Starting phenix.real_space_refine on Thu Jun 5 04:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qtk_14143/06_2025/7qtk_14143.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qtk_14143/06_2025/7qtk_14143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qtk_14143/06_2025/7qtk_14143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qtk_14143/06_2025/7qtk_14143.map" model { file = "/net/cci-nas-00/data/ceres_data/7qtk_14143/06_2025/7qtk_14143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qtk_14143/06_2025/7qtk_14143.cif" } resolution = 3.84 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= -0.000 sd= 0.029 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 19 5.16 5 C 3171 2.51 5 N 845 2.21 5 O 974 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 5009 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.80, per 1000 atoms: 0.76 Number of scatterers: 5009 At special positions: 0 Unit cell: (71.9316, 103.747, 125.88, 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 19 16.00 O 974 8.00 N 845 7.00 C 3171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.05 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN D 343 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 575.3 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 13 sheets defined 11.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'D' and resid 337 through 343 removed outlier: 4.320A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.875A pdb=" N TYR D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.035A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 4.756A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.766A pdb=" N ASP B 31 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.853A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.654A pdb=" N LYS C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.731A pdb=" N HIS C 189 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 354 through 358 removed outlier: 4.132A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 473 through 474 removed outlier: 4.001A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 50 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.334A pdb=" N GLY B 10 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE B 114 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.547A pdb=" N GLY B 151 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.650A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.665A pdb=" N VAL C 19 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.135A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 114 through 118 removed outlier: 3.804A pdb=" N VAL C 133 " --> pdb=" O PHE C 118 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.260A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS C 145 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL C 196 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 205 " --> pdb=" O VAL C 196 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 859 1.32 - 1.45: 1457 1.45 - 1.57: 2798 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 5134 Sorted by residual: bond pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.32e-02 5.74e+03 1.53e+01 bond pdb=" CA SER C 93 " pdb=" CB SER C 93 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.26e+01 bond pdb=" N THR C 109 " pdb=" CA THR C 109 " ideal model delta sigma weight residual 1.455 1.498 -0.042 1.33e-02 5.65e+03 1.00e+01 bond pdb=" N VAL C 110 " pdb=" CA VAL C 110 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.37e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.45e+00 ... (remaining 5129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6696 1.64 - 3.28: 220 3.28 - 4.92: 50 4.92 - 6.57: 13 6.57 - 8.21: 4 Bond angle restraints: 6983 Sorted by residual: angle pdb=" C VAL C 96 " pdb=" N THR C 97 " pdb=" CA THR C 97 " ideal model delta sigma weight residual 122.39 115.93 6.46 1.48e+00 4.57e-01 1.90e+01 angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.47 104.26 8.21 2.06e+00 2.36e-01 1.59e+01 angle pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta sigma weight residual 110.37 117.38 -7.01 1.78e+00 3.16e-01 1.55e+01 angle pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N PRO C 95 " ideal model delta sigma weight residual 118.44 124.39 -5.95 1.59e+00 3.96e-01 1.40e+01 angle pdb=" CA LYS B 129 " pdb=" C LYS B 129 " pdb=" O LYS B 129 " ideal model delta sigma weight residual 121.40 117.32 4.08 1.11e+00 8.12e-01 1.35e+01 ... (remaining 6978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 2781 16.64 - 33.28: 240 33.28 - 49.92: 47 49.92 - 66.56: 13 66.56 - 83.20: 4 Dihedral angle restraints: 3085 sinusoidal: 1216 harmonic: 1869 Sorted by residual: dihedral pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual 122.80 138.48 -15.68 0 2.50e+00 1.60e-01 3.93e+01 dihedral pdb=" C TYR C 94 " pdb=" N TYR C 94 " pdb=" CA TYR C 94 " pdb=" CB TYR C 94 " ideal model delta harmonic sigma weight residual -122.60 -135.93 13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual 93.00 50.33 42.67 1 1.00e+01 1.00e-02 2.54e+01 ... (remaining 3082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 755 0.122 - 0.245: 18 0.245 - 0.367: 1 0.367 - 0.489: 0 0.489 - 0.611: 1 Chirality restraints: 775 Sorted by residual: chirality pdb=" CA TYR C 94 " pdb=" N TYR C 94 " pdb=" C TYR C 94 " pdb=" CB TYR C 94 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.34e+00 chirality pdb=" CA VAL B 123 " pdb=" N VAL B 123 " pdb=" C VAL B 123 " pdb=" CB VAL B 123 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 129 " pdb=" N LYS B 129 " pdb=" C LYS B 129 " pdb=" CB LYS B 129 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 772 not shown) Planarity restraints: 899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS C 92 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C HIS C 92 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 92 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 93 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 97 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C THR C 97 " -0.033 2.00e-02 2.50e+03 pdb=" O THR C 97 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE C 98 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 94 " 0.018 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR C 94 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR C 94 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 94 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 94 " 0.005 2.00e-02 2.50e+03 ... (remaining 896 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 260 2.73 - 3.27: 4783 3.27 - 3.81: 7745 3.81 - 4.36: 9078 4.36 - 4.90: 15883 Nonbonded interactions: 37749 Sorted by model distance: nonbonded pdb=" OD1 ASP B 99 " pdb=" N ARG B 100 " model vdw 2.182 3.120 nonbonded pdb=" OG SER C 14 " pdb=" OD2 ASP C 17 " model vdw 2.210 3.040 nonbonded pdb=" OE2 GLU D 406 " pdb=" NE2 GLN D 409 " model vdw 2.279 3.120 nonbonded pdb=" O TYR C 192 " pdb=" OG SER C 208 " model vdw 2.287 3.040 nonbonded pdb=" OG SER B 17 " pdb=" ND2 ASN B 84 " model vdw 2.299 3.120 ... (remaining 37744 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.060 5145 Z= 0.238 Angle : 0.739 8.208 7007 Z= 0.421 Chirality : 0.054 0.611 775 Planarity : 0.004 0.033 898 Dihedral : 13.163 83.203 1864 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 0.54 % Allowed : 1.44 % Favored : 98.02 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.34), residues: 637 helix: -2.54 (0.93), residues: 22 sheet: 0.89 (0.34), residues: 244 loop : -0.47 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 115 HIS 0.003 0.001 HIS C 189 PHE 0.019 0.001 PHE D 392 TYR 0.023 0.002 TYR C 94 ARG 0.010 0.001 ARG C 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 1) link_NAG-ASN : angle 3.35267 ( 3) link_BETA1-4 : bond 0.00437 ( 1) link_BETA1-4 : angle 4.18155 ( 3) hydrogen bonds : bond 0.24191 ( 152) hydrogen bonds : angle 9.12790 ( 408) SS BOND : bond 0.00509 ( 9) SS BOND : angle 0.50101 ( 18) covalent geometry : bond 0.00385 ( 5134) covalent geometry : angle 0.73100 ( 6983) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.505 Fit side-chains REVERT: B 89 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7709 (mp0) REVERT: B 152 CYS cc_start: 0.3391 (m) cc_final: 0.3030 (m) REVERT: B 216 ASN cc_start: 0.7341 (m-40) cc_final: 0.6990 (p0) REVERT: C 49 TYR cc_start: 0.8696 (p90) cc_final: 0.8487 (p90) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.2392 time to fit residues: 24.4290 Evaluate side-chains 61 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN B 183 GLN B 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.121932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096912 restraints weight = 11828.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098570 restraints weight = 8283.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099653 restraints weight = 6572.045| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5145 Z= 0.194 Angle : 0.691 10.526 7007 Z= 0.354 Chirality : 0.049 0.392 775 Planarity : 0.004 0.034 898 Dihedral : 6.216 53.334 744 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 1.08 % Allowed : 9.91 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.34), residues: 637 helix: -2.51 (0.81), residues: 28 sheet: 0.74 (0.34), residues: 243 loop : -0.71 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 115 HIS 0.005 0.002 HIS C 198 PHE 0.018 0.002 PHE B 29 TYR 0.020 0.002 TYR D 369 ARG 0.007 0.001 ARG C 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 1) link_NAG-ASN : angle 2.96789 ( 3) link_BETA1-4 : bond 0.00161 ( 1) link_BETA1-4 : angle 2.69034 ( 3) hydrogen bonds : bond 0.03845 ( 152) hydrogen bonds : angle 6.46560 ( 408) SS BOND : bond 0.00356 ( 9) SS BOND : angle 0.87340 ( 18) covalent geometry : bond 0.00448 ( 5134) covalent geometry : angle 0.68575 ( 6983) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.667 Fit side-chains REVERT: D 406 GLU cc_start: 0.8075 (pt0) cc_final: 0.7817 (pt0) REVERT: B 29 PHE cc_start: 0.8136 (t80) cc_final: 0.7931 (t80) REVERT: B 89 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7747 (mp0) REVERT: B 114 ILE cc_start: 0.9060 (mm) cc_final: 0.8763 (mm) REVERT: B 216 ASN cc_start: 0.7110 (m-40) cc_final: 0.6293 (p0) REVERT: C 48 ILE cc_start: 0.9366 (tp) cc_final: 0.9120 (tp) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.2525 time to fit residues: 22.5258 Evaluate side-chains 64 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 62 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 59 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.121007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095647 restraints weight = 11855.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.097588 restraints weight = 7578.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098930 restraints weight = 5756.946| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5145 Z= 0.232 Angle : 0.727 11.607 7007 Z= 0.371 Chirality : 0.050 0.380 775 Planarity : 0.004 0.048 898 Dihedral : 6.098 48.997 744 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 0.90 % Allowed : 13.15 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.34), residues: 637 helix: -2.49 (0.95), residues: 26 sheet: 0.48 (0.34), residues: 238 loop : -0.90 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 115 HIS 0.005 0.002 HIS B 101 PHE 0.023 0.002 PHE D 515 TYR 0.025 0.002 TYR C 49 ARG 0.006 0.001 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 1) link_NAG-ASN : angle 3.25395 ( 3) link_BETA1-4 : bond 0.00261 ( 1) link_BETA1-4 : angle 3.20215 ( 3) hydrogen bonds : bond 0.04078 ( 152) hydrogen bonds : angle 6.32719 ( 408) SS BOND : bond 0.00313 ( 9) SS BOND : angle 1.07134 ( 18) covalent geometry : bond 0.00538 ( 5134) covalent geometry : angle 0.71996 ( 6983) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.630 Fit side-chains REVERT: D 378 LYS cc_start: 0.9040 (ttpt) cc_final: 0.8799 (pttm) REVERT: B 28 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7144 (ttp80) REVERT: B 29 PHE cc_start: 0.8268 (t80) cc_final: 0.7992 (t80) REVERT: B 32 TYR cc_start: 0.8752 (m-80) cc_final: 0.8207 (m-80) REVERT: B 89 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7846 (mp0) REVERT: C 18 ARG cc_start: 0.7285 (tpp80) cc_final: 0.6808 (mmm-85) REVERT: C 48 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9124 (tp) outliers start: 5 outliers final: 3 residues processed: 72 average time/residue: 0.2818 time to fit residues: 25.5970 Evaluate side-chains 62 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 15 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.093632 restraints weight = 12159.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095539 restraints weight = 8148.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096797 restraints weight = 6284.465| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5145 Z= 0.157 Angle : 0.652 10.518 7007 Z= 0.330 Chirality : 0.048 0.374 775 Planarity : 0.004 0.037 898 Dihedral : 5.912 50.977 744 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.80 % Allowed : 14.41 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.34), residues: 637 helix: -2.40 (0.89), residues: 28 sheet: 0.53 (0.34), residues: 230 loop : -0.80 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 PHE 0.016 0.001 PHE D 515 TYR 0.026 0.002 TYR C 49 ARG 0.004 0.001 ARG B 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 1) link_NAG-ASN : angle 2.99822 ( 3) link_BETA1-4 : bond 0.00338 ( 1) link_BETA1-4 : angle 3.39624 ( 3) hydrogen bonds : bond 0.03177 ( 152) hydrogen bonds : angle 5.90954 ( 408) SS BOND : bond 0.00345 ( 9) SS BOND : angle 0.94452 ( 18) covalent geometry : bond 0.00364 ( 5134) covalent geometry : angle 0.64487 ( 6983) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.843 Fit side-chains REVERT: B 29 PHE cc_start: 0.8224 (t80) cc_final: 0.7913 (t80) REVERT: B 32 TYR cc_start: 0.8707 (m-80) cc_final: 0.8064 (m-80) REVERT: B 89 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7773 (mp0) REVERT: B 209 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6761 (m-40) REVERT: C 18 ARG cc_start: 0.7104 (tpp80) cc_final: 0.6763 (mmm-85) REVERT: C 48 ILE cc_start: 0.9365 (tp) cc_final: 0.9005 (mm) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.3163 time to fit residues: 28.1881 Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.118892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097233 restraints weight = 12228.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095893 restraints weight = 11364.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097505 restraints weight = 10538.152| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5145 Z= 0.167 Angle : 0.687 12.134 7007 Z= 0.340 Chirality : 0.048 0.375 775 Planarity : 0.004 0.034 898 Dihedral : 5.805 43.900 744 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 2.34 % Allowed : 14.41 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.34), residues: 637 helix: -2.37 (0.95), residues: 26 sheet: 0.48 (0.34), residues: 227 loop : -0.87 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.003 0.001 HIS B 101 PHE 0.016 0.001 PHE D 515 TYR 0.021 0.002 TYR C 49 ARG 0.004 0.001 ARG B 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 1) link_NAG-ASN : angle 3.15781 ( 3) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 3.39862 ( 3) hydrogen bonds : bond 0.03255 ( 152) hydrogen bonds : angle 5.82649 ( 408) SS BOND : bond 0.00319 ( 9) SS BOND : angle 0.95323 ( 18) covalent geometry : bond 0.00389 ( 5134) covalent geometry : angle 0.68020 ( 6983) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.722 Fit side-chains REVERT: B 29 PHE cc_start: 0.8177 (t80) cc_final: 0.7893 (t80) REVERT: B 32 TYR cc_start: 0.8699 (m-80) cc_final: 0.8055 (m-80) REVERT: B 83 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7246 (mmm) REVERT: C 1 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7988 (p0) REVERT: C 18 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6743 (mmm-85) REVERT: C 48 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.8950 (mm) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.3056 time to fit residues: 27.7748 Evaluate side-chains 67 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 82 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.0010 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096322 restraints weight = 12117.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098179 restraints weight = 8229.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099421 restraints weight = 6400.375| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5145 Z= 0.106 Angle : 0.642 11.103 7007 Z= 0.316 Chirality : 0.047 0.368 775 Planarity : 0.004 0.033 898 Dihedral : 5.568 47.562 744 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 1.62 % Allowed : 14.95 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.34), residues: 637 helix: -2.48 (0.82), residues: 32 sheet: 0.64 (0.35), residues: 227 loop : -0.72 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.002 0.001 HIS C 198 PHE 0.012 0.001 PHE D 515 TYR 0.026 0.001 TYR C 49 ARG 0.003 0.000 ARG C 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 1) link_NAG-ASN : angle 2.79661 ( 3) link_BETA1-4 : bond 0.00511 ( 1) link_BETA1-4 : angle 3.55468 ( 3) hydrogen bonds : bond 0.02536 ( 152) hydrogen bonds : angle 5.52730 ( 408) SS BOND : bond 0.00349 ( 9) SS BOND : angle 1.02647 ( 18) covalent geometry : bond 0.00234 ( 5134) covalent geometry : angle 0.63393 ( 6983) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.515 Fit side-chains REVERT: B 29 PHE cc_start: 0.8157 (t80) cc_final: 0.7879 (t80) REVERT: B 32 TYR cc_start: 0.8579 (m-80) cc_final: 0.7881 (m-80) REVERT: B 156 ASP cc_start: 0.5925 (m-30) cc_final: 0.4961 (t0) REVERT: B 162 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.7126 (p) REVERT: C 1 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7874 (p0) REVERT: C 48 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8962 (mm) outliers start: 9 outliers final: 6 residues processed: 73 average time/residue: 0.2218 time to fit residues: 20.2580 Evaluate side-chains 69 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095156 restraints weight = 12080.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094539 restraints weight = 9738.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.094958 restraints weight = 9390.072| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5145 Z= 0.205 Angle : 0.715 12.951 7007 Z= 0.356 Chirality : 0.048 0.381 775 Planarity : 0.004 0.034 898 Dihedral : 5.619 32.647 744 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.94 % Rotamer: Outliers : 3.06 % Allowed : 14.59 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.34), residues: 637 helix: -2.59 (0.79), residues: 32 sheet: 0.57 (0.34), residues: 232 loop : -0.88 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 PHE 0.025 0.002 PHE D 515 TYR 0.017 0.002 TYR C 49 ARG 0.004 0.001 ARG C 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 1) link_NAG-ASN : angle 3.27907 ( 3) link_BETA1-4 : bond 0.00389 ( 1) link_BETA1-4 : angle 3.30117 ( 3) hydrogen bonds : bond 0.03408 ( 152) hydrogen bonds : angle 5.75954 ( 408) SS BOND : bond 0.00319 ( 9) SS BOND : angle 1.02066 ( 18) covalent geometry : bond 0.00474 ( 5134) covalent geometry : angle 0.70784 ( 6983) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.644 Fit side-chains REVERT: B 29 PHE cc_start: 0.8222 (t80) cc_final: 0.7934 (t80) REVERT: B 32 TYR cc_start: 0.8730 (m-80) cc_final: 0.8125 (m-80) REVERT: B 83 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7271 (mtm) REVERT: B 162 VAL cc_start: 0.7389 (OUTLIER) cc_final: 0.7101 (p) REVERT: C 1 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7943 (p0) REVERT: C 48 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8981 (mm) outliers start: 17 outliers final: 8 residues processed: 72 average time/residue: 0.2583 time to fit residues: 23.2348 Evaluate side-chains 65 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.0050 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.119332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096410 restraints weight = 12191.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095678 restraints weight = 7761.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096665 restraints weight = 7372.349| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5145 Z= 0.134 Angle : 0.679 13.169 7007 Z= 0.334 Chirality : 0.048 0.383 775 Planarity : 0.004 0.035 898 Dihedral : 5.427 31.830 744 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 2.70 % Allowed : 14.77 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.34), residues: 637 helix: -2.59 (0.81), residues: 32 sheet: 0.60 (0.34), residues: 233 loop : -0.92 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.002 0.001 HIS B 101 PHE 0.022 0.001 PHE D 515 TYR 0.021 0.001 TYR C 49 ARG 0.004 0.000 ARG C 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 1) link_NAG-ASN : angle 3.09934 ( 3) link_BETA1-4 : bond 0.00618 ( 1) link_BETA1-4 : angle 3.26187 ( 3) hydrogen bonds : bond 0.02849 ( 152) hydrogen bonds : angle 5.56625 ( 408) SS BOND : bond 0.00328 ( 9) SS BOND : angle 0.93046 ( 18) covalent geometry : bond 0.00317 ( 5134) covalent geometry : angle 0.67243 ( 6983) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: B 29 PHE cc_start: 0.8353 (t80) cc_final: 0.8026 (t80) REVERT: B 32 TYR cc_start: 0.8680 (m-80) cc_final: 0.8078 (m-80) REVERT: B 83 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7518 (mtm) REVERT: B 156 ASP cc_start: 0.6032 (m-30) cc_final: 0.5201 (t0) REVERT: B 162 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7207 (p) REVERT: C 1 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7994 (p0) REVERT: C 48 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9010 (mm) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.2197 time to fit residues: 19.8976 Evaluate side-chains 68 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.119891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095527 restraints weight = 12067.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096984 restraints weight = 8853.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098031 restraints weight = 7213.746| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5145 Z= 0.124 Angle : 0.666 12.541 7007 Z= 0.327 Chirality : 0.047 0.383 775 Planarity : 0.004 0.035 898 Dihedral : 5.345 36.225 744 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 2.34 % Allowed : 14.95 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.34), residues: 637 helix: -2.34 (0.84), residues: 32 sheet: 0.70 (0.35), residues: 233 loop : -0.87 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS B 101 PHE 0.021 0.001 PHE D 515 TYR 0.023 0.001 TYR C 49 ARG 0.004 0.000 ARG C 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 1) link_NAG-ASN : angle 2.92761 ( 3) link_BETA1-4 : bond 0.00560 ( 1) link_BETA1-4 : angle 3.23826 ( 3) hydrogen bonds : bond 0.02677 ( 152) hydrogen bonds : angle 5.36720 ( 408) SS BOND : bond 0.00314 ( 9) SS BOND : angle 0.88061 ( 18) covalent geometry : bond 0.00290 ( 5134) covalent geometry : angle 0.65976 ( 6983) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.595 Fit side-chains REVERT: B 29 PHE cc_start: 0.8206 (t80) cc_final: 0.7944 (t80) REVERT: B 32 TYR cc_start: 0.8596 (m-80) cc_final: 0.7917 (m-80) REVERT: B 62 GLU cc_start: 0.6618 (mp0) cc_final: 0.6389 (mp0) REVERT: B 83 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7335 (mtm) REVERT: B 89 GLU cc_start: 0.7012 (pm20) cc_final: 0.6751 (pm20) REVERT: B 156 ASP cc_start: 0.5762 (m-30) cc_final: 0.4822 (t0) REVERT: B 162 VAL cc_start: 0.7283 (OUTLIER) cc_final: 0.6974 (p) REVERT: C 1 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7802 (p0) REVERT: C 48 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.8962 (mm) outliers start: 13 outliers final: 8 residues processed: 73 average time/residue: 0.2211 time to fit residues: 19.9780 Evaluate side-chains 70 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.0570 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.120459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097041 restraints weight = 12310.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096450 restraints weight = 7775.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097045 restraints weight = 7069.287| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5145 Z= 0.117 Angle : 0.669 11.985 7007 Z= 0.327 Chirality : 0.047 0.381 775 Planarity : 0.004 0.034 898 Dihedral : 5.391 40.354 744 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 2.52 % Allowed : 15.32 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.34), residues: 637 helix: -1.68 (1.05), residues: 26 sheet: 0.70 (0.35), residues: 233 loop : -0.84 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 115 HIS 0.004 0.001 HIS B 101 PHE 0.020 0.001 PHE D 515 TYR 0.022 0.001 TYR C 49 ARG 0.006 0.001 ARG C 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 1) link_NAG-ASN : angle 2.82732 ( 3) link_BETA1-4 : bond 0.00483 ( 1) link_BETA1-4 : angle 3.27077 ( 3) hydrogen bonds : bond 0.02635 ( 152) hydrogen bonds : angle 5.33697 ( 408) SS BOND : bond 0.00315 ( 9) SS BOND : angle 0.90097 ( 18) covalent geometry : bond 0.00272 ( 5134) covalent geometry : angle 0.66251 ( 6983) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.627 Fit side-chains REVERT: B 29 PHE cc_start: 0.8362 (t80) cc_final: 0.8031 (t80) REVERT: B 32 TYR cc_start: 0.8678 (m-80) cc_final: 0.7983 (m-80) REVERT: B 83 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7542 (mtm) REVERT: B 89 GLU cc_start: 0.7329 (pm20) cc_final: 0.7077 (pm20) REVERT: B 156 ASP cc_start: 0.6177 (m-30) cc_final: 0.5070 (t0) REVERT: B 162 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7126 (p) REVERT: C 1 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7864 (p0) REVERT: C 48 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.8996 (mm) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.2411 time to fit residues: 20.9427 Evaluate side-chains 71 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 427 ASP Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 500 THR Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.117441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.095866 restraints weight = 12476.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095039 restraints weight = 10827.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096068 restraints weight = 11163.094| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5145 Z= 0.182 Angle : 0.712 11.579 7007 Z= 0.353 Chirality : 0.048 0.401 775 Planarity : 0.004 0.031 898 Dihedral : 5.775 44.356 744 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 2.52 % Allowed : 15.32 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.34), residues: 637 helix: -1.82 (0.99), residues: 26 sheet: 0.53 (0.35), residues: 234 loop : -0.93 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 115 HIS 0.002 0.001 HIS C 189 PHE 0.025 0.001 PHE D 515 TYR 0.018 0.002 TYR C 49 ARG 0.003 0.001 ARG C 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 1) link_NAG-ASN : angle 3.23971 ( 3) link_BETA1-4 : bond 0.00404 ( 1) link_BETA1-4 : angle 3.08868 ( 3) hydrogen bonds : bond 0.03161 ( 152) hydrogen bonds : angle 5.58809 ( 408) SS BOND : bond 0.00323 ( 9) SS BOND : angle 1.04437 ( 18) covalent geometry : bond 0.00426 ( 5134) covalent geometry : angle 0.70552 ( 6983) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.63 seconds wall clock time: 39 minutes 34.39 seconds (2374.39 seconds total)