Starting phenix.real_space_refine on Wed Mar 5 22:57:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ji0_36303/03_2025/8ji0_36303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ji0_36303/03_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_36303/03_2025/8ji0_36303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ji0_36303/03_2025/8ji0_36303.map" model { file = "/net/cci-nas-00/data/ceres_data/8ji0_36303/03_2025/8ji0_36303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ji0_36303/03_2025/8ji0_36303.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.100 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.48, per 1000 atoms: 0.88 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: 1.27 Conformation dependent library (CDL) restraints added in 460.3 milliseconds 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: 0.49 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: 1.06 Time building geometry restraints manager: 1.49 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: 1.090 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.030 Find NCS groups from input model: 0.040 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:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 4047 Z= 0.626 Angle : 1.197 20.716 5497 Z= 0.725 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 (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: -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 TRP 0.041 0.002 TRP B 306 HIS 0.004 0.001 HIS B 296 PHE 0.008 0.001 PHE B 156 TYR 0.038 0.002 TYR B 414 ARG 0.006 0.001 ARG B 409 *********************** 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 : 0.375 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: 0.8919 time to fit residues: 94.7918 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 : 0.386 ------------------------------------------------------------------------------- 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 41 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN B 451 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.246870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.214543 restraints weight = 4128.224| |-----------------------------------------------------------------------------| r_work (start): 0.4583 rms_B_bonded: 2.20 r_work: 0.4443 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4047 Z= 0.236 Angle : 0.677 9.380 5497 Z= 0.359 Chirality : 0.049 0.198 563 Planarity : 0.005 0.074 717 Dihedral : 9.041 77.759 564 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.72 % Favored : 92.07 % Rotamer: Outliers : 4.55 % Allowed : 25.12 % Favored : 70.33 % 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: -1.12 (0.39), residues: 492 helix: -0.28 (0.90), residues: 36 sheet: -2.02 (0.50), residues: 95 loop : -0.38 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 306 HIS 0.006 0.001 HIS B 296 PHE 0.013 0.001 PHE A2466 TYR 0.029 0.002 TYR A2563 ARG 0.003 0.000 ARG B 409 *********************** 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 87 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: B 210 MET cc_start: 0.7224 (mmm) cc_final: 0.6996 (mmt) REVERT: B 329 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6807 (pp20) REVERT: B 488 MET cc_start: 0.7296 (mtp) cc_final: 0.6632 (mpp) REVERT: A 2515 ARG cc_start: 0.6859 (tpp80) cc_final: 0.6533 (tpt170) REVERT: A 2612 LYS cc_start: 0.7384 (ttpp) cc_final: 0.7019 (ttpt) REVERT: A 2613 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6796 (mt0) outliers start: 19 outliers final: 8 residues processed: 78 average time/residue: 0.8681 time to fit residues: 70.9789 Evaluate side-chains 73 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 227 HIS 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 434 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2588 THR Chi-restraints excluded: chain A residue 2613 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 0.4980 chunk 9 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A2540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.246996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.215791 restraints weight = 4123.951| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 2.08 r_work: 0.4454 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4294 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4047 Z= 0.206 Angle : 0.609 6.274 5497 Z= 0.326 Chirality : 0.048 0.196 563 Planarity : 0.005 0.050 717 Dihedral : 6.829 51.339 547 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.31 % Allowed : 23.44 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.40), residues: 492 helix: 0.05 (0.94), residues: 36 sheet: -1.56 (0.53), residues: 94 loop : -0.31 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.008 0.001 PHE A2466 TYR 0.021 0.002 TYR A2563 ARG 0.003 0.000 ARG B 409 *********************** 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 89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8204 (ttp) REVERT: B 210 MET cc_start: 0.7412 (mmm) cc_final: 0.7191 (mmt) REVERT: B 488 MET cc_start: 0.7308 (mtp) cc_final: 0.6585 (mpp) REVERT: A 2515 ARG cc_start: 0.7031 (tpp80) cc_final: 0.6722 (tpt170) REVERT: A 2612 LYS cc_start: 0.7554 (ttpp) cc_final: 0.7006 (ttpt) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 0.9185 time to fit residues: 78.7377 Evaluate side-chains 74 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 287 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A2546 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.243656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.213232 restraints weight = 4225.518| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 2.06 r_work: 0.4429 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4269 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4047 Z= 0.256 Angle : 0.635 7.130 5497 Z= 0.339 Chirality : 0.050 0.186 563 Planarity : 0.005 0.044 717 Dihedral : 6.752 53.259 545 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 5.02 % Allowed : 23.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.40), residues: 492 helix: -0.03 (0.93), residues: 36 sheet: -1.64 (0.43), residues: 133 loop : -0.13 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 380 HIS 0.006 0.001 HIS B 296 PHE 0.009 0.001 PHE A2521 TYR 0.020 0.002 TYR A2563 ARG 0.003 0.001 ARG B 489 *********************** 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 90 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7080 (pp20) REVERT: B 413 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7140 (ptp90) REVERT: B 488 MET cc_start: 0.7280 (mtp) cc_final: 0.6567 (mpp) REVERT: A 2515 ARG cc_start: 0.7019 (tpp80) cc_final: 0.6747 (tpt170) REVERT: A 2612 LYS cc_start: 0.7547 (ttpp) cc_final: 0.7011 (ttpt) outliers start: 21 outliers final: 10 residues processed: 83 average time/residue: 0.9069 time to fit residues: 78.6320 Evaluate side-chains 73 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 413 ARG Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR 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 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 HIS B 336 ASN B 450 ASN B 451 ASN A2516 ASN A2540 ASN A2546 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4856 r_free = 0.4856 target = 0.245776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.214008 restraints weight = 4235.611| |-----------------------------------------------------------------------------| r_work (start): 0.4584 rms_B_bonded: 2.15 r_work: 0.4449 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4047 Z= 0.194 Angle : 0.609 6.170 5497 Z= 0.324 Chirality : 0.048 0.183 563 Planarity : 0.005 0.042 717 Dihedral : 6.451 55.009 545 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.26 % Allowed : 23.21 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.40), residues: 492 helix: 0.09 (0.94), residues: 36 sheet: -1.40 (0.45), residues: 131 loop : -0.10 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 PHE 0.006 0.001 PHE A2521 TYR 0.025 0.002 TYR A2563 ARG 0.002 0.000 ARG B 489 *********************** 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: 22 poor density : 66 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: B 488 MET cc_start: 0.7191 (mtp) cc_final: 0.6813 (mpp) REVERT: A 2515 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6661 (tpt170) REVERT: A 2612 LYS cc_start: 0.7426 (ttpp) cc_final: 0.6900 (ttpt) outliers start: 22 outliers final: 13 residues processed: 78 average time/residue: 0.8162 time to fit residues: 66.7871 Evaluate side-chains 76 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 287 THR 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 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 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 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 = 0.4839 r_free = 0.4839 target = 0.243397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.212376 restraints weight = 4114.934| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.10 r_work: 0.4435 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4276 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4047 Z= 0.223 Angle : 0.631 6.953 5497 Z= 0.333 Chirality : 0.049 0.177 563 Planarity : 0.005 0.043 717 Dihedral : 6.617 56.231 545 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 5.26 % Allowed : 23.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.40), residues: 492 helix: -0.05 (0.93), residues: 36 sheet: -1.47 (0.45), residues: 131 loop : -0.07 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 380 HIS 0.007 0.001 HIS B 296 PHE 0.007 0.001 PHE B 156 TYR 0.023 0.002 TYR A2563 ARG 0.003 0.000 ARG B 489 *********************** 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 89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6922 (mtt180) cc_final: 0.6706 (mtp85) REVERT: B 186 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7911 (mtp85) REVERT: B 329 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7122 (pp20) REVERT: B 488 MET cc_start: 0.7205 (mtp) cc_final: 0.6766 (mpp) REVERT: A 2515 ARG cc_start: 0.7026 (tpp80) cc_final: 0.6722 (tpt170) REVERT: A 2531 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7068 (mt-10) REVERT: A 2612 LYS cc_start: 0.7546 (ttpp) cc_final: 0.6997 (ttpt) outliers start: 22 outliers final: 12 residues processed: 80 average time/residue: 0.9317 time to fit residues: 77.6889 Evaluate side-chains 74 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 287 THR 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 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4840 r_free = 0.4840 target = 0.244084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.212847 restraints weight = 4123.652| |-----------------------------------------------------------------------------| r_work (start): 0.4580 rms_B_bonded: 2.09 r_work: 0.4446 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4285 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4047 Z= 0.212 Angle : 0.617 6.649 5497 Z= 0.326 Chirality : 0.049 0.179 563 Planarity : 0.005 0.044 717 Dihedral : 6.582 57.154 545 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.26 % Allowed : 24.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.40), residues: 492 helix: 0.30 (0.97), residues: 36 sheet: -1.45 (0.45), residues: 131 loop : -0.05 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 168 HIS 0.006 0.001 HIS B 296 PHE 0.006 0.001 PHE B 156 TYR 0.022 0.002 TYR A2563 ARG 0.002 0.000 ARG B 489 *********************** 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 89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6980 (mtt180) cc_final: 0.6562 (mtp85) REVERT: B 186 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7842 (mtp85) REVERT: B 329 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7107 (pp20) REVERT: B 488 MET cc_start: 0.7183 (mtp) cc_final: 0.6756 (mpp) REVERT: A 2515 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6774 (tpt170) REVERT: A 2531 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7072 (mt-10) REVERT: A 2612 LYS cc_start: 0.7406 (ttpp) cc_final: 0.6856 (ttpt) outliers start: 22 outliers final: 14 residues processed: 82 average time/residue: 0.9797 time to fit residues: 83.6486 Evaluate side-chains 79 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 287 THR 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 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 35 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.247255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.216371 restraints weight = 4080.616| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 2.08 r_work: 0.4456 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4285 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4047 Z= 0.176 Angle : 0.601 7.012 5497 Z= 0.321 Chirality : 0.048 0.178 563 Planarity : 0.005 0.046 717 Dihedral : 6.319 57.267 545 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.31 % Allowed : 24.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.41), residues: 492 helix: 0.38 (0.97), residues: 36 sheet: -1.38 (0.45), residues: 131 loop : 0.04 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 PHE 0.005 0.001 PHE A2533 TYR 0.022 0.002 TYR B 485 ARG 0.001 0.000 ARG B 489 *********************** 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 87 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6962 (mtt180) cc_final: 0.6728 (mtp85) REVERT: B 186 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7825 (mtp85) REVERT: B 329 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: B 488 MET cc_start: 0.7249 (mtp) cc_final: 0.6773 (mpp) REVERT: A 2466 PHE cc_start: 0.6604 (t80) cc_final: 0.6400 (t80) REVERT: A 2515 ARG cc_start: 0.7031 (tpp80) cc_final: 0.6752 (tpt170) REVERT: A 2531 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 2612 LYS cc_start: 0.7430 (ttpp) cc_final: 0.6864 (ttpt) outliers start: 18 outliers final: 12 residues processed: 80 average time/residue: 0.9553 time to fit residues: 79.8537 Evaluate side-chains 80 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 287 THR 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 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 2588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN ** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.243822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.212764 restraints weight = 4152.459| |-----------------------------------------------------------------------------| r_work (start): 0.4574 rms_B_bonded: 2.09 r_work: 0.4439 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4280 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4047 Z= 0.229 Angle : 0.640 6.619 5497 Z= 0.343 Chirality : 0.049 0.171 563 Planarity : 0.005 0.045 717 Dihedral : 6.591 58.707 545 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.55 % Allowed : 25.12 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.40), residues: 492 helix: 0.13 (0.95), residues: 36 sheet: -1.44 (0.45), residues: 131 loop : -0.04 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 380 HIS 0.007 0.001 HIS B 296 PHE 0.007 0.001 PHE B 156 TYR 0.023 0.002 TYR B 485 ARG 0.002 0.000 ARG B 489 *********************** 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 90 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6970 (mtt180) cc_final: 0.6746 (mtp85) REVERT: B 186 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7875 (mtp85) REVERT: B 329 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7114 (pp20) REVERT: B 401 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8322 (ttpp) REVERT: B 488 MET cc_start: 0.7176 (mtp) cc_final: 0.6746 (mpp) REVERT: A 2466 PHE cc_start: 0.6538 (t80) cc_final: 0.6333 (t80) REVERT: A 2515 ARG cc_start: 0.6951 (tpp80) cc_final: 0.6672 (tpt170) REVERT: A 2531 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7077 (mt-10) REVERT: A 2612 LYS cc_start: 0.7574 (ttpp) cc_final: 0.7028 (ttpt) outliers start: 19 outliers final: 13 residues processed: 83 average time/residue: 0.9614 time to fit residues: 83.1459 Evaluate side-chains 83 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 287 THR 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 394 SER Chi-restraints excluded: chain B residue 401 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR 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 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.245919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.215031 restraints weight = 4133.925| |-----------------------------------------------------------------------------| r_work (start): 0.4593 rms_B_bonded: 2.10 r_work: 0.4463 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4303 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4047 Z= 0.189 Angle : 0.618 7.657 5497 Z= 0.330 Chirality : 0.049 0.177 563 Planarity : 0.005 0.048 717 Dihedral : 6.317 57.608 545 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.55 % Allowed : 25.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.41), residues: 492 helix: 0.36 (0.97), residues: 35 sheet: -1.42 (0.45), residues: 131 loop : 0.01 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 168 HIS 0.006 0.001 HIS B 296 PHE 0.005 0.001 PHE A2491 TYR 0.023 0.002 TYR B 485 ARG 0.006 0.000 ARG B 470 ********************** 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 89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 165 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6753 (mtp85) REVERT: B 186 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7858 (mtp85) REVERT: B 329 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7108 (pp20) REVERT: B 488 MET cc_start: 0.7250 (mtp) cc_final: 0.6788 (mpp) REVERT: A 2466 PHE cc_start: 0.6465 (t80) cc_final: 0.6243 (t80) REVERT: A 2515 ARG cc_start: 0.7002 (tpp80) cc_final: 0.6745 (tpt170) REVERT: A 2531 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7048 (mt-10) REVERT: A 2612 LYS cc_start: 0.7479 (ttpp) cc_final: 0.6940 (ttpt) outliers start: 19 outliers final: 11 residues processed: 82 average time/residue: 1.0103 time to fit residues: 86.1968 Evaluate side-chains 80 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 287 THR 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 394 SER Chi-restraints excluded: chain B residue 441 SER Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 THR 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 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 5 optimal weight: 0.0030 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN ** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.245323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.214455 restraints weight = 4119.731| |-----------------------------------------------------------------------------| r_work (start): 0.4607 rms_B_bonded: 2.10 r_work: 0.4466 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4307 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4047 Z= 0.197 Angle : 0.622 7.311 5497 Z= 0.332 Chirality : 0.049 0.190 563 Planarity : 0.005 0.047 717 Dihedral : 6.218 57.364 544 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.59 % Allowed : 26.56 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.41), residues: 492 helix: 0.33 (0.97), residues: 35 sheet: -1.46 (0.45), residues: 131 loop : -0.01 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 168 HIS 0.006 0.001 HIS B 296 PHE 0.006 0.001 PHE B 156 TYR 0.026 0.002 TYR B 485 ARG 0.007 0.000 ARG B 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3380.75 seconds wall clock time: 58 minutes 45.28 seconds (3525.28 seconds total)