Starting phenix.real_space_refine on Sun Mar 10 14:34:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/03_2024/7xiz_33213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/03_2024/7xiz_33213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/03_2024/7xiz_33213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/03_2024/7xiz_33213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/03_2024/7xiz_33213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/03_2024/7xiz_33213.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 9 5.16 5 C 1386 2.51 5 N 364 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2161 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2161 Unusual residues: {'NAG': 2} Classifications: {'peptide': 267, 'undetermined': 2} Link IDs: {'PTRANS': 16, 'TRANS': 250, None: 2} Not linked: pdbres="PRO B 589 " pdbres="NAG B 601 " Not linked: pdbres="NAG B 601 " pdbres="NAG B 602 " Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.75, per 1000 atoms: 0.81 Number of scatterers: 2161 At special positions: 0 Unit cell: (76.96, 69.68, 76.96, 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 9 16.00 O 402 8.00 N 364 7.00 C 1386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 Links applied NAG-ASN " NAG B 601 " - " ASN B 331 " " NAG B 602 " - " ASN B 343 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 386.0 milliseconds 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 500 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 4.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.842A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.358A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 538 through 539 removed outlier: 4.825A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 542 through 543 34 hydrogen bonds defined for protein. 87 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.43 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 1 1.13 - 1.30: 345 1.30 - 1.48: 946 1.48 - 1.65: 918 1.65 - 1.82: 9 Bond restraints: 2219 Sorted by residual: bond pdb=" CG PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.503 0.960 0.543 3.40e-02 8.65e+02 2.56e+02 bond pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 1.473 1.574 -0.101 1.40e-02 5.10e+03 5.22e+01 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 1.472 1.439 0.032 1.34e-02 5.57e+03 5.79e+00 bond pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 ... (remaining 2214 not shown) Histogram of bond angle deviations from ideal: 78.55 - 89.61: 2 89.61 - 100.67: 2 100.67 - 111.74: 966 111.74 - 122.80: 1762 122.80 - 133.86: 286 Bond angle restraints: 3018 Sorted by residual: angle pdb=" N PRO B 384 " pdb=" CD PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 103.20 78.55 24.65 1.50e+00 4.44e-01 2.70e+02 angle pdb=" CA PRO B 384 " pdb=" N PRO B 384 " pdb=" CD PRO B 384 " ideal model delta sigma weight residual 112.00 96.26 15.74 1.40e+00 5.10e-01 1.26e+02 angle pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " pdb=" CG PRO B 384 " ideal model delta sigma weight residual 104.50 87.29 17.21 1.90e+00 2.77e-01 8.20e+01 angle pdb=" N PRO B 384 " pdb=" CA PRO B 384 " pdb=" CB PRO B 384 " ideal model delta sigma weight residual 103.26 97.25 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" C PHE B 377 " pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta sigma weight residual 121.54 129.63 -8.09 1.91e+00 2.74e-01 1.79e+01 ... (remaining 3013 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 1170 21.85 - 43.69: 142 43.69 - 65.53: 17 65.53 - 87.37: 8 87.37 - 109.21: 4 Dihedral angle restraints: 1341 sinusoidal: 560 harmonic: 781 Sorted by residual: dihedral pdb=" CA PHE B 377 " pdb=" C PHE B 377 " pdb=" N LYS B 378 " pdb=" CA LYS B 378 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE B 402 " pdb=" C ILE B 402 " pdb=" N ARG B 403 " pdb=" CA ARG B 403 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY B 476 " pdb=" C GLY B 476 " pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 1338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 191 0.039 - 0.078: 83 0.078 - 0.117: 42 0.117 - 0.155: 7 0.155 - 0.194: 8 Chirality restraints: 331 Sorted by residual: chirality pdb=" CB VAL B 367 " pdb=" CA VAL B 367 " pdb=" CG1 VAL B 367 " pdb=" CG2 VAL B 367 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA PHE B 377 " pdb=" N PHE B 377 " pdb=" C PHE B 377 " pdb=" CB PHE B 377 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 328 not shown) Planarity restraints: 395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 383 " -0.097 5.00e-02 4.00e+02 1.34e-01 2.85e+01 pdb=" N PRO B 384 " 0.230 5.00e-02 4.00e+02 pdb=" CA PRO B 384 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 384 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 378 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C LYS B 378 " 0.050 2.00e-02 2.50e+03 pdb=" O LYS B 378 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS B 379 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO B 521 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.037 5.00e-02 4.00e+02 ... (remaining 392 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 870 2.89 - 3.39: 1887 3.39 - 3.89: 3534 3.89 - 4.40: 3861 4.40 - 4.90: 6428 Nonbonded interactions: 16580 Sorted by model distance: nonbonded pdb=" N ASP B 571 " pdb=" OD1 ASP B 571 " model vdw 2.386 2.520 nonbonded pdb=" O GLN B 563 " pdb=" NH1 ARG B 577 " model vdw 2.395 2.520 nonbonded pdb=" NE2 GLN B 474 " pdb=" O ASN B 477 " model vdw 2.409 2.520 nonbonded pdb=" NE ARG B 457 " pdb=" O SER B 459 " model vdw 2.426 2.520 nonbonded pdb=" OG1 THR B 415 " pdb=" OD2 ASP B 420 " model vdw 2.440 2.440 ... (remaining 16575 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 6.920 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.013 0.543 2219 Z= 0.827 Angle : 1.111 24.653 3018 Z= 0.634 Chirality : 0.058 0.194 331 Planarity : 0.010 0.134 393 Dihedral : 19.025 109.212 832 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.75 % Allowed : 12.83 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 35.32 % Favored : 64.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.47), residues: 265 helix: -4.15 (0.66), residues: 19 sheet: -1.02 (0.70), residues: 48 loop : -2.57 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.019 0.002 PHE B 377 TYR 0.007 0.001 TYR B 451 ARG 0.001 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1235 time to fit residues: 3.3831 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN B 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2219 Z= 0.239 Angle : 0.695 6.618 3018 Z= 0.356 Chirality : 0.049 0.161 331 Planarity : 0.007 0.058 393 Dihedral : 13.034 95.902 337 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 3.40 % Allowed : 36.60 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.47), residues: 265 helix: -4.27 (0.52), residues: 25 sheet: -0.89 (0.67), residues: 50 loop : -2.64 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.013 0.001 PHE B 456 TYR 0.008 0.001 TYR B 396 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 17 time to evaluate : 0.253 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.0781 time to fit residues: 2.6978 Evaluate side-chains 20 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 532 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2219 Z= 0.207 Angle : 0.659 5.725 3018 Z= 0.334 Chirality : 0.048 0.157 331 Planarity : 0.006 0.056 393 Dihedral : 12.492 93.422 337 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 7.23 % Allowed : 34.04 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.46), residues: 265 helix: -4.30 (0.64), residues: 26 sheet: -0.39 (0.75), residues: 38 loop : -2.54 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.012 0.001 PHE B 456 TYR 0.007 0.001 TYR B 508 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 16 time to evaluate : 0.222 Fit side-chains REVERT: B 324 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6387 (mm-30) REVERT: B 571 ASP cc_start: 0.5322 (OUTLIER) cc_final: 0.4944 (t0) outliers start: 17 outliers final: 10 residues processed: 31 average time/residue: 0.0733 time to fit residues: 3.1807 Evaluate side-chains 28 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 16 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 571 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2219 Z= 0.165 Angle : 0.653 7.535 3018 Z= 0.325 Chirality : 0.047 0.162 331 Planarity : 0.006 0.056 393 Dihedral : 12.242 91.387 337 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 5.96 % Allowed : 36.60 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.48), residues: 265 helix: -4.34 (0.66), residues: 26 sheet: -0.39 (0.75), residues: 45 loop : -2.40 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.010 0.001 PHE B 456 TYR 0.007 0.001 TYR B 501 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 18 time to evaluate : 0.263 Fit side-chains REVERT: B 365 TYR cc_start: 0.7633 (m-80) cc_final: 0.7251 (m-80) REVERT: B 571 ASP cc_start: 0.5445 (OUTLIER) cc_final: 0.4996 (t0) outliers start: 14 outliers final: 11 residues processed: 31 average time/residue: 0.0702 time to fit residues: 3.1182 Evaluate side-chains 29 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 17 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 571 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 10.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2219 Z= 0.233 Angle : 0.684 7.180 3018 Z= 0.345 Chirality : 0.049 0.171 331 Planarity : 0.006 0.055 393 Dihedral : 12.604 94.403 337 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.98 % Favored : 82.26 % Rotamer: Outliers : 7.66 % Allowed : 34.89 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.49), residues: 265 helix: -4.27 (0.66), residues: 26 sheet: -0.36 (0.79), residues: 45 loop : -2.47 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 353 HIS 0.000 0.000 HIS B 505 PHE 0.011 0.001 PHE B 456 TYR 0.009 0.001 TYR B 501 ARG 0.002 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 18 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6524 (mm-30) outliers start: 18 outliers final: 15 residues processed: 34 average time/residue: 0.0978 time to fit residues: 4.3096 Evaluate side-chains 30 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 2219 Z= 0.365 Angle : 0.784 6.522 3018 Z= 0.404 Chirality : 0.054 0.210 331 Planarity : 0.006 0.047 393 Dihedral : 13.237 98.779 337 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.98 % Favored : 82.26 % Rotamer: Outliers : 9.79 % Allowed : 34.04 % Favored : 56.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.48), residues: 265 helix: -4.51 (0.56), residues: 25 sheet: -1.35 (0.79), residues: 44 loop : -2.57 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.014 0.002 PHE B 464 TYR 0.011 0.002 TYR B 396 ARG 0.003 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 15 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6708 (mm-30) outliers start: 23 outliers final: 21 residues processed: 36 average time/residue: 0.0893 time to fit residues: 4.2364 Evaluate side-chains 34 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 12 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 2219 Z= 0.213 Angle : 0.704 6.891 3018 Z= 0.354 Chirality : 0.050 0.162 331 Planarity : 0.005 0.053 393 Dihedral : 12.467 94.817 337 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer: Outliers : 9.79 % Allowed : 34.04 % Favored : 56.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.47), residues: 265 helix: -4.32 (0.53), residues: 31 sheet: -0.94 (0.74), residues: 49 loop : -2.73 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 436 HIS 0.000 0.000 HIS B 519 PHE 0.008 0.001 PHE B 497 TYR 0.010 0.001 TYR B 365 ARG 0.001 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 17 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 324 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6676 (mm-30) outliers start: 23 outliers final: 17 residues processed: 38 average time/residue: 0.0938 time to fit residues: 4.6761 Evaluate side-chains 34 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 16 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 439 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 2219 Z= 0.188 Angle : 0.699 8.291 3018 Z= 0.346 Chirality : 0.050 0.176 331 Planarity : 0.005 0.058 393 Dihedral : 11.998 89.443 337 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.72 % Favored : 84.53 % Rotamer: Outliers : 5.96 % Allowed : 36.17 % Favored : 57.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.47), residues: 265 helix: -4.86 (0.36), residues: 18 sheet: -0.94 (0.71), residues: 49 loop : -2.61 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.008 0.001 PHE B 456 TYR 0.012 0.001 TYR B 365 ARG 0.001 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 19 time to evaluate : 0.254 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 32 average time/residue: 0.1126 time to fit residues: 4.5651 Evaluate side-chains 25 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 15 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 2219 Z= 0.291 Angle : 0.775 8.675 3018 Z= 0.390 Chirality : 0.052 0.181 331 Planarity : 0.006 0.053 393 Dihedral : 12.659 94.137 337 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.36 % Favored : 81.89 % Rotamer: Outliers : 6.38 % Allowed : 36.17 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.47), residues: 265 helix: -4.39 (0.52), residues: 31 sheet: -1.09 (0.73), residues: 49 loop : -2.70 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 353 HIS 0.000 0.000 HIS B 505 PHE 0.011 0.002 PHE B 456 TYR 0.011 0.001 TYR B 365 ARG 0.003 0.000 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 16 time to evaluate : 0.234 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 14 residues processed: 31 average time/residue: 0.0948 time to fit residues: 3.8782 Evaluate side-chains 29 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 15 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 2219 Z= 0.303 Angle : 0.791 9.156 3018 Z= 0.399 Chirality : 0.053 0.175 331 Planarity : 0.006 0.049 393 Dihedral : 12.918 96.383 337 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.60 % Favored : 82.64 % Rotamer: Outliers : 7.66 % Allowed : 34.89 % Favored : 57.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.47), residues: 265 helix: -4.45 (0.50), residues: 31 sheet: -1.23 (0.74), residues: 49 loop : -2.85 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 353 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.002 PHE B 497 TYR 0.012 0.001 TYR B 365 ARG 0.002 0.000 ARG B 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 530 Ramachandran restraints generated. 265 Oldfield, 0 Emsley, 265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 15 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 347 PHE cc_start: 0.6086 (OUTLIER) cc_final: 0.5582 (m-10) outliers start: 18 outliers final: 15 residues processed: 33 average time/residue: 0.0978 time to fit residues: 4.2166 Evaluate side-chains 30 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 14 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 0.0270 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.077094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066291 restraints weight = 10012.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.067577 restraints weight = 6067.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.068453 restraints weight = 4263.756| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 2219 Z= 0.209 Angle : 0.744 9.008 3018 Z= 0.370 Chirality : 0.050 0.166 331 Planarity : 0.005 0.053 393 Dihedral : 12.287 92.636 337 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.85 % Favored : 83.40 % Rotamer: Outliers : 5.96 % Allowed : 35.74 % Favored : 58.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.47), residues: 265 helix: -4.46 (0.55), residues: 31 sheet: -0.91 (0.76), residues: 47 loop : -2.74 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.008 0.001 PHE B 497 TYR 0.015 0.001 TYR B 365 ARG 0.002 0.000 ARG B 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 952.78 seconds wall clock time: 17 minutes 45.74 seconds (1065.74 seconds total)