Starting phenix.real_space_refine on Thu Jul 24 16:31:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y6k_33642/07_2025/7y6k_33642.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y6k_33642/07_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_33642/07_2025/7y6k_33642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y6k_33642/07_2025/7y6k_33642.map" model { file = "/net/cci-nas-00/data/ceres_data/7y6k_33642/07_2025/7y6k_33642.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y6k_33642/07_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-5711/modules/chem_data/mon_lib" Total number of atoms: 6363 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1723 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Chain: "I" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1590 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "J" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1493 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.95, per 1000 atoms: 0.94 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: 1.57 Conformation dependent library (CDL) restraints added in 1.1 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: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.041A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.660A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.555A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.525A pdb=" N ASP E 219 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E 220 " --> pdb=" O SER E 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 216 through 220' Processing helix chain 'I' and resid 124 through 131 removed outlier: 3.616A pdb=" N LEU I 128 " --> pdb=" O SER I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 191 removed outlier: 4.222A pdb=" N GLU I 190 " --> pdb=" O LYS I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.678A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 170 through 172 No H-bonds generated for 'chain 'J' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.553A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.654A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 145 through 148 removed outlier: 3.849A pdb=" N ALA E 146 " --> pdb=" O LYS E 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 153 through 157 Processing sheet with id=AB1, first strand: chain 'E' and resid 182 through 185 removed outlier: 6.333A pdb=" N TRP E 172 " --> pdb=" O LEU E 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'I' and resid 17 through 23 Processing sheet with id=AB4, first strand: chain 'I' and resid 46 through 49 removed outlier: 6.306A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 46 through 49 removed outlier: 6.306A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 117 through 121 removed outlier: 3.529A pdb=" N VAL I 136 " --> pdb=" O PHE I 121 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR I 176 " --> pdb=" O ASN I 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER I 179 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 148 through 150 Processing sheet with id=AB8, first strand: chain 'I' and resid 194 through 195 removed outlier: 3.526A pdb=" N TYR I 195 " --> pdb=" O PHE I 212 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE I 212 " --> pdb=" O TYR I 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.845A pdb=" N MET J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TRP J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.680A pdb=" N VAL J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 134 through 138 removed outlier: 4.309A pdb=" N GLY J 153 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU J 152 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 190 " --> pdb=" O ASP J 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 165 through 168 236 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.92 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: 20.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.470 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:5.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.760 ------------------------------------------------------------------------------- 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 : 1.654 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: 0.3546 time to fit residues: 47.8299 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 : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain J residue 156 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 16 GLN I 28 ASN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN I 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130060 restraints weight = 7072.470| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.53 r_work: 0.3123 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 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 35.421 933 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.00 % Allowed : 11.13 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.30), residues: 820 helix: -3.30 (0.67), residues: 41 sheet: -0.57 (0.29), residues: 280 loop : -0.39 (0.30), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 50 HIS 0.004 0.001 HIS I 192 PHE 0.015 0.002 PHE B 338 TYR 0.020 0.002 TYR B 453 ARG 0.003 0.001 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 1) link_NAG-ASN : angle 1.95396 ( 3) hydrogen bonds : bond 0.03147 ( 211) hydrogen bonds : angle 6.69390 ( 573) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.23583 ( 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 : 1.663 Fit side-chains REVERT: E 164 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8149 (m110) REVERT: J 65 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8053 (mmtt) outliers start: 21 outliers final: 18 residues processed: 120 average time/residue: 0.3679 time to fit residues: 56.7642 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 : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 3 optimal weight: 0.0070 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.176619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.132866 restraints weight = 7123.248| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.71 r_work: 0.3138 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6526 Z= 0.177 Angle : 0.590 6.133 8885 Z= 0.307 Chirality : 0.044 0.167 974 Planarity : 0.005 0.045 1144 Dihedral : 4.982 39.338 933 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.14 % Allowed : 15.41 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.30), residues: 820 helix: -3.20 (0.67), residues: 41 sheet: -0.47 (0.30), residues: 281 loop : -0.33 (0.31), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.002 0.001 HIS I 192 PHE 0.011 0.002 PHE E 29 TYR 0.016 0.001 TYR I 50 ARG 0.003 0.000 ARG J 19 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 1) link_NAG-ASN : angle 1.71030 ( 3) hydrogen bonds : bond 0.02948 ( 211) hydrogen bonds : angle 6.43992 ( 573) SS BOND : bond 0.00294 ( 10) SS BOND : angle 0.96985 ( 20) covalent geometry : bond 0.00407 ( 6515) covalent geometry : angle 0.58788 ( 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 128 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.604 Fit side-chains REVERT: B 405 ASP cc_start: 0.8158 (m-30) cc_final: 0.7958 (m-30) REVERT: J 38 ARG cc_start: 0.8558 (ttp-170) cc_final: 0.8311 (ttp-170) REVERT: J 65 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8047 (mmtt) outliers start: 22 outliers final: 20 residues processed: 115 average time/residue: 0.5205 time to fit residues: 80.8593 Evaluate side-chains 113 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 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 = 0.3900 r_free = 0.3900 target = 0.175353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131921 restraints weight = 7090.135| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.56 r_work: 0.3121 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6526 Z= 0.194 Angle : 0.586 5.990 8885 Z= 0.306 Chirality : 0.044 0.167 974 Planarity : 0.005 0.045 1144 Dihedral : 5.019 41.178 933 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.85 % Allowed : 14.69 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 820 helix: -3.14 (0.68), residues: 41 sheet: -0.44 (0.29), residues: 292 loop : -0.31 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 50 HIS 0.003 0.001 HIS I 192 PHE 0.011 0.002 PHE B 400 TYR 0.017 0.001 TYR B 369 ARG 0.003 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 1) link_NAG-ASN : angle 1.70674 ( 3) hydrogen bonds : bond 0.02911 ( 211) hydrogen bonds : angle 6.37308 ( 573) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.92859 ( 20) covalent geometry : bond 0.00447 ( 6515) covalent geometry : angle 0.58459 ( 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 135 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.109 Fit side-chains REVERT: B 405 ASP cc_start: 0.8199 (m-30) cc_final: 0.7940 (m-30) REVERT: J 38 ARG cc_start: 0.8616 (ttp-170) cc_final: 0.8413 (ttp-170) REVERT: J 65 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8030 (mttt) outliers start: 34 outliers final: 28 residues processed: 121 average time/residue: 0.3499 time to fit residues: 57.2052 Evaluate side-chains 132 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 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: 4.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.172580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.127539 restraints weight = 7063.364| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.82 r_work: 0.3085 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 6526 Z= 0.257 Angle : 0.634 6.365 8885 Z= 0.332 Chirality : 0.045 0.172 974 Planarity : 0.005 0.048 1144 Dihedral : 5.294 43.896 933 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.71 % Allowed : 15.69 % Favored : 79.60 % 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: -0.91 (0.31), residues: 820 helix: -3.19 (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 0.013 0.002 TRP J 50 HIS 0.001 0.001 HIS J 178 PHE 0.014 0.002 PHE B 400 TYR 0.018 0.002 TYR I 50 ARG 0.004 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.88157 ( 3) hydrogen bonds : bond 0.03080 ( 211) hydrogen bonds : angle 6.52357 ( 573) SS BOND : bond 0.00296 ( 10) SS BOND : angle 1.04140 ( 20) covalent geometry : bond 0.00594 ( 6515) covalent geometry : angle 0.63203 ( 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 138 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.700 Fit side-chains REVERT: B 405 ASP cc_start: 0.8388 (m-30) cc_final: 0.8127 (m-30) REVERT: J 60 TYR cc_start: 0.8602 (m-80) cc_final: 0.7977 (m-80) REVERT: J 65 LYS cc_start: 0.8521 (mmtt) cc_final: 0.8091 (mttt) outliers start: 33 outliers final: 29 residues processed: 123 average time/residue: 0.2147 time to fit residues: 34.0585 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 : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 22 CYS Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 64 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.177328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.134526 restraints weight = 6990.475| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.42 r_work: 0.3141 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6526 Z= 0.173 Angle : 0.584 6.461 8885 Z= 0.305 Chirality : 0.044 0.156 974 Planarity : 0.004 0.050 1144 Dihedral : 5.165 45.066 933 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.42 % Allowed : 17.55 % 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: -0.90 (0.30), residues: 820 helix: -3.13 (0.66), residues: 41 sheet: -0.46 (0.29), residues: 292 loop : -0.37 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 50 HIS 0.001 0.001 HIS B 519 PHE 0.013 0.002 PHE E 29 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 0.00286 ( 1) link_NAG-ASN : angle 1.69618 ( 3) hydrogen bonds : bond 0.02767 ( 211) hydrogen bonds : angle 6.28925 ( 573) SS BOND : bond 0.00224 ( 10) SS BOND : angle 0.91226 ( 20) covalent geometry : bond 0.00399 ( 6515) covalent geometry : angle 0.58186 ( 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 130 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 0.746 Fit side-chains REVERT: B 405 ASP cc_start: 0.8366 (m-30) cc_final: 0.8142 (m-30) REVERT: E 110 TYR cc_start: 0.8864 (m-80) cc_final: 0.8604 (m-80) REVERT: I 106 LYS cc_start: 0.8581 (tptp) cc_final: 0.8314 (tptp) REVERT: J 60 TYR cc_start: 0.8569 (m-80) cc_final: 0.7740 (m-80) REVERT: J 65 LYS cc_start: 0.8470 (mmtt) cc_final: 0.8158 (mmtt) REVERT: J 114 MET cc_start: 0.9024 (ttm) cc_final: 0.8552 (mtt) outliers start: 31 outliers final: 29 residues processed: 116 average time/residue: 0.2074 time to fit residues: 31.2642 Evaluate side-chains 126 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 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 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 56 optimal weight: 10.0000 chunk 67 optimal weight: 0.0010 chunk 51 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 overall best weight: 0.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.181590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.138284 restraints weight = 6963.931| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.14 r_work: 0.3236 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6526 Z= 0.122 Angle : 0.554 6.669 8885 Z= 0.289 Chirality : 0.043 0.167 974 Planarity : 0.004 0.051 1144 Dihedral : 4.977 51.363 932 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.71 % Allowed : 18.26 % 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: -0.79 (0.30), residues: 820 helix: -2.91 (0.68), residues: 41 sheet: -0.31 (0.29), residues: 279 loop : -0.36 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.012 0.002 PHE E 29 TYR 0.013 0.001 TYR B 369 ARG 0.004 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 1) link_NAG-ASN : angle 1.56921 ( 3) hydrogen bonds : bond 0.02604 ( 211) hydrogen bonds : angle 6.02607 ( 573) SS BOND : bond 0.00247 ( 10) SS BOND : angle 0.75515 ( 20) covalent geometry : bond 0.00282 ( 6515) covalent geometry : angle 0.55289 ( 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 134 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.590 Fit side-chains REVERT: E 110 TYR cc_start: 0.8655 (m-80) cc_final: 0.8366 (m-80) REVERT: E 209 SER cc_start: 0.8952 (OUTLIER) cc_final: 0.8542 (m) REVERT: J 60 TYR cc_start: 0.8423 (m-80) cc_final: 0.7567 (m-80) REVERT: J 65 LYS cc_start: 0.8424 (mmtt) cc_final: 0.8152 (mmtt) REVERT: J 114 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8552 (mtt) outliers start: 26 outliers final: 21 residues processed: 120 average time/residue: 0.2296 time to fit residues: 34.9282 Evaluate side-chains 122 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 164 ASN 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 138 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 24 optimal weight: 0.0030 chunk 50 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.184151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141860 restraints weight = 6940.475| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.99 r_work: 0.3196 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6526 Z= 0.190 Angle : 0.595 6.611 8885 Z= 0.311 Chirality : 0.044 0.167 974 Planarity : 0.004 0.050 1144 Dihedral : 4.808 34.243 931 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.85 % Allowed : 17.97 % 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: -0.76 (0.30), residues: 820 helix: -3.03 (0.62), residues: 41 sheet: -0.29 (0.29), residues: 289 loop : -0.32 (0.31), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 172 HIS 0.001 0.000 HIS B 519 PHE 0.014 0.002 PHE E 68 TYR 0.016 0.002 TYR E 32 ARG 0.005 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 1) link_NAG-ASN : angle 1.69849 ( 3) hydrogen bonds : bond 0.02795 ( 211) hydrogen bonds : angle 6.08744 ( 573) SS BOND : bond 0.00230 ( 10) SS BOND : angle 0.83606 ( 20) covalent geometry : bond 0.00445 ( 6515) covalent geometry : angle 0.59333 ( 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 122 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.813 Fit side-chains REVERT: J 60 TYR cc_start: 0.8482 (m-80) cc_final: 0.7576 (m-80) REVERT: J 65 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8160 (mmtt) REVERT: J 114 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8594 (mtt) outliers start: 27 outliers final: 24 residues processed: 111 average time/residue: 0.2070 time to fit residues: 30.4737 Evaluate side-chains 119 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 164 ASN Chi-restraints excluded: chain E residue 188 ASP 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 30 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 165 THR Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.184259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141562 restraints weight = 7007.001| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.09 r_work: 0.3347 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6526 Z= 0.152 Angle : 0.583 7.372 8885 Z= 0.303 Chirality : 0.044 0.167 974 Planarity : 0.004 0.051 1144 Dihedral : 4.779 34.224 931 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.42 % Allowed : 18.26 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.30), residues: 820 helix: -3.07 (0.60), residues: 41 sheet: -0.25 (0.29), residues: 290 loop : -0.26 (0.31), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.012 0.002 PHE E 29 TYR 0.014 0.001 TYR I 50 ARG 0.005 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 1) link_NAG-ASN : angle 1.65668 ( 3) hydrogen bonds : bond 0.02685 ( 211) hydrogen bonds : angle 6.03255 ( 573) SS BOND : bond 0.00210 ( 10) SS BOND : angle 0.80044 ( 20) covalent geometry : bond 0.00356 ( 6515) covalent geometry : angle 0.58150 ( 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 123 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.716 Fit side-chains REVERT: E 110 TYR cc_start: 0.8722 (m-80) cc_final: 0.8386 (m-80) REVERT: J 60 TYR cc_start: 0.8449 (m-80) cc_final: 0.7654 (m-80) REVERT: J 65 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8113 (mttt) REVERT: J 114 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8528 (mtt) outliers start: 24 outliers final: 23 residues processed: 112 average time/residue: 0.1911 time to fit residues: 28.5941 Evaluate side-chains 120 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 164 ASN 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 30 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: 6.9990 chunk 40 optimal weight: 0.0040 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.186688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144134 restraints weight = 6976.417| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.09 r_work: 0.3315 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6526 Z= 0.143 Angle : 0.582 6.891 8885 Z= 0.302 Chirality : 0.044 0.177 974 Planarity : 0.004 0.051 1144 Dihedral : 4.746 34.132 931 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.42 % Allowed : 18.54 % 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: -0.64 (0.31), residues: 820 helix: -3.02 (0.60), residues: 41 sheet: -0.26 (0.29), residues: 297 loop : -0.18 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 50 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.002 PHE E 68 TYR 0.013 0.001 TYR I 50 ARG 0.005 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 1) link_NAG-ASN : angle 1.62827 ( 3) hydrogen bonds : bond 0.02665 ( 211) hydrogen bonds : angle 5.96915 ( 573) SS BOND : bond 0.00215 ( 10) SS BOND : angle 0.78377 ( 20) covalent geometry : bond 0.00334 ( 6515) covalent geometry : angle 0.58034 ( 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 121 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.720 Fit side-chains REVERT: E 110 TYR cc_start: 0.8682 (m-80) cc_final: 0.8320 (m-80) REVERT: E 209 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8607 (m) REVERT: J 60 TYR cc_start: 0.8404 (m-80) cc_final: 0.7658 (m-80) REVERT: J 65 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8093 (mttt) REVERT: J 114 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8526 (mtt) outliers start: 24 outliers final: 21 residues processed: 110 average time/residue: 0.1934 time to fit residues: 28.4900 Evaluate side-chains 117 residues out of total 703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 164 ASN 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 30 SER Chi-restraints excluded: chain J residue 114 MET Chi-restraints excluded: chain J residue 125 VAL Chi-restraints excluded: chain J residue 156 VAL Chi-restraints excluded: chain J residue 183 VAL Chi-restraints excluded: chain J residue 191 SER Chi-restraints excluded: chain J residue 192 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 GLN ** I 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.186019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.143223 restraints weight = 7140.382| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.10 r_work: 0.3207 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6526 Z= 0.163 Angle : 0.588 6.786 8885 Z= 0.306 Chirality : 0.044 0.174 974 Planarity : 0.004 0.051 1144 Dihedral : 4.748 34.510 931 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.42 % Allowed : 19.12 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.31), residues: 820 helix: -2.93 (0.61), residues: 41 sheet: -0.22 (0.29), residues: 297 loop : -0.17 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 172 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE E 68 TYR 0.014 0.001 TYR I 50 ARG 0.002 0.000 ARG I 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 1) link_NAG-ASN : angle 1.64122 ( 3) hydrogen bonds : bond 0.02690 ( 211) hydrogen bonds : angle 5.96971 ( 573) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.79481 ( 20) covalent geometry : bond 0.00381 ( 6515) covalent geometry : angle 0.58698 ( 8862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5171.14 seconds wall clock time: 93 minutes 42.90 seconds (5622.90 seconds total)