Starting phenix.real_space_refine on Sat May 10 09:57:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tld_41367/05_2025/8tld_41367.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tld_41367/05_2025/8tld_41367.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/8tld_41367/05_2025/8tld_41367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tld_41367/05_2025/8tld_41367.map" model { file = "/net/cci-nas-00/data/ceres_data/8tld_41367/05_2025/8tld_41367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tld_41367/05_2025/8tld_41367.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= 0.026 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 27 5.16 5 C 3776 2.51 5 N 1040 2.21 5 O 1139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5982 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 758 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 9, 'TRANS': 84} Chain breaks: 1 Chain: "C" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 879 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 942 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "F" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2471 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 291} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.69, per 1000 atoms: 0.62 Number of scatterers: 5982 At special positions: 0 Unit cell: (80.972, 112.316, 124.07, 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 27 16.00 O 1139 8.00 N 1040 7.00 C 3776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 106 " - pdb=" SG CYS D 64 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 155 " distance=2.03 Simple disulfide: pdb=" SG CYS F 182 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 269 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C 200 " - " ASN C 48 " " NAG F 501 " - " ASN F 35 " " NAG F 502 " - " ASN F 131 " " NAG F 503 " - " ASN F 216 " " NAG F 504 " - " ASN F 244 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 796.4 milliseconds 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1400 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 24.9% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 51 through 55 removed outlier: 3.859A pdb=" N ARG B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 51 through 55' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 64 through 78 Processing helix chain 'C' and resid 84 through 105 removed outlier: 3.673A pdb=" N ASN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 130 Processing helix chain 'D' and resid 29 through 41 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.536A pdb=" N LEU D 45 " --> pdb=" O HIS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 63 removed outlier: 3.721A pdb=" N LEU D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 64 through 79 Processing helix chain 'D' and resid 83 through 106 removed outlier: 4.037A pdb=" N ARG D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 130 Processing helix chain 'E' and resid 382 through 386 Processing helix chain 'F' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.293A pdb=" N GLU D 109 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 95 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 removed outlier: 4.293A pdb=" N GLU D 109 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER F 95 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 344 through 350 Processing sheet with id=AA6, first strand: chain 'E' and resid 387 through 392 Processing sheet with id=AA7, first strand: chain 'F' and resid 34 through 42 removed outlier: 5.518A pdb=" N ASN F 35 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS F 51 " --> pdb=" O ASN F 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 39 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR F 41 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLN F 45 " --> pdb=" O THR F 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 130 through 140 removed outlier: 5.696A pdb=" N ASN F 131 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU F 158 " --> pdb=" O ASN F 131 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL F 151 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ARG F 200 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ILE F 194 " --> pdb=" O TRP F 157 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER F 186 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'F' and resid 246 through 250 Processing sheet with id=AB2, first strand: chain 'F' and resid 284 through 289 280 hydrogen bonds defined for protein. 768 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: 1.65 Time building geometry restraints manager: 1.56 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: 1954 1.34 - 1.46: 1304 1.46 - 1.58: 2820 1.58 - 1.70: 2 1.70 - 1.82: 36 Bond restraints: 6116 Sorted by residual: bond pdb=" CG PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 1.503 1.296 0.207 3.40e-02 8.65e+02 3.70e+01 bond pdb=" CB PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.23e+01 bond pdb=" N PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.21e+01 bond pdb=" N PRO C 54 " pdb=" CA PRO C 54 " ideal model delta sigma weight residual 1.469 1.438 0.030 1.28e-02 6.10e+03 5.64e+00 bond pdb=" C1 NAG F 503 " pdb=" O5 NAG F 503 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 6111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 8264 3.60 - 7.20: 37 7.20 - 10.81: 5 10.81 - 14.41: 1 14.41 - 18.01: 1 Bond angle restraints: 8308 Sorted by residual: angle pdb=" CA PRO C 54 " pdb=" N PRO C 54 " pdb=" CD PRO C 54 " ideal model delta sigma weight residual 112.00 93.99 18.01 1.40e+00 5.10e-01 1.65e+02 angle pdb=" N PRO C 54 " pdb=" CD PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 103.20 90.46 12.74 1.50e+00 4.44e-01 7.21e+01 angle pdb=" CA PRO C 54 " pdb=" CB PRO C 54 " pdb=" CG PRO C 54 " ideal model delta sigma weight residual 104.50 94.84 9.66 1.90e+00 2.77e-01 2.59e+01 angle pdb=" CA PRO F 261 " pdb=" N PRO F 261 " pdb=" CD PRO F 261 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 angle pdb=" C GLU D 24 " pdb=" N ILE D 25 " pdb=" CA ILE D 25 " ideal model delta sigma weight residual 122.13 129.53 -7.40 1.85e+00 2.92e-01 1.60e+01 ... (remaining 8303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 3192 17.71 - 35.41: 429 35.41 - 53.12: 121 53.12 - 70.82: 18 70.82 - 88.53: 12 Dihedral angle restraints: 3772 sinusoidal: 1622 harmonic: 2150 Sorted by residual: dihedral pdb=" CA GLN C 102 " pdb=" C GLN C 102 " pdb=" N LYS C 103 " pdb=" CA LYS C 103 " ideal model delta harmonic sigma weight residual 180.00 152.91 27.09 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN C 48 " pdb=" C ASN C 48 " pdb=" N GLU C 49 " pdb=" CA GLU C 49 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS C 64 " pdb=" SG CYS C 64 " pdb=" SG CYS D 106 " pdb=" CB CYS D 106 " ideal model delta sinusoidal sigma weight residual -86.00 -45.06 -40.94 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 3769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 874 0.084 - 0.167: 70 0.167 - 0.251: 1 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG C 200 " pdb=" ND2 ASN C 48 " pdb=" C2 NAG C 200 " pdb=" O5 NAG C 200 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ASN D 60 " pdb=" N ASN D 60 " pdb=" C ASN D 60 " pdb=" CB ASN D 60 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C1 NAG F 501 " pdb=" ND2 ASN F 35 " pdb=" C2 NAG F 501 " pdb=" O5 NAG F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 943 not shown) Planarity restraints: 1059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 53 " -0.102 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO C 54 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO C 54 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 54 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 110 " -0.371 9.50e-02 1.11e+02 1.67e-01 1.80e+01 pdb=" NE ARG C 110 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 110 " 0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG C 110 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 110 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 260 " 0.063 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO F 261 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO F 261 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 261 " 0.050 5.00e-02 4.00e+02 ... (remaining 1056 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 343 2.72 - 3.27: 5661 3.27 - 3.81: 9630 3.81 - 4.36: 11263 4.36 - 4.90: 19145 Nonbonded interactions: 46042 Sorted by model distance: nonbonded pdb=" O PRO E 343 " pdb=" OG SER E 429 " model vdw 2.181 3.040 nonbonded pdb=" OG1 THR D 34 " pdb=" OD1 ASN D 91 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP B 104 " pdb=" NH1 ARG C 87 " model vdw 2.185 3.120 nonbonded pdb=" NZ LYS F 260 " pdb=" O PHE F 265 " model vdw 2.198 3.120 nonbonded pdb=" O THR C 50 " pdb=" NH1 ARG C 52 " model vdw 2.211 3.120 ... (remaining 46037 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 25 through 131) selection = (chain 'D' and resid 25 through 131) } 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: 0.250 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 : 0.005 0.207 6129 Z= 0.205 Angle : 0.759 18.009 8339 Z= 0.412 Chirality : 0.045 0.418 946 Planarity : 0.009 0.167 1054 Dihedral : 17.428 88.526 2348 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 0.60 % Allowed : 24.13 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.32), residues: 719 helix: 0.48 (0.41), residues: 169 sheet: 0.65 (0.36), residues: 226 loop : -0.96 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 322 HIS 0.006 0.001 HIS C 61 PHE 0.024 0.002 PHE D 116 TYR 0.009 0.001 TYR F 172 ARG 0.018 0.001 ARG C 110 Details of bonding type rmsd link_NAG-ASN : bond 0.01686 ( 5) link_NAG-ASN : angle 4.76115 ( 15) hydrogen bonds : bond 0.19589 ( 262) hydrogen bonds : angle 7.41462 ( 768) SS BOND : bond 0.00319 ( 8) SS BOND : angle 0.68439 ( 16) covalent geometry : bond 0.00532 ( 6116) covalent geometry : angle 0.73239 ( 8308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 126 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: D 123 PHE cc_start: 0.7327 (t80) cc_final: 0.6906 (t80) REVERT: F 186 SER cc_start: 0.8080 (m) cc_final: 0.7838 (p) REVERT: F 292 ASN cc_start: 0.7951 (OUTLIER) cc_final: 0.6940 (t0) REVERT: F 324 GLU cc_start: 0.7743 (tp30) cc_final: 0.7373 (tp30) outliers start: 4 outliers final: 0 residues processed: 127 average time/residue: 0.2055 time to fit residues: 33.1869 Evaluate side-chains 124 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132038 restraints weight = 9674.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.135129 restraints weight = 5759.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137227 restraints weight = 3882.246| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 6129 Z= 0.151 Angle : 0.638 12.369 8339 Z= 0.325 Chirality : 0.045 0.371 946 Planarity : 0.006 0.089 1054 Dihedral : 6.731 54.288 903 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 3.02 % Allowed : 23.68 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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 (0.32), residues: 719 helix: 1.03 (0.42), residues: 158 sheet: 0.78 (0.36), residues: 227 loop : -0.79 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 322 HIS 0.004 0.001 HIS F 277 PHE 0.012 0.002 PHE F 198 TYR 0.012 0.001 TYR E 376 ARG 0.007 0.001 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01489 ( 5) link_NAG-ASN : angle 4.90878 ( 15) hydrogen bonds : bond 0.04145 ( 262) hydrogen bonds : angle 5.52571 ( 768) SS BOND : bond 0.00373 ( 8) SS BOND : angle 0.79716 ( 16) covalent geometry : bond 0.00351 ( 6116) covalent geometry : angle 0.60368 ( 8308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 PRO cc_start: 0.6862 (Cg_exo) cc_final: 0.6636 (Cg_endo) REVERT: D 112 ARG cc_start: 0.7471 (mmt-90) cc_final: 0.7004 (mpt180) REVERT: D 123 PHE cc_start: 0.6981 (t80) cc_final: 0.6740 (t80) REVERT: F 40 VAL cc_start: 0.8317 (t) cc_final: 0.8068 (m) REVERT: F 292 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7051 (t0) REVERT: F 324 GLU cc_start: 0.7667 (tp30) cc_final: 0.7350 (tp30) outliers start: 20 outliers final: 9 residues processed: 147 average time/residue: 0.2088 time to fit residues: 38.7678 Evaluate side-chains 142 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN D 81 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.147628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.130710 restraints weight = 9722.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133666 restraints weight = 5854.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135657 restraints weight = 4004.978| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 6129 Z= 0.232 Angle : 0.676 12.077 8339 Z= 0.345 Chirality : 0.046 0.360 946 Planarity : 0.006 0.073 1054 Dihedral : 6.799 54.781 903 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.31 % Favored : 95.27 % Rotamer: Outliers : 4.37 % Allowed : 22.78 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.08 (0.32), residues: 719 helix: 0.74 (0.41), residues: 164 sheet: 0.58 (0.35), residues: 230 loop : -0.89 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 322 HIS 0.007 0.002 HIS F 106 PHE 0.019 0.002 PHE F 198 TYR 0.016 0.002 TYR E 376 ARG 0.004 0.001 ARG F 59 Details of bonding type rmsd link_NAG-ASN : bond 0.01394 ( 5) link_NAG-ASN : angle 4.22540 ( 15) hydrogen bonds : bond 0.04358 ( 262) hydrogen bonds : angle 5.40160 ( 768) SS BOND : bond 0.00634 ( 8) SS BOND : angle 1.03667 ( 16) covalent geometry : bond 0.00528 ( 6116) covalent geometry : angle 0.65163 ( 8308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7944 (m) REVERT: D 112 ARG cc_start: 0.7434 (mmt-90) cc_final: 0.7066 (mpt180) REVERT: F 40 VAL cc_start: 0.8363 (t) cc_final: 0.8138 (m) REVERT: F 85 LYS cc_start: 0.7819 (mttp) cc_final: 0.7588 (mttp) REVERT: F 292 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7234 (t0) REVERT: F 322 TRP cc_start: 0.7900 (m100) cc_final: 0.7693 (m-10) outliers start: 29 outliers final: 19 residues processed: 148 average time/residue: 0.2045 time to fit residues: 38.1834 Evaluate side-chains 152 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 292 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 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 = 0.3872 r_free = 0.3872 target = 0.149011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131561 restraints weight = 9781.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134694 restraints weight = 5885.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136793 restraints weight = 3988.145| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 6129 Z= 0.165 Angle : 0.612 12.235 8339 Z= 0.311 Chirality : 0.044 0.336 946 Planarity : 0.005 0.075 1054 Dihedral : 6.496 55.778 903 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.89 % Favored : 95.69 % Rotamer: Outliers : 4.52 % Allowed : 23.08 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.02 (0.31), residues: 719 helix: 0.87 (0.41), residues: 164 sheet: 0.55 (0.35), residues: 230 loop : -0.79 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 322 HIS 0.004 0.001 HIS C 61 PHE 0.012 0.002 PHE F 198 TYR 0.013 0.002 TYR E 376 ARG 0.002 0.000 ARG E 327 Details of bonding type rmsd link_NAG-ASN : bond 0.01341 ( 5) link_NAG-ASN : angle 3.91173 ( 15) hydrogen bonds : bond 0.03699 ( 262) hydrogen bonds : angle 5.14677 ( 768) SS BOND : bond 0.00457 ( 8) SS BOND : angle 0.81861 ( 16) covalent geometry : bond 0.00379 ( 6116) covalent geometry : angle 0.58902 ( 8308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8267 (t) cc_final: 0.8002 (p) REVERT: C 84 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7765 (m) REVERT: D 112 ARG cc_start: 0.7453 (mmt-90) cc_final: 0.7041 (mpt180) REVERT: E 421 TYR cc_start: 0.8338 (m-80) cc_final: 0.7623 (m-80) REVERT: F 40 VAL cc_start: 0.8385 (t) cc_final: 0.8147 (m) REVERT: F 135 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7914 (p) REVERT: F 292 ASN cc_start: 0.8302 (t0) cc_final: 0.7217 (t0) REVERT: F 322 TRP cc_start: 0.7966 (m100) cc_final: 0.7612 (m-10) outliers start: 30 outliers final: 21 residues processed: 149 average time/residue: 0.2001 time to fit residues: 38.4541 Evaluate side-chains 148 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 260 LYS Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.147006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.129448 restraints weight = 9748.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.132610 restraints weight = 5847.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134725 restraints weight = 3958.213| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 6129 Z= 0.217 Angle : 0.667 12.145 8339 Z= 0.339 Chirality : 0.045 0.334 946 Planarity : 0.006 0.084 1054 Dihedral : 6.426 55.803 901 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.01 % Favored : 94.58 % Rotamer: Outliers : 5.43 % Allowed : 22.62 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.10 (0.31), residues: 719 helix: 0.84 (0.41), residues: 164 sheet: 0.44 (0.34), residues: 230 loop : -0.87 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 322 HIS 0.006 0.001 HIS F 106 PHE 0.018 0.002 PHE F 198 TYR 0.015 0.002 TYR E 376 ARG 0.004 0.001 ARG D 52 Details of bonding type rmsd link_NAG-ASN : bond 0.01344 ( 5) link_NAG-ASN : angle 3.79486 ( 15) hydrogen bonds : bond 0.03936 ( 262) hydrogen bonds : angle 5.21068 ( 768) SS BOND : bond 0.00611 ( 8) SS BOND : angle 0.99645 ( 16) covalent geometry : bond 0.00495 ( 6116) covalent geometry : angle 0.64673 ( 8308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 112 ARG cc_start: 0.7408 (mmt-90) cc_final: 0.6965 (mpt180) REVERT: D 123 PHE cc_start: 0.7249 (t80) cc_final: 0.7006 (t80) REVERT: E 421 TYR cc_start: 0.8366 (m-80) cc_final: 0.7549 (m-80) REVERT: F 220 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6783 (pttt) REVERT: F 292 ASN cc_start: 0.8301 (t0) cc_final: 0.7162 (t0) REVERT: F 309 ARG cc_start: 0.6593 (mtp180) cc_final: 0.6087 (mtp180) REVERT: F 317 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6888 (ttm170) REVERT: F 322 TRP cc_start: 0.7972 (m100) cc_final: 0.7452 (m-10) outliers start: 36 outliers final: 25 residues processed: 154 average time/residue: 0.1860 time to fit residues: 37.0345 Evaluate side-chains 156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 131 TRP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 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 = 0.3868 r_free = 0.3868 target = 0.148630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131730 restraints weight = 9580.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134671 restraints weight = 5853.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136683 restraints weight = 4018.567| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6129 Z= 0.155 Angle : 0.615 12.272 8339 Z= 0.314 Chirality : 0.044 0.322 946 Planarity : 0.005 0.087 1054 Dihedral : 6.291 56.471 901 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.62 % Favored : 95.97 % Rotamer: Outliers : 5.43 % Allowed : 23.98 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.00 (0.32), residues: 719 helix: 0.86 (0.40), residues: 169 sheet: 0.47 (0.34), residues: 230 loop : -0.78 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 50 HIS 0.004 0.001 HIS C 61 PHE 0.019 0.002 PHE D 123 TYR 0.012 0.001 TYR E 376 ARG 0.004 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01285 ( 5) link_NAG-ASN : angle 3.77455 ( 15) hydrogen bonds : bond 0.03501 ( 262) hydrogen bonds : angle 5.03907 ( 768) SS BOND : bond 0.00454 ( 8) SS BOND : angle 0.75035 ( 16) covalent geometry : bond 0.00357 ( 6116) covalent geometry : angle 0.59441 ( 8308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8222 (t) cc_final: 0.7969 (p) REVERT: C 84 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7869 (m) REVERT: D 42 ARG cc_start: 0.5954 (OUTLIER) cc_final: 0.5163 (ttm110) REVERT: D 112 ARG cc_start: 0.7230 (mmt-90) cc_final: 0.6930 (mpt180) REVERT: D 123 PHE cc_start: 0.7328 (t80) cc_final: 0.6231 (t80) REVERT: E 421 TYR cc_start: 0.8378 (m-80) cc_final: 0.7552 (m-80) REVERT: F 220 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6581 (pttt) REVERT: F 272 TYR cc_start: 0.7713 (m-80) cc_final: 0.7331 (m-80) REVERT: F 292 ASN cc_start: 0.8274 (t0) cc_final: 0.7199 (t0) REVERT: F 317 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7028 (ttm170) outliers start: 36 outliers final: 23 residues processed: 142 average time/residue: 0.1970 time to fit residues: 35.6191 Evaluate side-chains 146 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131133 restraints weight = 9610.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134264 restraints weight = 5807.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136376 restraints weight = 3948.885| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 6129 Z= 0.172 Angle : 0.636 12.259 8339 Z= 0.321 Chirality : 0.044 0.320 946 Planarity : 0.005 0.063 1054 Dihedral : 6.324 55.931 901 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.73 % Favored : 94.85 % Rotamer: Outliers : 5.28 % Allowed : 23.23 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.05 (0.32), residues: 719 helix: 0.86 (0.40), residues: 169 sheet: 0.43 (0.34), residues: 232 loop : -0.82 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 50 HIS 0.005 0.001 HIS D 61 PHE 0.016 0.002 PHE D 123 TYR 0.012 0.002 TYR E 376 ARG 0.004 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01271 ( 5) link_NAG-ASN : angle 3.74546 ( 15) hydrogen bonds : bond 0.03543 ( 262) hydrogen bonds : angle 5.01286 ( 768) SS BOND : bond 0.00504 ( 8) SS BOND : angle 0.84336 ( 16) covalent geometry : bond 0.00400 ( 6116) covalent geometry : angle 0.61585 ( 8308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8172 (t) cc_final: 0.7917 (p) REVERT: C 84 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7723 (m) REVERT: D 42 ARG cc_start: 0.5932 (OUTLIER) cc_final: 0.5135 (ttm110) REVERT: D 112 ARG cc_start: 0.7238 (mmt-90) cc_final: 0.6921 (mpt180) REVERT: E 421 TYR cc_start: 0.8360 (m-80) cc_final: 0.7453 (m-80) REVERT: F 220 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6758 (pttt) REVERT: F 272 TYR cc_start: 0.7695 (m-80) cc_final: 0.7317 (m-80) REVERT: F 292 ASN cc_start: 0.8302 (t0) cc_final: 0.7145 (t0) REVERT: F 317 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6891 (ttm170) outliers start: 35 outliers final: 27 residues processed: 142 average time/residue: 0.1917 time to fit residues: 35.0095 Evaluate side-chains 150 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.149077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.131528 restraints weight = 9678.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134711 restraints weight = 5834.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136852 restraints weight = 3951.547| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6129 Z= 0.151 Angle : 0.627 12.273 8339 Z= 0.315 Chirality : 0.044 0.315 946 Planarity : 0.005 0.063 1054 Dihedral : 6.255 56.093 901 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.83 % Rotamer: Outliers : 4.98 % Allowed : 23.83 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.00 (0.32), residues: 719 helix: 0.91 (0.40), residues: 169 sheet: 0.47 (0.35), residues: 231 loop : -0.81 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 322 HIS 0.004 0.001 HIS C 61 PHE 0.014 0.002 PHE F 198 TYR 0.011 0.001 TYR E 376 ARG 0.002 0.000 ARG C 111 Details of bonding type rmsd link_NAG-ASN : bond 0.01240 ( 5) link_NAG-ASN : angle 3.74527 ( 15) hydrogen bonds : bond 0.03420 ( 262) hydrogen bonds : angle 4.93743 ( 768) SS BOND : bond 0.00432 ( 8) SS BOND : angle 0.75751 ( 16) covalent geometry : bond 0.00352 ( 6116) covalent geometry : angle 0.60642 ( 8308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8167 (t) cc_final: 0.7904 (p) REVERT: C 84 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7710 (m) REVERT: D 42 ARG cc_start: 0.5850 (OUTLIER) cc_final: 0.5043 (ttm110) REVERT: D 112 ARG cc_start: 0.7162 (mmt-90) cc_final: 0.6846 (mpt180) REVERT: D 127 MET cc_start: 0.6580 (mmp) cc_final: 0.6326 (mmm) REVERT: F 220 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6754 (pttt) REVERT: F 292 ASN cc_start: 0.8295 (t0) cc_final: 0.7201 (t0) REVERT: F 317 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6944 (ttm170) REVERT: F 322 TRP cc_start: 0.7910 (m100) cc_final: 0.7548 (m-10) outliers start: 33 outliers final: 28 residues processed: 143 average time/residue: 0.1934 time to fit residues: 35.5420 Evaluate side-chains 151 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 TYR Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 412 VAL Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN F 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.131369 restraints weight = 9777.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134465 restraints weight = 5961.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136556 restraints weight = 4086.244| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6129 Z= 0.135 Angle : 0.612 12.319 8339 Z= 0.307 Chirality : 0.043 0.309 946 Planarity : 0.005 0.063 1054 Dihedral : 6.195 56.115 901 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.03 % Favored : 95.55 % Rotamer: Outliers : 5.58 % Allowed : 23.08 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.15 (0.32), residues: 719 helix: 1.11 (0.41), residues: 164 sheet: 0.63 (0.35), residues: 226 loop : -0.77 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 434 HIS 0.004 0.001 HIS D 61 PHE 0.028 0.002 PHE D 123 TYR 0.014 0.001 TYR F 172 ARG 0.003 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01208 ( 5) link_NAG-ASN : angle 3.76594 ( 15) hydrogen bonds : bond 0.03267 ( 262) hydrogen bonds : angle 4.84504 ( 768) SS BOND : bond 0.00411 ( 8) SS BOND : angle 0.71503 ( 16) covalent geometry : bond 0.00318 ( 6116) covalent geometry : angle 0.59100 ( 8308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8142 (t) cc_final: 0.7898 (p) REVERT: C 84 THR cc_start: 0.8044 (OUTLIER) cc_final: 0.7740 (m) REVERT: C 112 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6173 (tpp80) REVERT: D 42 ARG cc_start: 0.5859 (OUTLIER) cc_final: 0.5081 (ttm110) REVERT: D 123 PHE cc_start: 0.7133 (t80) cc_final: 0.6346 (t80) REVERT: D 127 MET cc_start: 0.6561 (mmp) cc_final: 0.5999 (mmp) REVERT: E 421 TYR cc_start: 0.8438 (m-80) cc_final: 0.7700 (m-80) REVERT: F 193 ASN cc_start: 0.7626 (m-40) cc_final: 0.7355 (m110) REVERT: F 292 ASN cc_start: 0.8270 (t0) cc_final: 0.7155 (t0) REVERT: F 317 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6806 (ttm170) REVERT: F 322 TRP cc_start: 0.7876 (m100) cc_final: 0.7536 (m-10) outliers start: 37 outliers final: 29 residues processed: 141 average time/residue: 0.1894 time to fit residues: 34.4258 Evaluate side-chains 146 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 112 ARG Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.129827 restraints weight = 9760.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.133123 restraints weight = 5880.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135343 restraints weight = 3985.106| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 6129 Z= 0.153 Angle : 0.643 12.260 8339 Z= 0.320 Chirality : 0.044 0.309 946 Planarity : 0.005 0.062 1054 Dihedral : 6.250 55.917 901 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.62 % Favored : 95.97 % Rotamer: Outliers : 5.28 % Allowed : 23.23 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.08 (0.32), residues: 719 helix: 1.07 (0.41), residues: 164 sheet: 0.54 (0.35), residues: 232 loop : -0.81 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 322 HIS 0.004 0.001 HIS C 61 PHE 0.025 0.002 PHE D 123 TYR 0.010 0.001 TYR E 376 ARG 0.004 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01198 ( 5) link_NAG-ASN : angle 3.75485 ( 15) hydrogen bonds : bond 0.03339 ( 262) hydrogen bonds : angle 4.87634 ( 768) SS BOND : bond 0.00456 ( 8) SS BOND : angle 0.76132 ( 16) covalent geometry : bond 0.00357 ( 6116) covalent geometry : angle 0.62283 ( 8308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1438 Ramachandran restraints generated. 719 Oldfield, 0 Emsley, 719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.8147 (t) cc_final: 0.7899 (p) REVERT: C 84 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7757 (m) REVERT: D 42 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.5139 (ttm110) REVERT: D 112 ARG cc_start: 0.7084 (mmt-90) cc_final: 0.6747 (mpt180) REVERT: D 123 PHE cc_start: 0.7172 (t80) cc_final: 0.6367 (t80) REVERT: D 127 MET cc_start: 0.6560 (mmp) cc_final: 0.6106 (mmp) REVERT: E 421 TYR cc_start: 0.8458 (m-80) cc_final: 0.7696 (m-80) REVERT: F 193 ASN cc_start: 0.7631 (m-40) cc_final: 0.7406 (m110) REVERT: F 292 ASN cc_start: 0.8291 (t0) cc_final: 0.7210 (t0) REVERT: F 317 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6760 (ttm170) REVERT: F 322 TRP cc_start: 0.7897 (m100) cc_final: 0.7523 (m-10) outliers start: 35 outliers final: 28 residues processed: 145 average time/residue: 0.1972 time to fit residues: 36.7934 Evaluate side-chains 149 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 85 HIS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 93 CYS Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 42 ARG Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 426 SER Chi-restraints excluded: chain E residue 433 SER Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain F residue 186 SER Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 289 LEU Chi-restraints excluded: chain F residue 317 ARG Chi-restraints excluded: chain F residue 326 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS F 45 GLN F 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.149183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.130937 restraints weight = 9832.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134263 restraints weight = 5889.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136527 restraints weight = 3975.493| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6129 Z= 0.128 Angle : 0.632 12.263 8339 Z= 0.311 Chirality : 0.043 0.302 946 Planarity : 0.005 0.063 1054 Dihedral : 6.299 56.061 901 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.20 % Favored : 96.38 % Rotamer: Outliers : 5.28 % Allowed : 23.23 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.21 (0.32), residues: 719 helix: 1.16 (0.41), residues: 164 sheet: 0.74 (0.36), residues: 225 loop : -0.80 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 434 HIS 0.004 0.001 HIS D 61 PHE 0.025 0.002 PHE D 123 TYR 0.013 0.001 TYR F 172 ARG 0.006 0.000 ARG F 174 Details of bonding type rmsd link_NAG-ASN : bond 0.01150 ( 5) link_NAG-ASN : angle 3.79674 ( 15) hydrogen bonds : bond 0.03242 ( 262) hydrogen bonds : angle 4.80655 ( 768) SS BOND : bond 0.00356 ( 8) SS BOND : angle 0.64605 ( 16) covalent geometry : bond 0.00300 ( 6116) covalent geometry : angle 0.61198 ( 8308) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.07 seconds wall clock time: 39 minutes 31.31 seconds (2371.31 seconds total)