Starting phenix.real_space_refine on Wed Jul 23 07:10:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xc5_38237/07_2025/8xc5_38237.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xc5_38237/07_2025/8xc5_38237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xc5_38237/07_2025/8xc5_38237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xc5_38237/07_2025/8xc5_38237.map" model { file = "/net/cci-nas-00/data/ceres_data/8xc5_38237/07_2025/8xc5_38237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xc5_38237/07_2025/8xc5_38237.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 14 5.16 5 C 1179 2.51 5 N 320 2.21 5 O 379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 1892 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 180 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "B" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "C" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain breaks: 2 Chain: "A" 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" 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: 2.24, per 1000 atoms: 1.18 Number of scatterers: 1892 At special positions: 0 Unit cell: (50.4, 48.3, 94.5, 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 14 16.00 O 379 8.00 N 320 7.00 C 1179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 401 " - pdb=" SG CYS B 461 " distance=2.02 Simple disulfide: pdb=" SG CYS B 422 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 229 " - pdb=" SG CYS C 320 " distance=2.01 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 284 " distance=2.07 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 A 501 " - " ASN A 242 " " NAG B 601 " - " ASN B 362 " " NAG C 601 " - " ASN C 260 " " NAG C 602 " - " ASN C 291 " Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 835.2 milliseconds 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 450 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA2, first strand: chain 'A' and resid 234 through 236 Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 245 removed outlier: 3.767A pdb=" N ASN C 315 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 319 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 241 through 245 removed outlier: 3.767A pdb=" N ASN C 315 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 319 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ALA B 356 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY B 383 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 445 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 226 through 227 57 hydrogen bonds defined for protein. 141 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.42 Time building geometry restraints manager: 0.58 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: 628 1.34 - 1.46: 387 1.46 - 1.58: 888 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 1921 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N LEU A 241 " pdb=" CA LEU A 241 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.24e-02 6.50e+03 5.45e+00 bond pdb=" N TYR C 322 " pdb=" CA TYR C 322 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.51e-02 4.39e+03 5.35e+00 bond pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.84e+00 bond pdb=" N PRO B 475 " pdb=" CA PRO B 475 " ideal model delta sigma weight residual 1.469 1.448 0.021 1.28e-02 6.10e+03 2.59e+00 ... (remaining 1916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 2440 1.77 - 3.54: 134 3.54 - 5.30: 21 5.30 - 7.07: 4 7.07 - 8.84: 3 Bond angle restraints: 2602 Sorted by residual: angle pdb=" C ASN C 291 " pdb=" CA ASN C 291 " pdb=" CB ASN C 291 " ideal model delta sigma weight residual 109.54 115.04 -5.50 1.84e+00 2.95e-01 8.95e+00 angle pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " pdb=" C5 NAG B 601 " ideal model delta sigma weight residual 113.21 122.05 -8.84 3.00e+00 1.11e-01 8.68e+00 angle pdb=" N ASP C 228 " pdb=" CA ASP C 228 " pdb=" C ASP C 228 " ideal model delta sigma weight residual 110.44 113.87 -3.43 1.20e+00 6.94e-01 8.19e+00 angle pdb=" CA ASP C 228 " pdb=" C ASP C 228 " pdb=" O ASP C 228 " ideal model delta sigma weight residual 121.89 118.26 3.63 1.29e+00 6.01e-01 7.92e+00 angle pdb=" C PRO C 259 " pdb=" N ASN C 260 " pdb=" CA ASN C 260 " ideal model delta sigma weight residual 122.15 117.42 4.73 1.74e+00 3.30e-01 7.39e+00 ... (remaining 2597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.42: 1082 21.42 - 42.84: 129 42.84 - 64.25: 17 64.25 - 85.67: 3 85.67 - 107.08: 4 Dihedral angle restraints: 1235 sinusoidal: 548 harmonic: 687 Sorted by residual: dihedral pdb=" CB CYS B 422 " pdb=" SG CYS B 422 " pdb=" SG CYS B 477 " pdb=" CB CYS B 477 " ideal model delta sinusoidal sigma weight residual 93.00 -179.80 -87.20 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS B 466 " pdb=" SG CYS B 466 " pdb=" SG CYS B 473 " pdb=" CB CYS B 473 " ideal model delta sinusoidal sigma weight residual -86.00 -160.59 74.59 1 1.00e+01 1.00e-02 7.05e+01 dihedral pdb=" CA CYS B 422 " pdb=" C CYS B 422 " pdb=" N SER B 423 " pdb=" CA SER B 423 " ideal model delta harmonic sigma weight residual 180.00 153.85 26.15 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 1232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 283 0.103 - 0.206: 25 0.206 - 0.309: 2 0.309 - 0.412: 0 0.412 - 0.515: 1 Chirality restraints: 311 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 260 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C1 NAG C 602 " pdb=" ND2 ASN C 291 " pdb=" C2 NAG C 602 " pdb=" O5 NAG C 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 308 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 260 " -0.057 2.00e-02 2.50e+03 5.93e-02 4.40e+01 pdb=" CG ASN C 260 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 260 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 260 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG C 601 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 258 " -0.048 5.00e-02 4.00e+02 7.25e-02 8.41e+00 pdb=" N PRO C 259 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 291 " -0.023 2.00e-02 2.50e+03 2.21e-02 6.08e+00 pdb=" CG ASN C 291 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C 291 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 291 " 0.033 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " -0.027 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 175 2.74 - 3.28: 1869 3.28 - 3.82: 2820 3.82 - 4.36: 3254 4.36 - 4.90: 5653 Nonbonded interactions: 13771 Sorted by model distance: nonbonded pdb=" NE2 GLN B 359 " pdb=" O ASN B 365 " model vdw 2.195 3.120 nonbonded pdb=" O THR C 293 " pdb=" ND1 HIS C 294 " model vdw 2.219 3.120 nonbonded pdb=" O GLU B 377 " pdb=" NE2 GLN B 446 " model vdw 2.233 3.120 nonbonded pdb=" O THR C 300 " pdb=" OG1 THR C 300 " model vdw 2.265 3.040 nonbonded pdb=" NZ LYS A 227 " pdb=" OE2 GLU B 462 " model vdw 2.296 3.120 ... (remaining 13766 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: 1.660 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.540 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 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 : 0.008 0.168 1930 Z= 0.401 Angle : 1.407 32.602 2624 Z= 0.606 Chirality : 0.065 0.515 311 Planarity : 0.007 0.073 336 Dihedral : 17.640 107.083 770 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 31.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.35 % Favored : 85.65 % Rotamer: Outliers : 0.00 % Allowed : 33.96 % Favored : 66.04 % 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: -4.61 (0.47), residues: 223 helix: None (None), residues: 0 sheet: -2.19 (0.58), residues: 83 loop : -3.85 (0.37), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 464 PHE 0.014 0.002 PHE C 318 TYR 0.013 0.002 TYR B 402 ARG 0.003 0.001 ARG B 426 Details of bonding type rmsd link_NAG-ASN : bond 0.12352 ( 4) link_NAG-ASN : angle 15.45712 ( 12) hydrogen bonds : bond 0.22545 ( 44) hydrogen bonds : angle 11.50349 ( 141) SS BOND : bond 0.01783 ( 5) SS BOND : angle 1.44949 ( 10) covalent geometry : bond 0.00581 ( 1921) covalent geometry : angle 0.94208 ( 2602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.212 Fit side-chains REVERT: B 447 MET cc_start: 0.8230 (tpp) cc_final: 0.7952 (mmm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1622 time to fit residues: 10.8368 Evaluate side-chains 49 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 HIS B 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.184469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161966 restraints weight = 2328.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167663 restraints weight = 1330.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171665 restraints weight = 863.523| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1930 Z= 0.193 Angle : 0.923 10.402 2624 Z= 0.446 Chirality : 0.056 0.284 311 Planarity : 0.006 0.058 336 Dihedral : 10.494 59.011 332 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 8.02 % Allowed : 34.43 % Favored : 57.55 % 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: -4.27 (0.48), residues: 223 helix: None (None), residues: 0 sheet: -1.87 (0.57), residues: 82 loop : -3.66 (0.39), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 221 PHE 0.021 0.002 PHE C 318 TYR 0.013 0.002 TYR B 454 ARG 0.006 0.001 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00818 ( 4) link_NAG-ASN : angle 3.08431 ( 12) hydrogen bonds : bond 0.06003 ( 44) hydrogen bonds : angle 7.92907 ( 141) SS BOND : bond 0.00605 ( 5) SS BOND : angle 1.41436 ( 10) covalent geometry : bond 0.00430 ( 1921) covalent geometry : angle 0.89892 ( 2602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: B 447 MET cc_start: 0.8438 (tpp) cc_final: 0.8230 (mmm) REVERT: C 289 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6557 (tm-30) REVERT: C 294 HIS cc_start: 0.7877 (OUTLIER) cc_final: 0.6001 (t70) outliers start: 17 outliers final: 9 residues processed: 68 average time/residue: 0.1259 time to fit residues: 9.9877 Evaluate side-chains 60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.0770 chunk 7 optimal weight: 0.9990 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161762 restraints weight = 2379.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.167603 restraints weight = 1358.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.171642 restraints weight = 883.066| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1930 Z= 0.155 Angle : 0.859 9.079 2624 Z= 0.412 Chirality : 0.053 0.243 311 Planarity : 0.004 0.047 336 Dihedral : 9.557 57.372 332 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 9.43 % Allowed : 31.13 % Favored : 59.43 % 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: -4.04 (0.49), residues: 223 helix: None (None), residues: 0 sheet: -1.73 (0.58), residues: 82 loop : -3.49 (0.41), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 221 PHE 0.019 0.002 PHE C 307 TYR 0.010 0.001 TYR B 454 ARG 0.001 0.000 ARG B 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 4) link_NAG-ASN : angle 2.96041 ( 12) hydrogen bonds : bond 0.05047 ( 44) hydrogen bonds : angle 7.10097 ( 141) SS BOND : bond 0.00404 ( 5) SS BOND : angle 0.94081 ( 10) covalent geometry : bond 0.00334 ( 1921) covalent geometry : angle 0.83650 ( 2602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 388 GLN cc_start: 0.8035 (tp40) cc_final: 0.7645 (tt0) REVERT: B 447 MET cc_start: 0.8354 (tpp) cc_final: 0.8145 (mmm) REVERT: C 289 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6671 (tm-30) outliers start: 20 outliers final: 12 residues processed: 65 average time/residue: 0.1377 time to fit residues: 10.4092 Evaluate side-chains 60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain B residue 470 ASN Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.182860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159512 restraints weight = 2474.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.165304 restraints weight = 1423.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.169360 restraints weight = 930.887| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1930 Z= 0.163 Angle : 0.848 9.077 2624 Z= 0.411 Chirality : 0.053 0.245 311 Planarity : 0.004 0.044 336 Dihedral : 8.897 57.814 332 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 8.49 % Allowed : 30.66 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.94 (0.49), residues: 223 helix: None (None), residues: 0 sheet: -1.64 (0.58), residues: 82 loop : -3.43 (0.41), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 221 PHE 0.021 0.002 PHE C 307 TYR 0.013 0.002 TYR B 454 ARG 0.002 0.000 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 4) link_NAG-ASN : angle 2.96816 ( 12) hydrogen bonds : bond 0.04872 ( 44) hydrogen bonds : angle 6.67073 ( 141) SS BOND : bond 0.00439 ( 5) SS BOND : angle 0.86925 ( 10) covalent geometry : bond 0.00374 ( 1921) covalent geometry : angle 0.82547 ( 2602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 388 GLN cc_start: 0.8139 (tp40) cc_final: 0.7676 (tt0) REVERT: C 289 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6767 (tm-30) outliers start: 18 outliers final: 11 residues processed: 60 average time/residue: 0.1253 time to fit residues: 9.1195 Evaluate side-chains 60 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 285 ARG Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 11 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 1 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 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 = 0.4171 r_free = 0.4171 target = 0.184724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.161562 restraints weight = 2448.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.167227 restraints weight = 1414.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.171198 restraints weight = 927.643| |-----------------------------------------------------------------------------| r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1930 Z= 0.153 Angle : 0.843 9.100 2624 Z= 0.409 Chirality : 0.052 0.248 311 Planarity : 0.004 0.044 336 Dihedral : 8.587 57.560 332 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 7.55 % Allowed : 30.66 % Favored : 61.79 % 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: -3.80 (0.50), residues: 223 helix: None (None), residues: 0 sheet: -1.57 (0.58), residues: 82 loop : -3.32 (0.42), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 221 PHE 0.019 0.002 PHE C 307 TYR 0.012 0.001 TYR B 454 ARG 0.003 0.000 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 4) link_NAG-ASN : angle 2.86446 ( 12) hydrogen bonds : bond 0.04615 ( 44) hydrogen bonds : angle 6.41728 ( 141) SS BOND : bond 0.00396 ( 5) SS BOND : angle 0.77235 ( 10) covalent geometry : bond 0.00350 ( 1921) covalent geometry : angle 0.82225 ( 2602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 388 GLN cc_start: 0.8119 (tp40) cc_final: 0.7700 (tt0) REVERT: B 425 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: B 442 ARG cc_start: 0.7207 (ptp-170) cc_final: 0.6506 (mtt180) outliers start: 16 outliers final: 9 residues processed: 60 average time/residue: 0.1058 time to fit residues: 7.6788 Evaluate side-chains 54 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.0170 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 12 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.0040 chunk 19 optimal weight: 0.7980 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.187079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.164116 restraints weight = 2377.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.169803 restraints weight = 1330.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.173782 restraints weight = 858.995| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6528 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1930 Z= 0.140 Angle : 0.827 9.165 2624 Z= 0.403 Chirality : 0.052 0.252 311 Planarity : 0.004 0.041 336 Dihedral : 8.059 57.437 332 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 4.72 % Allowed : 33.96 % Favored : 61.32 % 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: -3.59 (0.50), residues: 223 helix: None (None), residues: 0 sheet: -1.15 (0.62), residues: 76 loop : -3.31 (0.40), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 221 PHE 0.016 0.002 PHE C 307 TYR 0.016 0.001 TYR B 402 ARG 0.004 0.000 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 2.78651 ( 12) hydrogen bonds : bond 0.04269 ( 44) hydrogen bonds : angle 6.28270 ( 141) SS BOND : bond 0.00355 ( 5) SS BOND : angle 0.76591 ( 10) covalent geometry : bond 0.00317 ( 1921) covalent geometry : angle 0.80744 ( 2602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.258 Fit side-chains REVERT: B 425 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: B 442 ARG cc_start: 0.6882 (ptp-170) cc_final: 0.6616 (mtt90) outliers start: 10 outliers final: 6 residues processed: 52 average time/residue: 0.1413 time to fit residues: 8.7495 Evaluate side-chains 48 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.0070 chunk 20 optimal weight: 0.6980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.186988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163829 restraints weight = 2343.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169455 restraints weight = 1354.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.173236 restraints weight = 890.999| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1930 Z= 0.139 Angle : 0.829 9.164 2624 Z= 0.398 Chirality : 0.051 0.252 311 Planarity : 0.004 0.041 336 Dihedral : 7.757 57.514 332 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 6.60 % Allowed : 33.02 % Favored : 60.38 % 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: -3.60 (0.50), residues: 223 helix: None (None), residues: 0 sheet: -1.28 (0.59), residues: 82 loop : -3.30 (0.42), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 221 PHE 0.018 0.002 PHE C 307 TYR 0.013 0.001 TYR B 402 ARG 0.002 0.000 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 2.69649 ( 12) hydrogen bonds : bond 0.04104 ( 44) hydrogen bonds : angle 6.07809 ( 141) SS BOND : bond 0.00302 ( 5) SS BOND : angle 0.96072 ( 10) covalent geometry : bond 0.00318 ( 1921) covalent geometry : angle 0.80964 ( 2602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.222 Fit side-chains REVERT: B 425 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: B 449 MET cc_start: 0.7136 (ppp) cc_final: 0.6931 (ppp) outliers start: 14 outliers final: 10 residues processed: 53 average time/residue: 0.1581 time to fit residues: 9.6184 Evaluate side-chains 51 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 401 CYS Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.183765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.163380 restraints weight = 2493.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.168526 restraints weight = 1481.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172116 restraints weight = 980.582| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1930 Z= 0.169 Angle : 0.833 9.101 2624 Z= 0.409 Chirality : 0.052 0.248 311 Planarity : 0.004 0.043 336 Dihedral : 7.771 57.598 332 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.90 % Favored : 86.10 % Rotamer: Outliers : 5.19 % Allowed : 35.85 % Favored : 58.96 % 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: -3.64 (0.49), residues: 223 helix: None (None), residues: 0 sheet: -1.34 (0.56), residues: 82 loop : -3.29 (0.41), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 460 PHE 0.023 0.003 PHE C 318 TYR 0.016 0.001 TYR B 454 ARG 0.002 0.000 ARG C 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 4) link_NAG-ASN : angle 2.68252 ( 12) hydrogen bonds : bond 0.04261 ( 44) hydrogen bonds : angle 6.18533 ( 141) SS BOND : bond 0.00417 ( 5) SS BOND : angle 0.83787 ( 10) covalent geometry : bond 0.00387 ( 1921) covalent geometry : angle 0.81477 ( 2602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.222 Fit side-chains REVERT: C 289 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6616 (tm-30) outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 0.1305 time to fit residues: 7.6260 Evaluate side-chains 48 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.177784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156215 restraints weight = 2623.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161246 restraints weight = 1609.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164708 restraints weight = 1095.832| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 1930 Z= 0.220 Angle : 0.884 8.959 2624 Z= 0.439 Chirality : 0.054 0.237 311 Planarity : 0.005 0.046 336 Dihedral : 8.200 57.832 332 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.35 % Favored : 85.65 % Rotamer: Outliers : 6.13 % Allowed : 33.49 % Favored : 60.38 % 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: -3.59 (0.48), residues: 223 helix: None (None), residues: 0 sheet: -1.26 (0.56), residues: 82 loop : -3.29 (0.41), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 460 PHE 0.030 0.003 PHE C 318 TYR 0.019 0.002 TYR B 454 ARG 0.004 0.001 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 4) link_NAG-ASN : angle 2.91321 ( 12) hydrogen bonds : bond 0.05058 ( 44) hydrogen bonds : angle 6.48990 ( 141) SS BOND : bond 0.00551 ( 5) SS BOND : angle 0.95783 ( 10) covalent geometry : bond 0.00523 ( 1921) covalent geometry : angle 0.86375 ( 2602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.228 Fit side-chains REVERT: B 388 GLN cc_start: 0.8120 (tp40) cc_final: 0.7894 (tt0) REVERT: C 289 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6597 (tm-30) outliers start: 13 outliers final: 13 residues processed: 54 average time/residue: 0.1330 time to fit residues: 8.4026 Evaluate side-chains 55 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 0.2980 chunk 7 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160844 restraints weight = 2540.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.165872 restraints weight = 1570.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.169357 restraints weight = 1071.807| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1930 Z= 0.160 Angle : 0.867 10.013 2624 Z= 0.424 Chirality : 0.052 0.248 311 Planarity : 0.004 0.042 336 Dihedral : 7.824 57.204 332 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 5.19 % Allowed : 34.91 % Favored : 59.91 % 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: -3.35 (0.51), residues: 223 helix: None (None), residues: 0 sheet: -0.89 (0.60), residues: 81 loop : -3.26 (0.42), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 460 PHE 0.019 0.002 PHE C 318 TYR 0.011 0.001 TYR B 454 ARG 0.004 0.001 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 4) link_NAG-ASN : angle 2.76599 ( 12) hydrogen bonds : bond 0.04390 ( 44) hydrogen bonds : angle 6.06097 ( 141) SS BOND : bond 0.00339 ( 5) SS BOND : angle 0.74144 ( 10) covalent geometry : bond 0.00374 ( 1921) covalent geometry : angle 0.84865 ( 2602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 446 Ramachandran restraints generated. 223 Oldfield, 0 Emsley, 223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.374 Fit side-chains REVERT: B 388 GLN cc_start: 0.8013 (tp40) cc_final: 0.7738 (tt0) REVERT: C 289 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6703 (tm-30) outliers start: 11 outliers final: 11 residues processed: 50 average time/residue: 0.1342 time to fit residues: 7.9481 Evaluate side-chains 51 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 431 HIS Chi-restraints excluded: chain B residue 454 TYR Chi-restraints excluded: chain B residue 466 CYS Chi-restraints excluded: chain C residue 221 HIS Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 294 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.179181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.157452 restraints weight = 2464.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.162900 restraints weight = 1470.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.166559 restraints weight = 976.067| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1930 Z= 0.174 Angle : 0.867 9.139 2624 Z= 0.426 Chirality : 0.052 0.249 311 Planarity : 0.005 0.048 336 Dihedral : 7.720 57.416 332 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.00 % Favored : 87.00 % Rotamer: Outliers : 6.13 % Allowed : 34.91 % Favored : 58.96 % 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: -3.27 (0.51), residues: 223 helix: None (None), residues: 0 sheet: -0.80 (0.60), residues: 81 loop : -3.23 (0.42), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 460 PHE 0.022 0.002 PHE C 318 TYR 0.014 0.002 TYR B 454 ARG 0.005 0.001 ARG B 442 Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 4) link_NAG-ASN : angle 2.69596 ( 12) hydrogen bonds : bond 0.04392 ( 44) hydrogen bonds : angle 6.21146 ( 141) SS BOND : bond 0.00374 ( 5) SS BOND : angle 0.77181 ( 10) covalent geometry : bond 0.00412 ( 1921) covalent geometry : angle 0.84951 ( 2602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1274.05 seconds wall clock time: 23 minutes 3.81 seconds (1383.81 seconds total)