Starting phenix.real_space_refine on Thu Nov 14 04:35:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/11_2024/8ji0_36303.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/11_2024/8ji0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/11_2024/8ji0_36303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/11_2024/8ji0_36303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/11_2024/8ji0_36303.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/11_2024/8ji0_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-5513/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: 3.15, per 1000 atoms: 0.80 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: 0.97 Conformation dependent library (CDL) restraints added in 480.5 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: 0.54 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: 1.09 Time building geometry restraints manager: 1.16 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: 1.310 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: 14.490 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: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- 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 : 0.433 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: 0.9545 time to fit residues: 101.2659 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 : 0.486 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 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 : 0.435 Fit side-chains revert: symmetry clash REVERT: B 210 MET cc_start: 0.7244 (mmm) cc_final: 0.7022 (mmt) REVERT: B 329 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6792 (pp20) REVERT: B 488 MET cc_start: 0.7309 (mtp) cc_final: 0.6683 (mpp) REVERT: A 2515 ARG cc_start: 0.6857 (tpp80) cc_final: 0.6507 (tpt170) REVERT: A 2612 LYS cc_start: 0.7304 (ttpp) cc_final: 0.7050 (ttpt) REVERT: A 2613 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6634 (mt0) outliers start: 19 outliers final: 8 residues processed: 78 average time/residue: 0.8972 time to fit residues: 73.2578 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 : 0.422 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.0470 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4047 Z= 0.216 Angle : 0.616 6.552 5497 Z= 0.330 Chirality : 0.049 0.197 563 Planarity : 0.005 0.051 717 Dihedral : 6.896 51.603 547 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.55 % Allowed : 22.97 % Favored : 72.49 % 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: 0.01 (0.94), residues: 36 sheet: -1.86 (0.48), residues: 106 loop : -0.21 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 461 HIS 0.005 0.001 HIS B 296 PHE 0.008 0.001 PHE A2521 TYR 0.022 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 88 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: B 210 MET cc_start: 0.7264 (mmm) cc_final: 0.7047 (mmt) REVERT: B 488 MET cc_start: 0.7285 (mtp) cc_final: 0.6606 (mpp) REVERT: A 2515 ARG cc_start: 0.6873 (tpp80) cc_final: 0.6517 (tpt170) REVERT: A 2612 LYS cc_start: 0.7405 (ttpp) cc_final: 0.7028 (ttpt) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 0.8625 time to fit residues: 73.2693 Evaluate side-chains 70 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 A2546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4047 Z= 0.157 Angle : 0.572 5.898 5497 Z= 0.303 Chirality : 0.047 0.195 563 Planarity : 0.005 0.040 717 Dihedral : 5.976 48.629 545 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.55 % Allowed : 23.68 % 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 (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: -0.69 (0.40), residues: 492 helix: 0.29 (0.96), residues: 36 sheet: -1.62 (0.50), residues: 97 loop : -0.13 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 168 HIS 0.005 0.001 HIS B 296 PHE 0.006 0.001 PHE A2466 TYR 0.015 0.001 TYR A2563 ARG 0.002 0.000 ARG B 409 *********************** 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 92 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: B 188 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8180 (tpp) REVERT: B 329 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6681 (pp20) REVERT: B 382 SER cc_start: 0.8694 (t) cc_final: 0.8487 (t) REVERT: B 413 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6617 (ptp90) REVERT: B 488 MET cc_start: 0.7302 (mtp) cc_final: 0.6564 (mpp) REVERT: A 2515 ARG cc_start: 0.6771 (tpp80) cc_final: 0.6420 (tpt170) REVERT: A 2612 LYS cc_start: 0.7270 (ttpp) cc_final: 0.6910 (ttpt) outliers start: 19 outliers final: 11 residues processed: 85 average time/residue: 0.7236 time to fit residues: 64.3229 Evaluate side-chains 78 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 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 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 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 35 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 A2511 ASN A2516 ASN A2540 ASN A2546 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4047 Z= 0.179 Angle : 0.598 5.982 5497 Z= 0.318 Chirality : 0.048 0.183 563 Planarity : 0.005 0.043 717 Dihedral : 5.887 48.854 545 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.55 % Allowed : 24.16 % 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 (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: -0.65 (0.40), residues: 492 helix: 0.24 (0.95), residues: 36 sheet: -1.37 (0.45), residues: 130 loop : 0.01 (0.38), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 168 HIS 0.005 0.001 HIS B 296 PHE 0.005 0.001 PHE B 156 TYR 0.017 0.002 TYR B 485 ARG 0.002 0.000 ARG B 409 *********************** 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 89 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6738 (pp20) REVERT: B 488 MET cc_start: 0.7208 (mtp) cc_final: 0.6803 (mpp) REVERT: A 2515 ARG cc_start: 0.6781 (tpp80) cc_final: 0.6421 (tpt170) REVERT: A 2612 LYS cc_start: 0.7273 (ttpp) cc_final: 0.6916 (ttpt) outliers start: 19 outliers final: 12 residues processed: 81 average time/residue: 0.8069 time to fit residues: 68.7529 Evaluate side-chains 79 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 0.0170 chunk 15 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.2618 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4047 Z= 0.134 Angle : 0.567 7.291 5497 Z= 0.298 Chirality : 0.047 0.177 563 Planarity : 0.004 0.045 717 Dihedral : 5.256 43.722 545 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.35 % Allowed : 24.40 % 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: -0.44 (0.41), residues: 492 helix: 0.40 (0.96), residues: 36 sheet: -1.32 (0.47), residues: 117 loop : 0.12 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 168 HIS 0.003 0.001 HIS B 296 PHE 0.005 0.001 PHE A2512 TYR 0.019 0.001 TYR B 485 ARG 0.002 0.000 ARG B 409 *********************** 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 90 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6555 (pp20) REVERT: B 488 MET cc_start: 0.7027 (mtp) cc_final: 0.6664 (mpp) REVERT: A 2515 ARG cc_start: 0.6775 (tpp80) cc_final: 0.6409 (tpt170) REVERT: A 2612 LYS cc_start: 0.7215 (ttpp) cc_final: 0.6875 (ttpt) outliers start: 14 outliers final: 7 residues processed: 85 average time/residue: 0.8978 time to fit residues: 79.7306 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 : 0.446 ------------------------------------------------------------------------------- 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 394 SER Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain A residue 2461 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.0470 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 A2540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3251 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= 0.186 Angle : 0.608 6.495 5497 Z= 0.319 Chirality : 0.048 0.169 563 Planarity : 0.005 0.046 717 Dihedral : 5.344 46.319 543 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.07 % Allowed : 25.12 % Favored : 70.81 % 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: -0.48 (0.41), residues: 492 helix: 0.54 (0.99), residues: 36 sheet: -1.35 (0.45), residues: 131 loop : 0.16 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 380 HIS 0.006 0.001 HIS B 296 PHE 0.006 0.001 PHE B 156 TYR 0.026 0.002 TYR A2563 ARG 0.003 0.000 ARG B 470 *********************** 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 85 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6731 (pp20) REVERT: B 401 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8169 (ttpp) REVERT: B 488 MET cc_start: 0.7063 (mtp) cc_final: 0.6633 (mpp) REVERT: A 2515 ARG cc_start: 0.6767 (tpp80) cc_final: 0.6413 (tpt170) REVERT: A 2612 LYS cc_start: 0.7255 (ttpp) cc_final: 0.6909 (ttpt) outliers start: 17 outliers final: 8 residues processed: 77 average time/residue: 0.8785 time to fit residues: 70.7858 Evaluate side-chains 75 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 401 LYS 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 A residue 2588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4047 Z= 0.276 Angle : 0.671 6.975 5497 Z= 0.354 Chirality : 0.050 0.167 563 Planarity : 0.005 0.046 717 Dihedral : 6.199 59.162 543 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.31 % Allowed : 24.40 % 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 (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 (0.40), residues: 492 helix: 0.21 (0.97), residues: 36 sheet: -1.41 (0.45), residues: 131 loop : -0.02 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 380 HIS 0.009 0.002 HIS B 296 PHE 0.009 0.002 PHE B 156 TYR 0.030 0.002 TYR A2563 ARG 0.003 0.001 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 83 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6751 (pp20) REVERT: B 488 MET cc_start: 0.7106 (mtp) cc_final: 0.6711 (mpp) REVERT: A 2515 ARG cc_start: 0.6770 (tpp80) cc_final: 0.6404 (tpt170) REVERT: A 2531 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 2612 LYS cc_start: 0.7290 (ttpp) cc_final: 0.6882 (ttpt) outliers start: 18 outliers final: 9 residues processed: 77 average time/residue: 0.9544 time to fit residues: 76.8494 Evaluate side-chains 71 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS 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 2461 ASN 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 39 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3347 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= 0.257 Angle : 0.671 7.032 5497 Z= 0.356 Chirality : 0.050 0.165 563 Planarity : 0.005 0.048 717 Dihedral : 6.194 57.657 543 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.63 % Allowed : 27.03 % 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: -0.75 (0.40), residues: 492 helix: 0.11 (0.94), residues: 36 sheet: -1.41 (0.45), residues: 131 loop : -0.06 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 168 HIS 0.008 0.001 HIS B 296 PHE 0.008 0.001 PHE A2605 TYR 0.028 0.002 TYR A2563 ARG 0.005 0.001 ARG B 470 *********************** 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 77 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6762 (pp20) REVERT: B 488 MET cc_start: 0.7019 (mtp) cc_final: 0.6645 (mpp) REVERT: A 2515 ARG cc_start: 0.6794 (tpp80) cc_final: 0.6485 (tpt170) REVERT: A 2531 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 2612 LYS cc_start: 0.7434 (ttpp) cc_final: 0.7015 (ttpt) outliers start: 11 outliers final: 8 residues processed: 73 average time/residue: 0.9834 time to fit residues: 74.8528 Evaluate side-chains 72 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS 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 2588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4047 Z= 0.299 Angle : 0.702 6.871 5497 Z= 0.372 Chirality : 0.051 0.161 563 Planarity : 0.005 0.048 717 Dihedral : 6.355 57.612 543 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.87 % Allowed : 26.32 % Favored : 70.81 % 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: -0.08 (0.92), residues: 36 sheet: -1.52 (0.45), residues: 131 loop : -0.19 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 168 HIS 0.009 0.002 HIS B 296 PHE 0.009 0.002 PHE A2605 TYR 0.031 0.003 TYR A2563 ARG 0.005 0.001 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 75 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: B 329 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6760 (pp20) REVERT: B 488 MET cc_start: 0.7129 (mtp) cc_final: 0.6766 (mpp) REVERT: A 2515 ARG cc_start: 0.6850 (tpp80) cc_final: 0.6474 (tpt170) REVERT: A 2531 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7069 (mt-10) REVERT: A 2612 LYS cc_start: 0.7392 (ttpp) cc_final: 0.6964 (ttpt) outliers start: 12 outliers final: 8 residues processed: 71 average time/residue: 0.9480 time to fit residues: 70.2343 Evaluate side-chains 71 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS 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 2588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 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 = 0.4852 r_free = 0.4852 target = 0.246589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.215839 restraints weight = 4122.179| |-----------------------------------------------------------------------------| r_work (start): 0.4582 rms_B_bonded: 2.06 r_work: 0.4453 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.4296 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4047 Z= 0.213 Angle : 0.652 7.671 5497 Z= 0.345 Chirality : 0.049 0.166 563 Planarity : 0.005 0.047 717 Dihedral : 6.119 57.710 543 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.63 % Allowed : 26.56 % Favored : 70.81 % 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: -0.82 (0.40), residues: 492 helix: 0.18 (0.95), residues: 36 sheet: -1.48 (0.45), residues: 131 loop : -0.11 (0.38), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 168 HIS 0.007 0.001 HIS B 296 PHE 0.007 0.001 PHE A2605 TYR 0.026 0.002 TYR B 485 ARG 0.010 0.001 ARG B 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.02 seconds wall clock time: 39 minutes 46.00 seconds (2386.00 seconds total)