start: 27 outliers final: 25 residues processed: 115 average time/residue: 0.1947 time to fit residues: 29.4284 Evaluate side-chains 125 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 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 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.177174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134877 restraints weight = 7089.398| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.27 r_work: 0.3135 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6526 Z= 0.189 Angle : 0.593 6.682 8885 Z= 0.312 Chirality : 0.044 0.156 974 Planarity : 0.005 0.051 1144 Dihedral : 5.148 44.381 932 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.14 % Allowed : 18.26 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.30), residues: 820 helix: -2.96 (0.66), residues: 41 sheet: -0.47 (0.29), residues: 299 loop : -0.31 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.002 0.000 HIS B 519 PHE 0.018 0.002 PHE E 68 TYR 0.016 0.001 TYR I 50 ARG 0.004 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 1.72032 ( 3) hydrogen bonds : bond 0.02792 ( 211) hydrogen bonds : angle 6.21977 ( 573) SS BOND : bond 0.00252 ( 10) SS BOND : angle 0.86374 ( 20) covalent geometry : bond 0.00440 ( 6515) covalent geometry : angle 0.59199 ( 8862) *********************** 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 to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.684 Fit side-chains REVERT: B 405 ASP cc_start: 0.8276 (m-30) cc_final: 0.8073 (m-30) REVERT: I 57 SER cc_start: 0.8416 (m) cc_final: 0.8195 (p) REVERT: I 106 LYS cc_start: 0.8562 (tptp) cc_final: 0.8287 (tptp) REVERT: J 60 TYR cc_start: 0.8530 (m-80) cc_final: 0.7719 (m-80) REVERT: J 65 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8101 (mttt) REVERT: J 114 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8649 (mtt) outliers start: 29 outliers final: 27 residues processed: 117 average time/residue: 0.1917 time to fit residues: 29.4729 Evaluate side-chains 126 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 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 60 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.180717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137764 restraints weight = 7045.746| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.04 r_work: 0.3164 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6526 Z= 0.197 Angle : 0.603 7.714 8885 Z= 0.315 Chirality : 0.044 0.157 974 Planarity : 0.005 0.051 1144 Dihedral : 5.166 43.989 932 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.14 % Allowed : 17.97 % 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: -0.84 (0.30), residues: 820 helix: -2.82 (0.69), residues: 41 sheet: -0.46 (0.29), residues: 299 loop : -0.30 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.002 0.000 HIS B 519 PHE 0.018 0.002 PHE E 68 TYR 0.017 0.001 TYR I 50 ARG 0.005 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 1) link_NAG-ASN : angle 1.73227 ( 3) hydrogen bonds : bond 0.02802 ( 211) hydrogen bonds : angle 6.25300 ( 573) SS BOND : bond 0.00223 ( 10) SS BOND : angle 0.89366 ( 20) covalent geometry : bond 0.00457 ( 6515) covalent geometry : angle 0.60124 ( 8862) ********************** 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 128 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.691 Fit side-chains REVERT: E 43 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7714 (ttmm) REVERT: I 57 SER cc_start: 0.8430 (m) cc_final: 0.8228 (p) REVERT: I 106 LYS cc_start: 0.8564 (tptp) cc_final: 0.8294 (tptp) REVERT: J 60 TYR cc_start: 0.8518 (m-80) cc_final: 0.7646 (m-80) REVERT: J 65 LYS cc_start: 0.8458 (mmtt) cc_final: 0.8088 (mttt) REVERT: J 114 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8655 (mtt) outliers start: 29 outliers final: 27 residues processed: 116 average time/residue: 0.2088 time to fit residues: 31.6709 Evaluate side-chains 125 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 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 12 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.0570 overall best weight: 0.5076 ------------------------------------------------------------------------------- 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** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.184117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.141301 restraints weight = 7144.029| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.05 r_work: 0.3191 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6526 Z= 0.161 Angle : 0.587 7.349 8885 Z= 0.306 Chirality : 0.044 0.154 974 Planarity : 0.004 0.051 1144 Dihedral : 5.095 43.790 932 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.71 % Allowed : 18.12 % 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: -0.80 (0.30), residues: 820 helix: -2.90 (0.63), residues: 41 sheet: -0.39 (0.29), residues: 297 loop : -0.30 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE E 68 TYR 0.015 0.001 TYR I 50 ARG 0.005 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 1) link_NAG-ASN : angle 1.64557 ( 3) hydrogen bonds : bond 0.02692 ( 211) hydrogen bonds : angle 6.13604 ( 573) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.82125 ( 20) covalent geometry : bond 0.00374 ( 6515) covalent geometry : angle 0.58567 ( 8862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.12 seconds wall clock time: 67 minutes 22.37 seconds (4042.37 seconds total)