Starting phenix.real_space_refine on Sun Apr 27 07:20:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lyp_63514/04_2025/9lyp_63514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lyp_63514/04_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_63514/04_2025/9lyp_63514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lyp_63514/04_2025/9lyp_63514.map" model { file = "/net/cci-nas-00/data/ceres_data/9lyp_63514/04_2025/9lyp_63514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lyp_63514/04_2025/9lyp_63514.cif" } resolution = 3.6 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= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.66, per 1000 atoms: 0.95 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: 1.27 Conformation dependent library (CDL) restraints added in 614.1 milliseconds 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: 0.60 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: 1.31 Time building geometry restraints manager: 1.51 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: 6.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.250 Find NCS groups from input model: 0.060 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- 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 (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: -0.89 (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 TRP 0.027 0.006 TRP j 110 HIS 0.015 0.005 HIS j 171 PHE 0.023 0.004 PHE B 377 TYR 0.065 0.007 TYR B 495 ARG 0.023 0.005 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 1) link_NAG-ASN : angle 3.95305 ( 3) link_BETA1-4 : bond 0.00304 ( 1) link_BETA1-4 : angle 1.48723 ( 3) hydrogen bonds : bond 0.24050 ( 150) hydrogen bonds : angle 9.41510 ( 411) SS BOND : bond 0.00609 ( 9) SS BOND : angle 1.65043 ( 18) covalent geometry : bond 0.00375 ( 5001) covalent geometry : angle 0.87149 ( 6807) *********************** 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 : 0.541 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: 0.1844 time to fit residues: 19.4830 Evaluate side-chains 57 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.0040 overall best weight: 0.5910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 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 = 0.4050 r_free = 0.4050 target = 0.117026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.084417 restraints weight = 13256.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.086884 restraints weight = 6828.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.088403 restraints weight = 4608.755| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5012 Z= 0.148 Angle : 0.705 6.791 6831 Z= 0.367 Chirality : 0.048 0.161 755 Planarity : 0.005 0.053 876 Dihedral : 5.599 37.705 737 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.72 % Favored : 94.12 % Rotamer: Outliers : 0.92 % Allowed : 8.10 % Favored : 90.98 % 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: 0.14 (0.33), residues: 629 helix: -2.74 (0.57), residues: 41 sheet: 1.72 (0.33), residues: 215 loop : -0.58 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP i 152 HIS 0.006 0.002 HIS i 193 PHE 0.021 0.002 PHE B 377 TYR 0.019 0.002 TYR i 190 ARG 0.005 0.001 ARG B 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 1) link_NAG-ASN : angle 2.79193 ( 3) link_BETA1-4 : bond 0.00612 ( 1) link_BETA1-4 : angle 0.97666 ( 3) hydrogen bonds : bond 0.04099 ( 150) hydrogen bonds : angle 6.18935 ( 411) SS BOND : bond 0.00298 ( 9) SS BOND : angle 1.35018 ( 18) covalent geometry : bond 0.00327 ( 5001) covalent geometry : angle 0.69985 ( 6807) *********************** 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 73 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8633 (m-80) cc_final: 0.8312 (m-80) REVERT: i 49 MET cc_start: 0.8242 (mmm) cc_final: 0.8016 (mmm) REVERT: j 32 TYR cc_start: 0.7172 (m-80) cc_final: 0.6756 (m-10) REVERT: j 89 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8252 (mp0) outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.1531 time to fit residues: 14.3085 Evaluate side-chains 60 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 456 PHE 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 57 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 206 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 = 0.4020 r_free = 0.4020 target = 0.115110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.081716 restraints weight = 13216.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084258 restraints weight = 6743.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.085765 restraints weight = 4531.966| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5012 Z= 0.159 Angle : 0.656 5.965 6831 Z= 0.342 Chirality : 0.046 0.162 755 Planarity : 0.004 0.035 876 Dihedral : 5.495 41.115 737 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.21 % Allowed : 8.66 % Favored : 89.13 % 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: 629 helix: -2.58 (0.68), residues: 35 sheet: 1.68 (0.34), residues: 216 loop : -0.36 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP i 152 HIS 0.007 0.001 HIS i 193 PHE 0.017 0.002 PHE j 153 TYR 0.014 0.002 TYR j 35 ARG 0.003 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 1) link_NAG-ASN : angle 2.06200 ( 3) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 1.14437 ( 3) hydrogen bonds : bond 0.03759 ( 150) hydrogen bonds : angle 5.87342 ( 411) SS BOND : bond 0.00287 ( 9) SS BOND : angle 1.28001 ( 18) covalent geometry : bond 0.00355 ( 5001) covalent geometry : angle 0.65166 ( 6807) *********************** 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 79 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: B 365 TYR cc_start: 0.8675 (m-80) cc_final: 0.8332 (m-80) REVERT: i 49 MET cc_start: 0.8329 (mmm) cc_final: 0.8113 (mmm) REVERT: j 34 MET cc_start: 0.8800 (mmm) cc_final: 0.8222 (mmp) outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.1578 time to fit residues: 15.3246 Evaluate side-chains 64 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 47 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4012 r_free = 0.4012 target = 0.115325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.082056 restraints weight = 13358.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084546 restraints weight = 6883.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086069 restraints weight = 4676.726| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5012 Z= 0.136 Angle : 0.637 5.863 6831 Z= 0.333 Chirality : 0.045 0.151 755 Planarity : 0.004 0.041 876 Dihedral : 5.357 39.186 737 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.39 % Allowed : 10.68 % Favored : 86.92 % 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: 0.42 (0.34), residues: 629 helix: -2.66 (0.69), residues: 35 sheet: 1.78 (0.33), residues: 224 loop : -0.39 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP i 152 HIS 0.007 0.001 HIS i 193 PHE 0.010 0.001 PHE i 143 TYR 0.015 0.002 TYR B 501 ARG 0.004 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 1) link_NAG-ASN : angle 2.07020 ( 3) link_BETA1-4 : bond 0.00234 ( 1) link_BETA1-4 : angle 1.01438 ( 3) hydrogen bonds : bond 0.03385 ( 150) hydrogen bonds : angle 5.69961 ( 411) SS BOND : bond 0.00229 ( 9) SS BOND : angle 1.05270 ( 18) covalent geometry : bond 0.00302 ( 5001) covalent geometry : angle 0.63441 ( 6807) *********************** 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 75 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 THR cc_start: 0.8044 (p) cc_final: 0.7800 (p) REVERT: B 365 TYR cc_start: 0.8681 (m-80) cc_final: 0.8331 (m-80) REVERT: B 498 GLN cc_start: 0.8747 (mt0) cc_final: 0.7726 (mt0) REVERT: j 32 TYR cc_start: 0.7638 (m-80) cc_final: 0.7290 (m-80) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.1581 time to fit residues: 14.8887 Evaluate side-chains 66 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain i residue 198 CYS Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER 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 47 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3972 r_free = 0.3972 target = 0.113788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.080500 restraints weight = 13558.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.083076 restraints weight = 6793.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.084638 restraints weight = 4545.844| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3815 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= 0.127 Angle : 0.611 5.810 6831 Z= 0.319 Chirality : 0.044 0.144 755 Planarity : 0.004 0.039 876 Dihedral : 5.221 39.394 737 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.39 % Allowed : 11.97 % Favored : 85.64 % 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 (0.35), residues: 629 helix: -2.77 (0.70), residues: 35 sheet: 1.79 (0.34), residues: 224 loop : -0.47 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP i 152 HIS 0.006 0.001 HIS i 193 PHE 0.012 0.001 PHE i 143 TYR 0.018 0.001 TYR B 501 ARG 0.004 0.001 ARG i 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 1) link_NAG-ASN : angle 1.89821 ( 3) link_BETA1-4 : bond 0.00498 ( 1) link_BETA1-4 : angle 1.07213 ( 3) hydrogen bonds : bond 0.03111 ( 150) hydrogen bonds : angle 5.58341 ( 411) SS BOND : bond 0.00201 ( 9) SS BOND : angle 1.00806 ( 18) covalent geometry : bond 0.00280 ( 5001) covalent geometry : angle 0.60846 ( 6807) *********************** 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 76 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 THR cc_start: 0.8091 (p) cc_final: 0.7844 (p) REVERT: B 365 TYR cc_start: 0.8733 (m-80) cc_final: 0.8359 (m-80) REVERT: i 49 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7699 (mtp) REVERT: j 83 MET cc_start: 0.8612 (mtm) cc_final: 0.8395 (ptp) outliers start: 13 outliers final: 11 residues processed: 73 average time/residue: 0.2032 time to fit residues: 20.0946 Evaluate side-chains 65 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 49 MET Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 198 CYS Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3941 r_free = 0.3941 target = 0.112438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078257 restraints weight = 13500.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.080648 restraints weight = 6939.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.082155 restraints weight = 4755.338| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4194 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= 0.193 Angle : 0.668 7.285 6831 Z= 0.346 Chirality : 0.045 0.152 755 Planarity : 0.004 0.040 876 Dihedral : 5.366 38.146 737 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.76 % Allowed : 12.34 % 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 (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: 0.17 (0.35), residues: 629 helix: -2.69 (0.73), residues: 35 sheet: 1.62 (0.34), residues: 225 loop : -0.59 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP i 152 HIS 0.005 0.001 HIS i 193 PHE 0.017 0.002 PHE i 143 TYR 0.021 0.002 TYR B 501 ARG 0.002 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 1) link_NAG-ASN : angle 2.00693 ( 3) link_BETA1-4 : bond 0.00578 ( 1) link_BETA1-4 : angle 1.08110 ( 3) hydrogen bonds : bond 0.03411 ( 150) hydrogen bonds : angle 5.57288 ( 411) SS BOND : bond 0.00232 ( 9) SS BOND : angle 1.09743 ( 18) covalent geometry : bond 0.00438 ( 5001) covalent geometry : angle 0.66504 ( 6807) *********************** 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 73 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 THR cc_start: 0.8148 (p) cc_final: 0.7811 (p) REVERT: B 365 TYR cc_start: 0.8787 (m-80) cc_final: 0.8441 (m-80) REVERT: i 49 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7764 (mtp) REVERT: i 174 ASP cc_start: 0.8560 (t0) cc_final: 0.8304 (p0) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.1458 time to fit residues: 13.7536 Evaluate side-chains 65 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 49 MET Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 160 SER Chi-restraints excluded: chain i residue 198 CYS Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 54 optimal weight: 6.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** 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 = 0.3951 r_free = 0.3951 target = 0.112049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.078922 restraints weight = 13255.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.081321 restraints weight = 6752.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.082825 restraints weight = 4590.996| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5012 Z= 0.156 Angle : 0.634 5.876 6831 Z= 0.330 Chirality : 0.045 0.145 755 Planarity : 0.004 0.040 876 Dihedral : 5.205 38.003 737 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.76 % Allowed : 12.71 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.34), residues: 629 helix: -2.81 (0.69), residues: 35 sheet: 1.62 (0.34), residues: 224 loop : -0.64 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP i 152 HIS 0.005 0.001 HIS i 193 PHE 0.017 0.001 PHE i 143 TYR 0.019 0.001 TYR B 501 ARG 0.002 0.001 ARG B 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 1) link_NAG-ASN : angle 1.90436 ( 3) link_BETA1-4 : bond 0.00402 ( 1) link_BETA1-4 : angle 1.01797 ( 3) hydrogen bonds : bond 0.03150 ( 150) hydrogen bonds : angle 5.52364 ( 411) SS BOND : bond 0.00229 ( 9) SS BOND : angle 1.04816 ( 18) covalent geometry : bond 0.00350 ( 5001) covalent geometry : angle 0.63159 ( 6807) *********************** 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 73 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 345 THR cc_start: 0.8211 (p) cc_final: 0.7906 (p) REVERT: B 365 TYR cc_start: 0.8770 (m-80) cc_final: 0.8415 (m-80) REVERT: i 49 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7875 (mtp) REVERT: i 144 TYR cc_start: 0.7287 (t80) cc_final: 0.6474 (t80) REVERT: i 165 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8472 (tp30) REVERT: i 174 ASP cc_start: 0.8431 (t0) cc_final: 0.8170 (p0) outliers start: 15 outliers final: 11 residues processed: 70 average time/residue: 0.1947 time to fit residues: 18.5446 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 : 0.639 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 49 MET Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 198 CYS Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 193 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.077386 restraints weight = 13553.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.079786 restraints weight = 7131.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.081258 restraints weight = 4901.250| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5012 Z= 0.222 Angle : 0.686 6.228 6831 Z= 0.358 Chirality : 0.046 0.155 755 Planarity : 0.004 0.040 876 Dihedral : 5.407 36.961 737 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.95 % Allowed : 12.71 % 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 (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: -0.04 (0.35), residues: 629 helix: -2.60 (0.74), residues: 35 sheet: 1.37 (0.34), residues: 225 loop : -0.68 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP i 152 HIS 0.005 0.001 HIS i 193 PHE 0.014 0.002 PHE i 143 TYR 0.018 0.002 TYR B 501 ARG 0.003 0.001 ARG B 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 1) link_NAG-ASN : angle 2.00715 ( 3) link_BETA1-4 : bond 0.00537 ( 1) link_BETA1-4 : angle 1.05255 ( 3) hydrogen bonds : bond 0.03600 ( 150) hydrogen bonds : angle 5.72713 ( 411) SS BOND : bond 0.00355 ( 9) SS BOND : angle 1.56095 ( 18) covalent geometry : bond 0.00507 ( 5001) covalent geometry : angle 0.68125 ( 6807) *********************** 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 66 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8248 (p) cc_final: 0.7949 (p) REVERT: B 365 TYR cc_start: 0.8779 (m-80) cc_final: 0.8413 (m-80) REVERT: i 49 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7846 (mtp) REVERT: i 144 TYR cc_start: 0.7389 (t80) cc_final: 0.6483 (t80) REVERT: i 165 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8480 (tp30) outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.1948 time to fit residues: 17.6139 Evaluate side-chains 61 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 473 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 49 MET Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 138 CYS Chi-restraints excluded: chain i residue 198 CYS Chi-restraints excluded: chain j residue 118 VAL Chi-restraints excluded: chain j residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 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 = 0.3954 r_free = 0.3954 target = 0.111673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077995 restraints weight = 13191.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.080525 restraints weight = 6725.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.082038 restraints weight = 4537.909| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5012 Z= 0.151 Angle : 0.651 5.872 6831 Z= 0.339 Chirality : 0.045 0.145 755 Planarity : 0.004 0.039 876 Dihedral : 5.240 37.553 737 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.76 % Allowed : 13.08 % 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 (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: -0.07 (0.34), residues: 629 helix: -2.65 (0.71), residues: 35 sheet: 1.27 (0.35), residues: 227 loop : -0.65 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP i 152 HIS 0.002 0.001 HIS j 207 PHE 0.013 0.001 PHE i 143 TYR 0.018 0.001 TYR i 51 ARG 0.001 0.000 ARG B 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 1) link_NAG-ASN : angle 1.88046 ( 3) link_BETA1-4 : bond 0.00403 ( 1) link_BETA1-4 : angle 1.03614 ( 3) hydrogen bonds : bond 0.03237 ( 150) hydrogen bonds : angle 5.54561 ( 411) SS BOND : bond 0.00306 ( 9) SS BOND : angle 1.23018 ( 18) covalent geometry : bond 0.00340 ( 5001) covalent geometry : angle 0.64716 ( 6807) *********************** 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 67 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8195 (p) cc_final: 0.7909 (p) REVERT: B 365 TYR cc_start: 0.8704 (m-80) cc_final: 0.8368 (m-80) REVERT: i 144 TYR cc_start: 0.7342 (t80) cc_final: 0.6455 (t80) REVERT: i 165 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8444 (tp30) outliers start: 15 outliers final: 13 residues processed: 63 average time/residue: 0.1355 time to fit residues: 11.8715 Evaluate side-chains 62 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 455 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain i residue 48 LEU Chi-restraints excluded: chain i residue 91 ASN Chi-restraints excluded: chain i residue 198 CYS 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 36 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 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 = 0.3974 r_free = 0.3974 target = 0.112726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.081265 restraints weight = 13162.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083734 restraints weight = 6408.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085259 restraints weight = 4209.924| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5012 Z= 0.125 Angle : 0.642 5.939 6831 Z= 0.333 Chirality : 0.044 0.141 755 Planarity : 0.004 0.040 876 Dihedral : 5.053 37.440 737 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.84 % Allowed : 14.73 % Favored : 83.43 % 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: -0.11 (0.35), residues: 629 helix: -2.84 (0.67), residues: 43 sheet: 1.32 (0.35), residues: 226 loop : -0.65 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP i 152 HIS 0.002 0.001 HIS j 207 PHE 0.009 0.001 PHE i 143 TYR 0.019 0.001 TYR i 51 ARG 0.002 0.000 ARG j 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 1) link_NAG-ASN : angle 1.83024 ( 3) link_BETA1-4 : bond 0.00451 ( 1) link_BETA1-4 : angle 1.01722 ( 3) hydrogen bonds : bond 0.03058 ( 150) hydrogen bonds : angle 5.42559 ( 411) SS BOND : bond 0.00294 ( 9) SS BOND : angle 1.04807 ( 18) covalent geometry : bond 0.00279 ( 5001) covalent geometry : angle 0.63897 ( 6807) ********************** 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 65 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: B 345 THR cc_start: 0.8194 (p) cc_final: 0.7926 (p) REVERT: B 365 TYR cc_start: 0.8696 (m-80) cc_final: 0.8318 (m-80) REVERT: i 144 TYR cc_start: 0.7311 (t80) cc_final: 0.6502 (t80) REVERT: i 165 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8424 (tp30) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.1844 time to fit residues: 15.8976 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 : 0.597 ------------------------------------------------------------------------------- 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 512 VAL Chi-restraints excluded: chain i residue 198 CYS 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 27 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 53 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 0.0060 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 112 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.112541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079249 restraints weight = 13556.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.081786 restraints weight = 6813.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.083355 restraints weight = 4576.844| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5012 Z= 0.143 Angle : 0.646 6.799 6831 Z= 0.334 Chirality : 0.044 0.144 755 Planarity : 0.004 0.040 876 Dihedral : 5.052 37.132 737 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.21 % Allowed : 14.18 % Favored : 83.61 % 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: -0.11 (0.35), residues: 629 helix: -2.91 (0.63), residues: 43 sheet: 1.33 (0.35), residues: 227 loop : -0.65 (0.34), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP i 152 HIS 0.002 0.001 HIS j 207 PHE 0.011 0.001 PHE i 143 TYR 0.018 0.001 TYR i 51 ARG 0.002 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 1) link_NAG-ASN : angle 1.88259 ( 3) link_BETA1-4 : bond 0.00401 ( 1) link_BETA1-4 : angle 0.98849 ( 3) hydrogen bonds : bond 0.03070 ( 150) hydrogen bonds : angle 5.37139 ( 411) SS BOND : bond 0.00296 ( 9) SS BOND : angle 1.09225 ( 18) covalent geometry : bond 0.00325 ( 5001) covalent geometry : angle 0.64289 ( 6807) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.65 seconds wall clock time: 46 minutes 12.08 seconds (2772.08 seconds total)