Starting phenix.real_space_refine on Thu Jul 18 21:56:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/07_2024/8ji0_36303.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/07_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_36303/07_2024/8ji0_36303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/07_2024/8ji0_36303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/07_2024/8ji0_36303.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ji0_36303/07_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 Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ASP 440": "OD1" <-> "OD2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "A TYR 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2508": "OD1" <-> "OD2" Residue "A GLU 2531": "OE1" <-> "OE2" Residue "A ASP 2565": "OD1" <-> "OD2" Residue "A ASP 2587": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 2.86, per 1000 atoms: 0.73 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 - 3.50 Amino acid : False - 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: 1.46 Conformation dependent library (CDL) restraints added in 709.6 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: 1.12 Time building geometry restraints manager: 1.62 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: 91.65 - 100.73: 16 100.73 - 109.81: 579 109.81 - 118.89: 2588 118.89 - 127.97: 2257 127.97 - 137.04: 57 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 2.440 nonbonded pdb=" OG1 THR A2506 " pdb=" OD1 ASN A2511 " model vdw 1.965 2.440 nonbonded pdb=" OH TYR A2550 " pdb=" O PHE A2554 " model vdw 2.001 2.440 nonbonded pdb=" O LYS B 300 " pdb=" NZ LYS B 300 " model vdw 2.035 2.520 nonbonded pdb=" O MET B 371 " pdb=" NZ LYS B 449 " model vdw 2.067 2.520 ... (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 ========== 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: 0.710 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.520 Find NCS groups from input model: 0.050 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 0.457 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: 0.9397 time to fit residues: 99.9662 Evaluate side-chains 78 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 0.9980 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4047 Z= 0.246 Angle : 0.671 8.871 5497 Z= 0.356 Chirality : 0.049 0.201 563 Planarity : 0.005 0.072 717 Dihedral : 9.273 93.497 564 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.54 % Favored : 91.26 % Rotamer: Outliers : 6.46 % Allowed : 23.92 % Favored : 69.62 % 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: -1.13 (0.39), residues: 492 helix: -0.34 (0.90), residues: 36 sheet: -2.01 (0.48), residues: 105 loop : -0.33 (0.36), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 461 HIS 0.005 0.001 HIS B 296 PHE 0.013 0.002 PHE A2466 TYR 0.031 0.002 TYR A2563 ARG 0.004 0.001 ARG A2490 *********************** 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 96 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 69 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 488 MET cc_start: 0.7295 (mtp) cc_final: 0.6675 (mpp) REVERT: A 2515 ARG cc_start: 0.6844 (tpp80) cc_final: 0.6535 (tpt170) REVERT: A 2612 LYS cc_start: 0.7282 (ttpp) cc_final: 0.7028 (ttpt) outliers start: 27 outliers final: 12 residues processed: 86 average time/residue: 0.8726 time to fit residues: 78.6364 Evaluate side-chains 73 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 333 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 382 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 2572 THR Chi-restraints excluded: chain A residue 2588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 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 336 ASN B 450 ASN A2516 ASN A2540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4047 Z= 0.223 Angle : 0.611 6.234 5497 Z= 0.327 Chirality : 0.049 0.197 563 Planarity : 0.005 0.050 717 Dihedral : 6.627 52.146 545 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 6.46 % Allowed : 22.97 % 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: -1.01 (0.40), residues: 492 helix: -0.02 (0.93), residues: 36 sheet: -2.13 (0.45), residues: 113 loop : -0.13 (0.37), residues: 343 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 0.009 0.001 PHE A2521 TYR 0.023 0.002 TYR A2563 ARG 0.003 0.001 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 98 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 71 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: B 352 GLN cc_start: 0.7131 (mt0) cc_final: 0.6921 (mt0) REVERT: B 488 MET cc_start: 0.7252 (mtp) cc_final: 0.6560 (mpp) REVERT: A 2515 ARG cc_start: 0.6836 (tpp80) cc_final: 0.6500 (tpt170) REVERT: A 2612 LYS cc_start: 0.7393 (ttpp) cc_final: 0.6954 (ttpt) outliers start: 27 outliers final: 14 residues processed: 85 average time/residue: 0.9087 time to fit residues: 80.7167 Evaluate side-chains 76 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 377 GLN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 382 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 2572 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: 0.0040 chunk 21 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 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 450 ASN A2516 ASN A2546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4047 Z= 0.189 Angle : 0.585 5.798 5497 Z= 0.312 Chirality : 0.048 0.192 563 Planarity : 0.005 0.040 717 Dihedral : 6.408 51.335 545 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.55 % Allowed : 25.60 % 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: -0.82 (0.39), residues: 492 helix: 0.27 (0.95), residues: 36 sheet: -1.70 (0.50), residues: 92 loop : -0.27 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.007 0.001 PHE A2533 TYR 0.018 0.002 TYR A2563 ARG 0.003 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 fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.437 Fit side-chains REVERT: B 488 MET cc_start: 0.7337 (mtp) cc_final: 0.6633 (mpp) REVERT: A 2515 ARG cc_start: 0.6788 (tpp80) cc_final: 0.6402 (tpt170) REVERT: A 2612 LYS cc_start: 0.7412 (ttpp) cc_final: 0.6980 (ttpt) outliers start: 19 outliers final: 12 residues processed: 85 average time/residue: 0.8547 time to fit residues: 76.1145 Evaluate side-chains 73 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 355 LEU 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 2507 LEU Chi-restraints excluded: chain A residue 2572 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 35 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2461 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: 0.7118 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4047 Z= 0.212 Angle : 0.612 5.870 5497 Z= 0.325 Chirality : 0.048 0.175 563 Planarity : 0.005 0.041 717 Dihedral : 6.513 54.084 545 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.02 % Allowed : 25.60 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.40), residues: 492 helix: 0.13 (0.92), residues: 36 sheet: -1.83 (0.45), residues: 124 loop : -0.08 (0.37), residues: 332 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 0.007 0.001 PHE A2530 TYR 0.018 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 89 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: B 488 MET cc_start: 0.7334 (mtp) cc_final: 0.6607 (mpp) REVERT: A 2515 ARG cc_start: 0.6789 (tpp80) cc_final: 0.6401 (tpt170) REVERT: A 2609 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.6285 (p0) REVERT: A 2612 LYS cc_start: 0.7411 (ttpp) cc_final: 0.6994 (ttpt) outliers start: 21 outliers final: 15 residues processed: 81 average time/residue: 0.8135 time to fit residues: 69.3414 Evaluate side-chains 77 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 381 ILE 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 2507 LEU Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2588 THR Chi-restraints excluded: chain A residue 2609 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4047 Z= 0.251 Angle : 0.639 6.703 5497 Z= 0.337 Chirality : 0.049 0.169 563 Planarity : 0.005 0.042 717 Dihedral : 6.751 56.237 545 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 6.46 % Allowed : 23.92 % Favored : 69.62 % 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: -0.92 (0.40), residues: 492 helix: -0.03 (0.91), residues: 36 sheet: -1.59 (0.44), residues: 134 loop : -0.12 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.008 0.001 PHE A2530 TYR 0.030 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 92 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: B 186 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: B 488 MET cc_start: 0.7314 (mtp) cc_final: 0.6565 (mpp) REVERT: A 2515 ARG cc_start: 0.6820 (tpp80) cc_final: 0.6463 (tpt170) REVERT: A 2612 LYS cc_start: 0.7417 (ttpp) cc_final: 0.6979 (ttpt) outliers start: 27 outliers final: 16 residues processed: 85 average time/residue: 0.9493 time to fit residues: 84.1787 Evaluate side-chains 80 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 63 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 ASP 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 355 LEU 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 2572 THR 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 26 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN B 450 ASN A2461 ASN A2516 ASN A2540 ASN A2546 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4047 Z= 0.234 Angle : 0.629 7.473 5497 Z= 0.331 Chirality : 0.049 0.168 563 Planarity : 0.005 0.044 717 Dihedral : 6.833 59.960 545 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.98 % Allowed : 24.88 % Favored : 69.14 % 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 (0.39), residues: 492 helix: 0.06 (0.93), residues: 36 sheet: -1.46 (0.46), residues: 120 loop : -0.30 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.007 0.001 PHE A2530 TYR 0.027 0.002 TYR A2563 ARG 0.004 0.001 ARG B 413 *********************** 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 99 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 186 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7712 (mtp85) REVERT: B 467 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6363 (tmtp) REVERT: B 488 MET cc_start: 0.7036 (mtp) cc_final: 0.6655 (mpp) REVERT: A 2515 ARG cc_start: 0.6870 (tpp80) cc_final: 0.6496 (tpt170) REVERT: A 2612 LYS cc_start: 0.7407 (ttpp) cc_final: 0.6955 (ttpt) outliers start: 25 outliers final: 15 residues processed: 90 average time/residue: 0.8694 time to fit residues: 81.7591 Evaluate side-chains 79 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 ASP 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 355 LEU 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 B residue 467 LYS Chi-restraints excluded: chain A residue 2572 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: 3.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 0.0060 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2461 ASN A2516 ASN A2540 ASN A2546 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.3359 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= 0.221 Angle : 0.625 6.786 5497 Z= 0.333 Chirality : 0.049 0.163 563 Planarity : 0.005 0.044 717 Dihedral : 6.717 56.858 545 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.26 % Allowed : 26.08 % Favored : 68.66 % 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: -0.88 (0.40), residues: 492 helix: 0.36 (0.97), residues: 36 sheet: -1.47 (0.44), residues: 132 loop : -0.20 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.006 0.001 PHE A2530 TYR 0.024 0.002 TYR A2563 ARG 0.011 0.001 ARG B 470 *********************** 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 92 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: B 186 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7676 (mtp85) REVERT: B 488 MET cc_start: 0.7087 (mtp) cc_final: 0.6669 (mpp) REVERT: A 2466 PHE cc_start: 0.6876 (t80) cc_final: 0.6674 (t80) REVERT: A 2515 ARG cc_start: 0.6896 (tpp80) cc_final: 0.6541 (tpt170) REVERT: A 2612 LYS cc_start: 0.7383 (ttpp) cc_final: 0.6980 (ttpt) outliers start: 22 outliers final: 17 residues processed: 84 average time/residue: 0.8538 time to fit residues: 75.2033 Evaluate side-chains 83 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 186 ARG 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 355 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 382 SER 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 2572 THR Chi-restraints excluded: chain A residue 2588 THR Chi-restraints excluded: chain A residue 2600 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.0070 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2461 ASN A2516 ASN A2540 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4047 Z= 0.174 Angle : 0.591 7.135 5497 Z= 0.316 Chirality : 0.047 0.166 563 Planarity : 0.005 0.047 717 Dihedral : 6.197 55.821 545 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.55 % Allowed : 27.75 % Favored : 67.70 % 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: -0.78 (0.40), residues: 492 helix: 0.67 (0.99), residues: 35 sheet: -1.63 (0.48), residues: 109 loop : -0.19 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 168 HIS 0.005 0.001 HIS B 296 PHE 0.005 0.001 PHE A2533 TYR 0.024 0.002 TYR B 485 ARG 0.003 0.000 ARG B 413 *********************** 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 93 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: B 186 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: B 488 MET cc_start: 0.7196 (mtp) cc_final: 0.6760 (mpp) REVERT: A 2466 PHE cc_start: 0.6853 (t80) cc_final: 0.6610 (t80) REVERT: A 2515 ARG cc_start: 0.6911 (tpp80) cc_final: 0.6542 (tpt170) REVERT: A 2612 LYS cc_start: 0.7376 (ttpp) cc_final: 0.7008 (ttpt) outliers start: 19 outliers final: 13 residues processed: 85 average time/residue: 0.8620 time to fit residues: 76.7611 Evaluate side-chains 81 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 188 MET 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 381 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain A residue 2461 ASN Chi-restraints excluded: chain A residue 2572 THR Chi-restraints excluded: chain A residue 2588 THR Chi-restraints excluded: chain A residue 2600 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7125 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4047 Z= 0.243 Angle : 0.643 6.818 5497 Z= 0.343 Chirality : 0.050 0.227 563 Planarity : 0.005 0.046 717 Dihedral : 6.452 55.980 545 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.31 % Allowed : 28.47 % Favored : 67.22 % 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: -0.87 (0.40), residues: 492 helix: 0.27 (0.95), residues: 36 sheet: -1.49 (0.45), residues: 132 loop : -0.18 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.008 0.001 PHE A2530 TYR 0.030 0.002 TYR B 222 ARG 0.003 0.001 ARG B 413 ********************** 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 88 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: B 186 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7718 (mtp85) REVERT: B 488 MET cc_start: 0.7251 (mtp) cc_final: 0.6774 (mpp) REVERT: A 2515 ARG cc_start: 0.6813 (tpp80) cc_final: 0.6452 (tpt170) REVERT: A 2612 LYS cc_start: 0.7349 (ttpp) cc_final: 0.6961 (ttpt) outliers start: 18 outliers final: 13 residues processed: 80 average time/residue: 0.9433 time to fit residues: 78.5901 Evaluate side-chains 81 residues out of total 418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 382 SER 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 2572 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: 3.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 ASN A2540 ASN A2546 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.245045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.214663 restraints weight = 4083.925| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 2.07 r_work: 0.4467 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4310 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 0.039 4047 Z= 0.197 Angle : 0.614 7.491 5497 Z= 0.327 Chirality : 0.049 0.207 563 Planarity : 0.005 0.048 717 Dihedral : 6.285 56.249 545 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.07 % Allowed : 28.47 % Favored : 67.46 % 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: 0.34 (0.95), residues: 36 sheet: -1.44 (0.45), residues: 132 loop : -0.06 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 380 HIS 0.005 0.001 HIS B 296 PHE 0.006 0.001 PHE A2533 TYR 0.027 0.002 TYR B 485 ARG 0.003 0.000 ARG B 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.77 seconds wall clock time: 36 minutes 32.37 seconds (2192.37 seconds total)