Starting phenix.real_space_refine on Wed Sep 17 05:17:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lyp_63514/09_2025/9lyp_63514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lyp_63514/09_2025/9lyp_63514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lyp_63514/09_2025/9lyp_63514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lyp_63514/09_2025/9lyp_63514.map" model { file = "/net/cci-nas-00/data/ceres_data/9lyp_63514/09_2025/9lyp_63514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lyp_63514/09_2025/9lyp_63514.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.022 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 21 5.16 5 C 3079 2.51 5 N 811 2.21 5 O 971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4882 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "i" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "j" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1674 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 211} Chain: "P" 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: 1.29, per 1000 atoms: 0.26 Number of scatterers: 4882 At special positions: 0 Unit cell: (58.59, 93, 123.69, 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 21 16.00 O 971 8.00 N 811 7.00 C 3079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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 i 22 " - pdb=" SG CYS i 90 " distance=2.04 Simple disulfide: pdb=" SG CYS i 138 " - pdb=" SG CYS i 198 " distance=2.04 Simple disulfide: pdb=" SG CYS i 218 " - pdb=" SG CYS j 223 " distance=2.03 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 96 " distance=2.04 Simple disulfide: pdb=" SG CYS j 147 " - pdb=" SG CYS j 203 " 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 P 1 " - " NAG P 2 " NAG-ASN " NAG P 1 " - " ASN B 343 " Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 204.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1162 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 14 sheets defined 13.5% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.067A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.791A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 498 through 500 No H-bonds generated for 'chain 'B' and resid 498 through 500' Processing helix chain 'B' and resid 501 through 506 removed outlier: 3.690A pdb=" N TYR B 505 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 55 Processing helix chain 'i' and resid 124 through 132 Processing helix chain 'i' and resid 186 through 193 Processing helix chain 'i' and resid 216 through 218 No H-bonds generated for 'chain 'i' and resid 216 through 218' Processing helix chain 'j' and resid 87 through 91 removed outlier: 3.743A pdb=" N THR j 91 " --> pdb=" O THR j 88 " (cutoff:3.500A) Processing helix chain 'j' and resid 163 through 166 Processing helix chain 'j' and resid 193 through 197 removed outlier: 3.630A pdb=" N GLY j 197 " --> pdb=" O SER j 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 193 through 197' Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.931A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'i' and resid 9 through 12 removed outlier: 6.515A pdb=" N VAL i 10 " --> pdb=" O THR i 108 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'i' and resid 17 through 23 Processing sheet with id=AA5, first strand: chain 'i' and resid 47 through 50 removed outlier: 6.325A pdb=" N TRP i 37 " --> pdb=" O MET i 49 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP i 87 " --> pdb=" O GLN i 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'i' and resid 118 through 122 removed outlier: 4.710A pdb=" N SER i 135 " --> pdb=" O LEU i 185 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU i 185 " --> pdb=" O SER i 135 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL i 137 " --> pdb=" O LEU i 183 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU i 183 " --> pdb=" O VAL i 137 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LEU i 139 " --> pdb=" O SER i 181 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER i 181 " --> pdb=" O LEU i 139 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN i 141 " --> pdb=" O LEU i 179 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU i 179 " --> pdb=" O ASN i 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'i' and resid 157 through 159 removed outlier: 4.164A pdb=" N TRP i 152 " --> pdb=" O GLN i 159 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'j' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'j' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'j' and resid 58 through 60 removed outlier: 5.368A pdb=" N TRP j 47 " --> pdb=" O ARG j 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG j 38 " --> pdb=" O TRP j 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'j' and resid 58 through 60 removed outlier: 5.368A pdb=" N TRP j 47 " --> pdb=" O ARG j 38 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG j 38 " --> pdb=" O TRP j 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'j' and resid 127 through 130 removed outlier: 3.853A pdb=" N SER j 127 " --> pdb=" O LYS j 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'j' and resid 158 through 161 removed outlier: 4.412A pdb=" N TYR j 201 " --> pdb=" O VAL j 218 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N HIS j 207 " --> pdb=" O THR j 212 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR j 212 " --> pdb=" O HIS j 207 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 176 through 177 162 hydrogen bonds defined for protein. 411 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: 0.71 Time building geometry restraints manager: 0.59 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: 1554 1.34 - 1.46: 1298 1.46 - 1.58: 2125 1.58 - 1.71: 0 1.71 - 1.83: 24 Bond restraints: 5001 Sorted by residual: bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" N GLN j 1 " pdb=" CA GLN j 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.12e+00 bond pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N GLN i 1 " pdb=" CA GLN i 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 4996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 6188 1.39 - 2.79: 496 2.79 - 4.18: 92 4.18 - 5.58: 23 5.58 - 6.97: 8 Bond angle restraints: 6807 Sorted by residual: angle pdb=" N GLY j 113 " pdb=" CA GLY j 113 " pdb=" C GLY j 113 " ideal model delta sigma weight residual 111.93 118.90 -6.97 1.15e+00 7.56e-01 3.67e+01 angle pdb=" N ASN i 141 " pdb=" CA ASN i 141 " pdb=" C ASN i 141 " ideal model delta sigma weight residual 109.40 115.21 -5.81 1.63e+00 3.76e-01 1.27e+01 angle pdb=" N VAL B 362 " pdb=" CA VAL B 362 " pdb=" C VAL B 362 " ideal model delta sigma weight residual 107.80 102.71 5.09 1.45e+00 4.76e-01 1.23e+01 angle pdb=" N ASN i 142 " pdb=" CA ASN i 142 " pdb=" C ASN i 142 " ideal model delta sigma weight residual 111.30 115.63 -4.33 1.36e+00 5.41e-01 1.01e+01 angle pdb=" N TYR B 421 " pdb=" CA TYR B 421 " pdb=" C TYR B 421 " ideal model delta sigma weight residual 112.04 116.60 -4.56 1.44e+00 4.82e-01 1.00e+01 ... (remaining 6802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 2780 16.69 - 33.38: 170 33.38 - 50.08: 28 50.08 - 66.77: 11 66.77 - 83.46: 4 Dihedral angle restraints: 2993 sinusoidal: 1159 harmonic: 1834 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 93.00 140.55 -47.55 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS i 138 " pdb=" SG CYS i 138 " pdb=" SG CYS i 198 " pdb=" CB CYS i 198 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 dihedral pdb=" CB CYS j 22 " pdb=" SG CYS j 22 " pdb=" SG CYS j 96 " pdb=" CB CYS j 96 " ideal model delta sinusoidal sigma weight residual 93.00 60.86 32.14 1 1.00e+01 1.00e-02 1.47e+01 ... (remaining 2990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 481 0.038 - 0.076: 165 0.076 - 0.114: 80 0.114 - 0.152: 27 0.152 - 0.190: 2 Chirality restraints: 755 Sorted by residual: chirality pdb=" CB ILE B 472 " pdb=" CA ILE B 472 " pdb=" CG1 ILE B 472 " pdb=" CG2 ILE B 472 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA VAL B 362 " pdb=" N VAL B 362 " pdb=" C VAL B 362 " pdb=" CB VAL B 362 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA VAL j 93 " pdb=" N VAL j 93 " pdb=" C VAL j 93 " pdb=" CB VAL j 93 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 ... (remaining 752 not shown) Planarity restraints: 877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 495 " 0.011 2.00e-02 2.50e+03 3.50e-02 2.45e+01 pdb=" CG TYR B 495 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 495 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 495 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 495 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR B 495 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR B 495 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 495 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR i 88 " 0.007 2.00e-02 2.50e+03 2.23e-02 9.91e+00 pdb=" CG TYR i 88 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR i 88 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR i 88 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR i 88 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR i 88 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR i 88 " -0.028 2.00e-02 2.50e+03 pdb=" OH TYR i 88 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 457 " -0.251 9.50e-02 1.11e+02 1.13e-01 9.41e+00 pdb=" NE ARG B 457 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG B 457 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 457 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 457 " -0.002 2.00e-02 2.50e+03 ... (remaining 874 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 190 2.70 - 3.25: 5203 3.25 - 3.80: 7410 3.80 - 4.35: 9969 4.35 - 4.90: 16814 Nonbonded interactions: 39586 Sorted by model distance: nonbonded pdb=" O3 NAG P 1 " pdb=" O7 NAG P 1 " model vdw 2.150 3.040 nonbonded pdb=" O SER i 82 " pdb=" OE1 GLU i 85 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 438 " pdb=" OD2 ASP B 442 " model vdw 2.279 3.040 nonbonded pdb=" N GLU B 471 " pdb=" OE1 GLU B 471 " model vdw 2.288 3.120 nonbonded pdb=" O GLN i 81 " pdb=" OE1 GLU i 83 " model vdw 2.314 3.040 ... (remaining 39581 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: 3.840 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.330 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 0.046 5012 Z= 0.172 Angle : 0.879 6.969 6831 Z= 0.500 Chirality : 0.050 0.190 755 Planarity : 0.009 0.113 876 Dihedral : 11.362 83.460 1804 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.32), residues: 629 helix: -3.30 (0.45), residues: 48 sheet: 1.38 (0.33), residues: 224 loop : -1.61 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.005 ARG B 355 TYR 0.065 0.007 TYR B 495 PHE 0.023 0.004 PHE B 377 TRP 0.027 0.006 TRP j 110 HIS 0.015 0.005 HIS j 171 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5001) covalent geometry : angle 0.87149 ( 6807) SS BOND : bond 0.00609 ( 9) SS BOND : angle 1.65043 ( 18) hydrogen bonds : bond 0.24050 ( 150) hydrogen bonds : angle 9.41510 ( 411) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.48723 ( 3) link_NAG-ASN : bond 0.00438 ( 1) link_NAG-ASN : angle 3.95305 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8671 (m-80) cc_final: 0.8281 (m-80) REVERT: i 38 TYR cc_start: 0.8126 (m-80) cc_final: 0.7877 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0816 time to fit residues: 8.6967 Evaluate side-chains 56 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 142 ASN i 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.115877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082612 restraints weight = 13302.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085121 restraints weight = 6729.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.086667 restraints weight = 4531.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.087676 restraints weight = 3561.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088333 restraints weight = 3082.392| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5012 Z= 0.175 Angle : 0.724 6.685 6831 Z= 0.378 Chirality : 0.049 0.174 755 Planarity : 0.005 0.057 876 Dihedral : 5.744 36.896 737 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.88 % Favored : 93.96 % Rotamer: Outliers : 1.29 % Allowed : 7.18 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.33), residues: 629 helix: -2.49 (0.67), residues: 35 sheet: 1.72 (0.33), residues: 215 loop : -0.68 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 357 TYR 0.019 0.002 TYR i 190 PHE 0.027 0.002 PHE B 377 TRP 0.019 0.002 TRP i 152 HIS 0.004 0.002 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5001) covalent geometry : angle 0.71843 ( 6807) SS BOND : bond 0.00291 ( 9) SS BOND : angle 1.40975 ( 18) hydrogen bonds : bond 0.04233 ( 150) hydrogen bonds : angle 6.15403 ( 411) link_BETA1-4 : bond 0.00098 ( 1) link_BETA1-4 : angle 0.96989 ( 3) link_NAG-ASN : bond 0.00963 ( 1) link_NAG-ASN : angle 3.00852 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8625 (m-80) cc_final: 0.8318 (m-80) REVERT: i 28 ASP cc_start: 0.7472 (m-30) cc_final: 0.7104 (m-30) REVERT: i 49 MET cc_start: 0.8320 (mmm) cc_final: 0.8078 (mmm) REVERT: j 32 TYR cc_start: 0.7239 (m-80) cc_final: 0.7034 (m-10) REVERT: j 89 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8266 (mp0) outliers start: 7 outliers final: 2 residues processed: 70 average time/residue: 0.0590 time to fit residues: 5.5528 Evaluate side-chains 57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 6 optimal weight: 0.0170 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.115741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082975 restraints weight = 13279.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.085440 restraints weight = 6770.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.086983 restraints weight = 4572.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.087918 restraints weight = 3617.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088421 restraints weight = 3144.666| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5012 Z= 0.136 Angle : 0.655 5.959 6831 Z= 0.341 Chirality : 0.045 0.159 755 Planarity : 0.004 0.034 876 Dihedral : 5.581 41.700 737 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.84 % Allowed : 10.31 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.34), residues: 629 helix: -2.53 (0.67), residues: 35 sheet: 1.71 (0.33), residues: 226 loop : -0.40 (0.35), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.013 0.002 TYR j 35 PHE 0.014 0.001 PHE j 153 TRP 0.019 0.001 TRP i 152 HIS 0.007 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5001) covalent geometry : angle 0.65052 ( 6807) SS BOND : bond 0.00445 ( 9) SS BOND : angle 1.30298 ( 18) hydrogen bonds : bond 0.03622 ( 150) hydrogen bonds : angle 5.99436 ( 411) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 1.20574 ( 3) link_NAG-ASN : bond 0.00460 ( 1) link_NAG-ASN : angle 2.10962 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.141 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8639 (m-80) cc_final: 0.8295 (m-80) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 0.0514 time to fit residues: 4.7526 Evaluate side-chains 63 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 55 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 193 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.114838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081910 restraints weight = 13330.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.084327 restraints weight = 6832.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.085839 restraints weight = 4619.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.086794 restraints weight = 3664.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087256 restraints weight = 3191.260| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5012 Z= 0.157 Angle : 0.639 5.953 6831 Z= 0.334 Chirality : 0.045 0.153 755 Planarity : 0.004 0.035 876 Dihedral : 5.480 39.365 737 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.03 % Allowed : 10.68 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.34), residues: 629 helix: -2.57 (0.70), residues: 35 sheet: 1.67 (0.33), residues: 225 loop : -0.43 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 357 TYR 0.014 0.002 TYR j 35 PHE 0.012 0.001 PHE i 143 TRP 0.023 0.001 TRP i 152 HIS 0.007 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 5001) covalent geometry : angle 0.63519 ( 6807) SS BOND : bond 0.00341 ( 9) SS BOND : angle 1.16658 ( 18) hydrogen bonds : bond 0.03532 ( 150) hydrogen bonds : angle 5.76054 ( 411) link_BETA1-4 : bond 0.00535 ( 1) link_BETA1-4 : angle 1.08933 ( 3) link_NAG-ASN : bond 0.00279 ( 1) link_NAG-ASN : angle 2.09486 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 355 ARG cc_start: 0.8589 (mtp180) cc_final: 0.8373 (mtp85) REVERT: B 365 TYR cc_start: 0.8698 (m-80) cc_final: 0.8341 (m-80) REVERT: i 28 ASP cc_start: 0.7689 (m-30) cc_final: 0.7320 (m-30) outliers start: 11 outliers final: 9 residues processed: 71 average time/residue: 0.0764 time to fit residues: 7.1070 Evaluate side-chains 63 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 193 HIS ** 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 = 0.3962 r_free = 0.3962 target = 0.112855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.081417 restraints weight = 13332.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.083868 restraints weight = 6585.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.085415 restraints weight = 4370.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.086361 restraints weight = 3412.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086944 restraints weight = 2940.974| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5012 Z= 0.144 Angle : 0.632 5.894 6831 Z= 0.331 Chirality : 0.044 0.147 755 Planarity : 0.004 0.033 876 Dihedral : 5.337 39.355 737 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.39 % Allowed : 12.15 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.34), residues: 629 helix: -2.68 (0.71), residues: 35 sheet: 1.67 (0.33), residues: 224 loop : -0.49 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 112 TYR 0.024 0.002 TYR B 501 PHE 0.013 0.001 PHE i 143 TRP 0.025 0.001 TRP i 152 HIS 0.006 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5001) covalent geometry : angle 0.62868 ( 6807) SS BOND : bond 0.00298 ( 9) SS BOND : angle 1.07873 ( 18) hydrogen bonds : bond 0.03233 ( 150) hydrogen bonds : angle 5.60802 ( 411) link_BETA1-4 : bond 0.00435 ( 1) link_BETA1-4 : angle 1.04405 ( 3) link_NAG-ASN : bond 0.00355 ( 1) link_NAG-ASN : angle 1.88345 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 THR cc_start: 0.8125 (p) cc_final: 0.7871 (p) REVERT: B 365 TYR cc_start: 0.8706 (m-80) cc_final: 0.8347 (m-80) REVERT: i 28 ASP cc_start: 0.7646 (m-30) cc_final: 0.7261 (m-30) outliers start: 13 outliers final: 9 residues processed: 69 average time/residue: 0.0597 time to fit residues: 5.6172 Evaluate side-chains 61 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.0370 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 164 GLN ** i 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079696 restraints weight = 13685.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.082225 restraints weight = 6844.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083745 restraints weight = 4580.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.084689 restraints weight = 3618.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.085114 restraints weight = 3137.715| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5012 Z= 0.143 Angle : 0.624 5.892 6831 Z= 0.324 Chirality : 0.044 0.145 755 Planarity : 0.004 0.034 876 Dihedral : 5.236 38.718 737 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.21 % Allowed : 11.60 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.35), residues: 629 helix: -2.72 (0.72), residues: 35 sheet: 1.67 (0.34), residues: 225 loop : -0.46 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 355 TYR 0.031 0.002 TYR B 501 PHE 0.013 0.001 PHE i 143 TRP 0.028 0.002 TRP i 152 HIS 0.006 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5001) covalent geometry : angle 0.62021 ( 6807) SS BOND : bond 0.00206 ( 9) SS BOND : angle 1.11887 ( 18) hydrogen bonds : bond 0.03242 ( 150) hydrogen bonds : angle 5.60539 ( 411) link_BETA1-4 : bond 0.00393 ( 1) link_BETA1-4 : angle 1.03769 ( 3) link_NAG-ASN : bond 0.00301 ( 1) link_NAG-ASN : angle 1.97205 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 THR cc_start: 0.8100 (p) cc_final: 0.7767 (p) REVERT: B 365 TYR cc_start: 0.8770 (m-80) cc_final: 0.8418 (m-80) REVERT: i 28 ASP cc_start: 0.7736 (m-30) cc_final: 0.7336 (m-30) REVERT: i 87 ASP cc_start: 0.7780 (p0) cc_final: 0.7171 (p0) REVERT: i 174 ASP cc_start: 0.8510 (t0) cc_final: 0.8283 (p0) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.0680 time to fit residues: 6.3158 Evaluate side-chains 62 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 160 SER Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.111231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079327 restraints weight = 13283.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081709 restraints weight = 6739.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.083167 restraints weight = 4539.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.084103 restraints weight = 3587.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.084676 restraints weight = 3101.946| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5012 Z= 0.188 Angle : 0.647 6.020 6831 Z= 0.337 Chirality : 0.045 0.149 755 Planarity : 0.004 0.035 876 Dihedral : 5.333 37.826 737 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.39 % Allowed : 12.15 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.34), residues: 629 helix: -2.70 (0.69), residues: 43 sheet: 1.59 (0.34), residues: 225 loop : -0.58 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG i 112 TYR 0.027 0.002 TYR B 501 PHE 0.015 0.001 PHE i 143 TRP 0.033 0.002 TRP i 152 HIS 0.005 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 5001) covalent geometry : angle 0.64253 ( 6807) SS BOND : bond 0.00209 ( 9) SS BOND : angle 1.42359 ( 18) hydrogen bonds : bond 0.03397 ( 150) hydrogen bonds : angle 5.59145 ( 411) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 1.01648 ( 3) link_NAG-ASN : bond 0.00301 ( 1) link_NAG-ASN : angle 1.98232 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8163 (p) cc_final: 0.7821 (p) REVERT: B 365 TYR cc_start: 0.8752 (m-80) cc_final: 0.8394 (m-80) REVERT: i 28 ASP cc_start: 0.7730 (m-30) cc_final: 0.7258 (m-30) REVERT: i 174 ASP cc_start: 0.8427 (t0) cc_final: 0.8196 (p0) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.0674 time to fit residues: 5.9180 Evaluate side-chains 58 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 160 SER Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.112034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.079533 restraints weight = 13475.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.081901 restraints weight = 6885.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083320 restraints weight = 4675.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.084218 restraints weight = 3738.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.084808 restraints weight = 3262.414| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5012 Z= 0.149 Angle : 0.643 5.915 6831 Z= 0.333 Chirality : 0.044 0.146 755 Planarity : 0.004 0.035 876 Dihedral : 5.271 37.691 737 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.03 % Allowed : 13.08 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.34), residues: 629 helix: -2.72 (0.69), residues: 43 sheet: 1.50 (0.34), residues: 227 loop : -0.66 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.016 0.001 TYR i 51 PHE 0.013 0.001 PHE i 143 TRP 0.029 0.002 TRP i 152 HIS 0.002 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5001) covalent geometry : angle 0.63941 ( 6807) SS BOND : bond 0.00270 ( 9) SS BOND : angle 1.19675 ( 18) hydrogen bonds : bond 0.03189 ( 150) hydrogen bonds : angle 5.37049 ( 411) link_BETA1-4 : bond 0.00311 ( 1) link_BETA1-4 : angle 0.99826 ( 3) link_NAG-ASN : bond 0.00306 ( 1) link_NAG-ASN : angle 1.89350 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8165 (p) cc_final: 0.7842 (p) REVERT: B 365 TYR cc_start: 0.8730 (m-80) cc_final: 0.8364 (m-80) REVERT: i 28 ASP cc_start: 0.7747 (m-30) cc_final: 0.7276 (m-30) REVERT: i 144 TYR cc_start: 0.7366 (t80) cc_final: 0.6478 (t80) REVERT: i 174 ASP cc_start: 0.8425 (t0) cc_final: 0.8217 (p0) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.0524 time to fit residues: 4.6374 Evaluate side-chains 58 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.0370 chunk 54 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.111483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078589 restraints weight = 13188.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.081025 restraints weight = 6640.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.082526 restraints weight = 4476.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083421 restraints weight = 3546.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084003 restraints weight = 3092.145| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5012 Z= 0.151 Angle : 0.656 6.659 6831 Z= 0.340 Chirality : 0.044 0.145 755 Planarity : 0.004 0.034 876 Dihedral : 5.252 37.702 737 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.03 % Allowed : 13.26 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.34), residues: 629 helix: -2.66 (0.70), residues: 43 sheet: 1.37 (0.35), residues: 227 loop : -0.67 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.018 0.001 TYR i 51 PHE 0.010 0.001 PHE i 143 TRP 0.046 0.002 TRP i 152 HIS 0.002 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5001) covalent geometry : angle 0.65256 ( 6807) SS BOND : bond 0.00273 ( 9) SS BOND : angle 1.17728 ( 18) hydrogen bonds : bond 0.03292 ( 150) hydrogen bonds : angle 5.53064 ( 411) link_BETA1-4 : bond 0.00380 ( 1) link_BETA1-4 : angle 1.02311 ( 3) link_NAG-ASN : bond 0.00332 ( 1) link_NAG-ASN : angle 1.89437 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8193 (p) cc_final: 0.7905 (p) REVERT: B 365 TYR cc_start: 0.8737 (m-80) cc_final: 0.8416 (m-80) REVERT: i 28 ASP cc_start: 0.7748 (m-30) cc_final: 0.7333 (m-30) REVERT: i 139 LEU cc_start: 0.8391 (mm) cc_final: 0.8170 (mm) REVERT: i 144 TYR cc_start: 0.7418 (t80) cc_final: 0.6446 (t80) REVERT: i 165 GLU cc_start: 0.8601 (tp30) cc_final: 0.7681 (tp30) outliers start: 11 outliers final: 10 residues processed: 62 average time/residue: 0.0658 time to fit residues: 5.6199 Evaluate side-chains 60 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 138 CYS Chi-restraints excluded: chain j residue 118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 24 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.110590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077871 restraints weight = 13382.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080206 restraints weight = 6833.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081691 restraints weight = 4641.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082389 restraints weight = 3680.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.083037 restraints weight = 3264.069| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5012 Z= 0.182 Angle : 0.663 6.808 6831 Z= 0.346 Chirality : 0.045 0.149 755 Planarity : 0.004 0.034 876 Dihedral : 5.314 36.752 737 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.21 % Allowed : 13.63 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.35), residues: 629 helix: -2.61 (0.70), residues: 43 sheet: 1.29 (0.34), residues: 237 loop : -0.70 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 355 TYR 0.018 0.002 TYR i 51 PHE 0.017 0.002 PHE i 143 TRP 0.049 0.002 TRP i 152 HIS 0.002 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 5001) covalent geometry : angle 0.65924 ( 6807) SS BOND : bond 0.00279 ( 9) SS BOND : angle 1.27571 ( 18) hydrogen bonds : bond 0.03309 ( 150) hydrogen bonds : angle 5.46021 ( 411) link_BETA1-4 : bond 0.00432 ( 1) link_BETA1-4 : angle 0.99958 ( 3) link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 1.95467 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1258 Ramachandran restraints generated. 629 Oldfield, 0 Emsley, 629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8253 (p) cc_final: 0.7987 (p) REVERT: B 365 TYR cc_start: 0.8751 (m-80) cc_final: 0.8391 (m-80) REVERT: i 28 ASP cc_start: 0.7795 (m-30) cc_final: 0.7289 (m-30) REVERT: i 144 TYR cc_start: 0.7371 (t80) cc_final: 0.6510 (t80) REVERT: i 174 ASP cc_start: 0.8549 (t0) cc_final: 0.8272 (p0) outliers start: 12 outliers final: 11 residues processed: 63 average time/residue: 0.0619 time to fit residues: 5.4521 Evaluate side-chains 61 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.110851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.077973 restraints weight = 13653.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080360 restraints weight = 6895.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081858 restraints weight = 4673.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082780 restraints weight = 3700.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.083264 restraints weight = 3217.619| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5012 Z= 0.186 Angle : 0.669 6.318 6831 Z= 0.348 Chirality : 0.045 0.149 755 Planarity : 0.004 0.034 876 Dihedral : 5.334 36.762 737 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.39 % Allowed : 13.26 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.35), residues: 629 helix: -2.60 (0.69), residues: 43 sheet: 1.23 (0.34), residues: 237 loop : -0.70 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.018 0.002 TYR i 51 PHE 0.011 0.001 PHE i 143 TRP 0.046 0.002 TRP i 152 HIS 0.002 0.001 HIS i 193 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5001) covalent geometry : angle 0.66612 ( 6807) SS BOND : bond 0.00220 ( 9) SS BOND : angle 1.20762 ( 18) hydrogen bonds : bond 0.03280 ( 150) hydrogen bonds : angle 5.51090 ( 411) link_BETA1-4 : bond 0.00457 ( 1) link_BETA1-4 : angle 1.02059 ( 3) link_NAG-ASN : bond 0.00339 ( 1) link_NAG-ASN : angle 1.96199 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1115.55 seconds wall clock time: 20 minutes 0.13 seconds (1200.13 seconds total)