Starting phenix.real_space_refine on Fri Aug 22 14:18:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ji0_36303/08_2025/8ji0_36303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ji0_36303/08_2025/8ji0_36303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ji0_36303/08_2025/8ji0_36303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ji0_36303/08_2025/8ji0_36303.map" model { file = "/net/cci-nas-00/data/ceres_data/8ji0_36303/08_2025/8ji0_36303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ji0_36303/08_2025/8ji0_36303.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.100 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 24 5.16 5 C 2512 2.51 5 N 665 2.21 5 O 733 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3934 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2669 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1265 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 6, 'TRANS': 150} Time building chain proxies: 1.20, per 1000 atoms: 0.31 Number of scatterers: 3934 At special positions: 0 Unit cell: (81.525, 83.699, 81.525, 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 24 16.00 O 733 8.00 N 665 7.00 C 2512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 426 " 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 Time building additional restraints: 0.31 Conformation dependent library (CDL) restraints added in 152.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 900 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 11 sheets defined 10.2% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.588A pdb=" N GLY B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.616A pdb=" N LYS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 225' Processing helix chain 'B' and resid 294 through 299 removed outlier: 4.013A pdb=" N VAL B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 406 through 411 Processing helix chain 'B' and resid 477 through 492 removed outlier: 4.795A pdb=" N ASP B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP B 483 " --> pdb=" O VAL B 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA2, first strand: chain 'B' and resid 196 through 201 Processing sheet with id=AA3, first strand: chain 'B' and resid 279 through 282 removed outlier: 3.673A pdb=" N CYS B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 379 through 383 removed outlier: 3.527A pdb=" N GLY B 383 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN B 398 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS B 426 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 473 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 445 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER B 382 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2462 through 2466 removed outlier: 3.641A pdb=" N LYS A2462 " --> pdb=" O PHE A2473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2484 through 2486 Processing sheet with id=AA7, first strand: chain 'A' and resid 2502 through 2507 removed outlier: 3.505A pdb=" N LYS A2505 " --> pdb=" O PHE A2512 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A2512 " --> pdb=" O LYS A2505 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2522 through 2523 Processing sheet with id=AA9, first strand: chain 'A' and resid 2553 through 2557 removed outlier: 3.854A pdb=" N LYS A2553 " --> pdb=" O PHE A2564 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A2564 " --> pdb=" O LYS A2553 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2573 through 2577 Processing sheet with id=AB2, first strand: chain 'A' and resid 2595 through 2597 removed outlier: 3.689A pdb=" N PHE A2606 " --> pdb=" O GLY A2595 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A2605 " --> pdb=" O GLN A2613 " (cutoff:3.500A) 104 hydrogen bonds defined for protein. 246 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: 0.57 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 13 1.20 - 1.35: 1258 1.35 - 1.51: 1295 1.51 - 1.66: 1447 1.66 - 1.81: 34 Bond restraints: 4047 Sorted by residual: bond pdb=" C ASN B 304 " pdb=" O ASN B 304 " ideal model delta sigma weight residual 1.235 1.045 0.190 1.45e-02 4.76e+03 1.72e+02 bond pdb=" C PRO B 301 " pdb=" O PRO B 301 " ideal model delta sigma weight residual 1.237 1.115 0.122 1.20e-02 6.94e+03 1.04e+02 bond pdb=" C TRP B 306 " pdb=" O TRP B 306 " ideal model delta sigma weight residual 1.236 1.117 0.119 1.23e-02 6.61e+03 9.39e+01 bond pdb=" C PRO B 305 " pdb=" O PRO B 305 " ideal model delta sigma weight residual 1.235 1.111 0.124 1.30e-02 5.92e+03 9.04e+01 bond pdb=" C ASN B 303 " pdb=" O ASN B 303 " ideal model delta sigma weight residual 1.237 1.122 0.115 1.39e-02 5.18e+03 6.88e+01 ... (remaining 4042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 5422 4.14 - 8.29: 54 8.29 - 12.43: 12 12.43 - 16.57: 7 16.57 - 20.72: 2 Bond angle restraints: 5497 Sorted by residual: angle pdb=" N TYR B 414 " pdb=" CA TYR B 414 " pdb=" C TYR B 414 " ideal model delta sigma weight residual 114.16 93.44 20.72 1.48e+00 4.57e-01 1.96e+02 angle pdb=" N TRP B 306 " pdb=" CA TRP B 306 " pdb=" CB TRP B 306 " ideal model delta sigma weight residual 110.98 97.28 13.70 1.32e+00 5.74e-01 1.08e+02 angle pdb=" C PRO B 305 " pdb=" CA PRO B 305 " pdb=" CB PRO B 305 " ideal model delta sigma weight residual 111.56 95.17 16.39 1.65e+00 3.67e-01 9.87e+01 angle pdb=" C TRP B 306 " pdb=" CA TRP B 306 " pdb=" CB TRP B 306 " ideal model delta sigma weight residual 109.27 123.51 -14.24 1.64e+00 3.72e-01 7.54e+01 angle pdb=" CB LYS B 342 " pdb=" CG LYS B 342 " pdb=" CD LYS B 342 " ideal model delta sigma weight residual 111.30 91.65 19.65 2.30e+00 1.89e-01 7.30e+01 ... (remaining 5492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.41: 1927 14.41 - 28.82: 275 28.82 - 43.23: 91 43.23 - 57.64: 37 57.64 - 72.05: 9 Dihedral angle restraints: 2339 sinusoidal: 917 harmonic: 1422 Sorted by residual: dihedral pdb=" C ILE A2608 " pdb=" N ILE A2608 " pdb=" CA ILE A2608 " pdb=" CB ILE A2608 " ideal model delta harmonic sigma weight residual -122.00 -148.04 26.04 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C LYS B 342 " pdb=" N LYS B 342 " pdb=" CA LYS B 342 " pdb=" CB LYS B 342 " ideal model delta harmonic sigma weight residual -122.60 -145.93 23.33 0 2.50e+00 1.60e-01 8.71e+01 dihedral pdb=" N ILE A2608 " pdb=" C ILE A2608 " pdb=" CA ILE A2608 " pdb=" CB ILE A2608 " ideal model delta harmonic sigma weight residual 123.40 143.42 -20.02 0 2.50e+00 1.60e-01 6.42e+01 ... (remaining 2336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 553 0.202 - 0.404: 4 0.404 - 0.606: 3 0.606 - 0.808: 1 0.808 - 1.010: 2 Chirality restraints: 563 Sorted by residual: chirality pdb=" CA LYS B 342 " pdb=" N LYS B 342 " pdb=" C LYS B 342 " pdb=" CB LYS B 342 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA ILE A2608 " pdb=" N ILE A2608 " pdb=" C ILE A2608 " pdb=" CB ILE A2608 " both_signs ideal model delta sigma weight residual False 2.43 1.61 0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" CA ARG B 413 " pdb=" N ARG B 413 " pdb=" C ARG B 413 " pdb=" CB ARG B 413 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 560 not shown) Planarity restraints: 717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 306 " 0.032 2.00e-02 2.50e+03 6.87e-02 4.72e+01 pdb=" C TRP B 306 " -0.119 2.00e-02 2.50e+03 pdb=" O TRP B 306 " 0.047 2.00e-02 2.50e+03 pdb=" N HIS B 307 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 300 " 0.028 2.00e-02 2.50e+03 5.61e-02 3.15e+01 pdb=" C LYS B 300 " -0.097 2.00e-02 2.50e+03 pdb=" O LYS B 300 " 0.036 2.00e-02 2.50e+03 pdb=" N PRO B 301 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 414 " 0.023 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C TYR B 414 " -0.086 2.00e-02 2.50e+03 pdb=" O TYR B 414 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL B 415 " 0.029 2.00e-02 2.50e+03 ... (remaining 714 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.50: 38 2.50 - 3.10: 2929 3.10 - 3.70: 5689 3.70 - 4.30: 8474 4.30 - 4.90: 14441 Nonbonded interactions: 31571 Sorted by model distance: nonbonded pdb=" OH TYR B 416 " pdb=" O PRO B 471 " model vdw 1.905 3.040 nonbonded pdb=" OG1 THR A2506 " pdb=" OD1 ASN A2511 " model vdw 1.965 3.040 nonbonded pdb=" OH TYR A2550 " pdb=" O PHE A2554 " model vdw 2.001 3.040 nonbonded pdb=" O LYS B 300 " pdb=" NZ LYS B 300 " model vdw 2.035 3.120 nonbonded pdb=" O MET B 371 " pdb=" NZ LYS B 449 " model vdw 2.067 3.120 ... (remaining 31566 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 individual isotropic 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.420 Find NCS groups from input model: 0.010 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:8.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 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 : 0.009 0.190 4052 Z= 0.587 Angle : 1.196 20.716 5507 Z= 0.724 Chirality : 0.089 1.010 563 Planarity : 0.007 0.069 717 Dihedral : 16.497 72.050 1424 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.94 % Favored : 90.45 % Rotamer: Outliers : 6.46 % Allowed : 22.73 % Favored : 70.81 % Cbeta Deviations : 1.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.39), residues: 492 helix: -1.24 (0.87), residues: 36 sheet: -2.20 (0.47), residues: 114 loop : -0.70 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 409 TYR 0.038 0.002 TYR B 414 PHE 0.008 0.001 PHE B 156 TRP 0.041 0.002 TRP B 306 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00929 ( 4047) covalent geometry : angle 1.19679 ( 5497) SS BOND : bond 0.00225 ( 5) SS BOND : angle 0.89427 ( 10) hydrogen bonds : bond 0.24372 ( 104) hydrogen bonds : angle 10.25244 ( 246) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.6891 (pp20) cc_final: 0.6635 (pp20) REVERT: A 2515 ARG cc_start: 0.6933 (tpp80) cc_final: 0.6678 (tpt170) REVERT: A 2612 LYS cc_start: 0.7175 (ttpp) cc_final: 0.6955 (ttpt) outliers start: 27 outliers final: 15 residues processed: 102 average time/residue: 0.4673 time to fit residues: 49.4246 Evaluate side-chains 78 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 227 HIS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 413 ARG Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain A residue 2508 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 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 307 HIS B 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.250218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.218907 restraints weight = 4172.570| |-----------------------------------------------------------------------------| r_work (start): 0.4619 rms_B_bonded: 2.16 r_work: 0.4476 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4052 Z= 0.138 Angle : 0.651 8.363 5507 Z= 0.344 Chirality : 0.048 0.209 563 Planarity : 0.005 0.069 717 Dihedral : 8.636 69.285 564 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.07 % Rotamer: Outliers : 4.78 % Allowed : 23.44 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.40), residues: 492 helix: -0.03 (0.94), residues: 36 sheet: -2.01 (0.50), residues: 95 loop : -0.31 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.027 0.002 TYR A2563 PHE 0.013 0.001 PHE A2466 TRP 0.014 0.002 TRP B 461 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4047) covalent geometry : angle 0.65010 ( 5497) SS BOND : bond 0.00223 ( 5) SS BOND : angle 0.88318 ( 10) hydrogen bonds : bond 0.03624 ( 104) hydrogen bonds : angle 6.62552 ( 246) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: B 210 MET cc_start: 0.7204 (mmm) cc_final: 0.6978 (mmt) REVERT: B 329 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6700 (pp20) REVERT: B 382 SER cc_start: 0.8753 (t) cc_final: 0.8547 (t) REVERT: B 488 MET cc_start: 0.7302 (mtp) cc_final: 0.6636 (mpp) REVERT: A 2515 ARG cc_start: 0.6871 (tpp80) cc_final: 0.6586 (tpt170) REVERT: A 2612 LYS cc_start: 0.7331 (ttpp) cc_final: 0.6983 (ttpt) outliers start: 20 outliers final: 7 residues processed: 84 average time/residue: 0.4261 time to fit residues: 37.3332 Evaluate side-chains 72 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 45 optimal weight: 0.0670 chunk 36 optimal weight: 3.9990 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN B 418 ASN B 450 ASN A2516 ASN A2540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.251166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.218346 restraints weight = 4120.044| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 2.25 r_work: 0.4489 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4052 Z= 0.111 Angle : 0.574 6.205 5507 Z= 0.306 Chirality : 0.048 0.199 563 Planarity : 0.004 0.044 717 Dihedral : 6.002 56.630 545 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.59 % Allowed : 22.97 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.40), residues: 492 helix: 0.38 (0.99), residues: 36 sheet: -1.89 (0.48), residues: 109 loop : -0.01 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 409 TYR 0.016 0.001 TYR A2563 PHE 0.005 0.001 PHE A2533 TRP 0.013 0.001 TRP B 380 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4047) covalent geometry : angle 0.57374 ( 5497) SS BOND : bond 0.00152 ( 5) SS BOND : angle 0.68655 ( 10) hydrogen bonds : bond 0.03144 ( 104) hydrogen bonds : angle 6.12903 ( 246) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: B 488 MET cc_start: 0.7412 (mtp) cc_final: 0.6617 (mpp) REVERT: A 2515 ARG cc_start: 0.6840 (tpp80) cc_final: 0.6586 (tpt170) REVERT: A 2612 LYS cc_start: 0.7472 (ttpp) cc_final: 0.6958 (ttpt) outliers start: 15 outliers final: 5 residues processed: 83 average time/residue: 0.4358 time to fit residues: 37.8038 Evaluate side-chains 70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2600 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN B 450 ASN B 451 ASN A2511 ASN A2516 ASN A2540 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.241982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.211133 restraints weight = 4158.698| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 2.04 r_work: 0.4419 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4264 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4052 Z= 0.221 Angle : 0.690 6.727 5507 Z= 0.368 Chirality : 0.051 0.178 563 Planarity : 0.005 0.044 717 Dihedral : 6.594 53.265 544 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.26 % Allowed : 22.97 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.39), residues: 492 helix: -0.28 (0.91), residues: 36 sheet: -1.42 (0.46), residues: 118 loop : -0.30 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 489 TYR 0.024 0.002 TYR A2563 PHE 0.012 0.002 PHE A2521 TRP 0.011 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 4047) covalent geometry : angle 0.68799 ( 5497) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.43657 ( 10) hydrogen bonds : bond 0.04078 ( 104) hydrogen bonds : angle 6.62869 ( 246) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6943 (mtt180) cc_final: 0.6711 (mtp85) REVERT: B 329 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7042 (pp20) REVERT: B 488 MET cc_start: 0.7303 (mtp) cc_final: 0.6571 (mpp) REVERT: A 2515 ARG cc_start: 0.7012 (tpp80) cc_final: 0.6636 (tpt170) REVERT: A 2612 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7025 (ttpt) outliers start: 22 outliers final: 12 residues processed: 83 average time/residue: 0.4395 time to fit residues: 37.9254 Evaluate side-chains 78 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2461 ASN A2516 ASN A2540 ASN A2546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.245220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.214459 restraints weight = 4127.689| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 2.05 r_work: 0.4444 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4286 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4052 Z= 0.152 Angle : 0.619 5.968 5507 Z= 0.329 Chirality : 0.049 0.173 563 Planarity : 0.005 0.046 717 Dihedral : 6.299 55.533 544 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.78 % Allowed : 23.21 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.40), residues: 492 helix: -0.06 (0.93), residues: 36 sheet: -1.45 (0.45), residues: 131 loop : -0.20 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.018 0.002 TYR A2563 PHE 0.007 0.001 PHE A2521 TRP 0.013 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4047) covalent geometry : angle 0.61838 ( 5497) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.87244 ( 10) hydrogen bonds : bond 0.03439 ( 104) hydrogen bonds : angle 6.39502 ( 246) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6988 (pp20) REVERT: B 371 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7013 (mmt) REVERT: B 488 MET cc_start: 0.7228 (mtp) cc_final: 0.6821 (mpp) REVERT: A 2515 ARG cc_start: 0.6985 (tpp80) cc_final: 0.6680 (tpt170) REVERT: A 2612 LYS cc_start: 0.7415 (ttpp) cc_final: 0.6877 (ttpt) outliers start: 20 outliers final: 11 residues processed: 81 average time/residue: 0.4332 time to fit residues: 36.4966 Evaluate side-chains 75 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2461 ASN Chi-restraints excluded: chain A residue 2507 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 11 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2516 ASN A2540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.243819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.212537 restraints weight = 4144.436| |-----------------------------------------------------------------------------| r_work (start): 0.4573 rms_B_bonded: 2.09 r_work: 0.4438 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4279 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4052 Z= 0.151 Angle : 0.625 6.103 5507 Z= 0.330 Chirality : 0.049 0.175 563 Planarity : 0.005 0.045 717 Dihedral : 6.301 55.881 544 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.78 % Allowed : 23.92 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.40), residues: 492 helix: -0.07 (0.93), residues: 36 sheet: -1.49 (0.44), residues: 131 loop : -0.16 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.028 0.002 TYR A2563 PHE 0.007 0.001 PHE A2521 TRP 0.014 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4047) covalent geometry : angle 0.62460 ( 5497) SS BOND : bond 0.00197 ( 5) SS BOND : angle 0.90411 ( 10) hydrogen bonds : bond 0.03304 ( 104) hydrogen bonds : angle 6.34847 ( 246) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6917 (mtt180) cc_final: 0.6646 (mtp85) REVERT: B 329 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7047 (pp20) REVERT: B 371 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7211 (mmt) REVERT: B 488 MET cc_start: 0.7227 (mtp) cc_final: 0.6808 (mpp) REVERT: A 2515 ARG cc_start: 0.6999 (tpp80) cc_final: 0.6721 (tpt170) REVERT: A 2531 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 2612 LYS cc_start: 0.7546 (ttpp) cc_final: 0.6995 (ttpt) outliers start: 20 outliers final: 12 residues processed: 79 average time/residue: 0.4581 time to fit residues: 37.7530 Evaluate side-chains 77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2461 ASN Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.0000 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 HIS B 450 ASN A2516 ASN A2540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.247987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.217872 restraints weight = 4248.417| |-----------------------------------------------------------------------------| r_work (start): 0.4610 rms_B_bonded: 2.05 r_work: 0.4477 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4321 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4052 Z= 0.120 Angle : 0.602 7.694 5507 Z= 0.319 Chirality : 0.048 0.175 563 Planarity : 0.005 0.045 717 Dihedral : 5.953 56.068 544 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.07 % Allowed : 24.88 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.40), residues: 492 helix: 0.43 (0.99), residues: 36 sheet: -1.35 (0.47), residues: 118 loop : -0.14 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.021 0.002 TYR B 485 PHE 0.006 0.001 PHE A2533 TRP 0.016 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4047) covalent geometry : angle 0.60209 ( 5497) SS BOND : bond 0.00114 ( 5) SS BOND : angle 0.69884 ( 10) hydrogen bonds : bond 0.02910 ( 104) hydrogen bonds : angle 6.11060 ( 246) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6971 (mtt180) cc_final: 0.6722 (mtp85) REVERT: B 329 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7038 (pp20) REVERT: B 488 MET cc_start: 0.7306 (mtp) cc_final: 0.6929 (mpp) REVERT: A 2466 PHE cc_start: 0.6579 (t80) cc_final: 0.6339 (t80) REVERT: A 2515 ARG cc_start: 0.7007 (tpp80) cc_final: 0.6732 (tpt170) REVERT: A 2531 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7026 (mt-10) REVERT: A 2612 LYS cc_start: 0.7369 (ttpp) cc_final: 0.6820 (ttpt) outliers start: 17 outliers final: 7 residues processed: 77 average time/residue: 0.4725 time to fit residues: 37.8642 Evaluate side-chains 73 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 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 450 ASN A2461 ASN ** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.245504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.214937 restraints weight = 4175.432| |-----------------------------------------------------------------------------| r_work (start): 0.4580 rms_B_bonded: 2.06 r_work: 0.4448 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4291 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4052 Z= 0.153 Angle : 0.623 6.474 5507 Z= 0.332 Chirality : 0.049 0.171 563 Planarity : 0.005 0.046 717 Dihedral : 6.243 57.184 544 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.59 % Allowed : 25.12 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.40), residues: 492 helix: 0.27 (0.98), residues: 36 sheet: -1.42 (0.45), residues: 131 loop : -0.11 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 489 TYR 0.023 0.002 TYR A2563 PHE 0.007 0.001 PHE B 156 TRP 0.016 0.002 TRP B 380 HIS 0.008 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4047) covalent geometry : angle 0.62250 ( 5497) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.88783 ( 10) hydrogen bonds : bond 0.03241 ( 104) hydrogen bonds : angle 6.27693 ( 246) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.142 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6735 (mtp85) REVERT: B 329 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7059 (pp20) REVERT: B 488 MET cc_start: 0.7190 (mtp) cc_final: 0.6772 (mpp) REVERT: A 2466 PHE cc_start: 0.6595 (t80) cc_final: 0.6369 (t80) REVERT: A 2515 ARG cc_start: 0.7041 (tpp80) cc_final: 0.6731 (tpt170) REVERT: A 2531 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 2612 LYS cc_start: 0.7562 (ttpp) cc_final: 0.7024 (ttpt) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.4468 time to fit residues: 35.9005 Evaluate side-chains 75 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 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 450 ASN A2461 ASN A2540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.245456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.214763 restraints weight = 4241.606| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 2.08 r_work: 0.4448 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4052 Z= 0.153 Angle : 0.635 7.207 5507 Z= 0.338 Chirality : 0.049 0.170 563 Planarity : 0.005 0.047 717 Dihedral : 6.298 59.981 544 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.83 % Allowed : 26.08 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.40), residues: 492 helix: 0.19 (0.96), residues: 36 sheet: -1.43 (0.45), residues: 131 loop : -0.11 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 489 TYR 0.023 0.002 TYR A2563 PHE 0.006 0.001 PHE B 156 TRP 0.016 0.002 TRP B 380 HIS 0.007 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4047) covalent geometry : angle 0.63450 ( 5497) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.84649 ( 10) hydrogen bonds : bond 0.03237 ( 104) hydrogen bonds : angle 6.33199 ( 246) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: B 470 ARG cc_start: 0.5946 (mpt180) cc_final: 0.5743 (mpp-170) REVERT: B 488 MET cc_start: 0.7192 (mtp) cc_final: 0.6783 (mpp) REVERT: A 2466 PHE cc_start: 0.6429 (t80) cc_final: 0.6217 (t80) REVERT: A 2515 ARG cc_start: 0.6984 (tpp80) cc_final: 0.6703 (tpt170) REVERT: A 2531 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7054 (mt-10) REVERT: A 2612 LYS cc_start: 0.7500 (ttpp) cc_final: 0.6953 (ttpt) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.4722 time to fit residues: 38.3516 Evaluate side-chains 78 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2588 THR Chi-restraints excluded: chain A residue 2600 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.0170 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS B 450 ASN A2461 ASN ** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.248754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.218570 restraints weight = 4174.922| |-----------------------------------------------------------------------------| r_work (start): 0.4611 rms_B_bonded: 2.06 r_work: 0.4482 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4324 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4052 Z= 0.122 Angle : 0.602 7.663 5507 Z= 0.321 Chirality : 0.048 0.175 563 Planarity : 0.005 0.049 717 Dihedral : 6.016 58.911 544 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.35 % Allowed : 26.08 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.41), residues: 492 helix: 0.30 (0.96), residues: 36 sheet: -1.39 (0.45), residues: 131 loop : 0.04 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 489 TYR 0.026 0.002 TYR B 485 PHE 0.006 0.001 PHE B 429 TRP 0.017 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4047) covalent geometry : angle 0.60210 ( 5497) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.66164 ( 10) hydrogen bonds : bond 0.02851 ( 104) hydrogen bonds : angle 6.11864 ( 246) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: B 488 MET cc_start: 0.7301 (mtp) cc_final: 0.6870 (mpp) REVERT: A 2515 ARG cc_start: 0.6948 (tpp80) cc_final: 0.6578 (ttt180) REVERT: A 2531 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6990 (mt-10) REVERT: A 2612 LYS cc_start: 0.7331 (ttpp) cc_final: 0.6803 (ttpt) outliers start: 14 outliers final: 8 residues processed: 78 average time/residue: 0.4488 time to fit residues: 36.4935 Evaluate side-chains 77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2461 ASN Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 HIS B 450 ASN ** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.248250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.218005 restraints weight = 4158.314| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 2.06 r_work: 0.4478 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4322 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.160 4052 Z= 0.304 Angle : 1.226 59.199 5507 Z= 0.743 Chirality : 0.053 0.530 563 Planarity : 0.005 0.049 717 Dihedral : 5.924 58.923 543 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.39 % Allowed : 27.03 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.41), residues: 492 helix: 0.26 (0.96), residues: 36 sheet: -1.43 (0.46), residues: 121 loop : 0.06 (0.38), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 470 TYR 0.025 0.002 TYR B 485 PHE 0.005 0.001 PHE A2491 TRP 0.015 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 4047) covalent geometry : angle 1.22696 ( 5497) SS BOND : bond 0.00070 ( 5) SS BOND : angle 0.67656 ( 10) hydrogen bonds : bond 0.02901 ( 104) hydrogen bonds : angle 6.12540 ( 246) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1672.31 seconds wall clock time: 29 minutes 18.47 seconds (1758.47 seconds total)