Starting phenix.real_space_refine on Thu Dec 7 16:10:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/12_2023/7xiz_33213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/12_2023/7xiz_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_33213/12_2023/7xiz_33213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/12_2023/7xiz_33213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/12_2023/7xiz_33213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/12_2023/7xiz_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-1.21rc1-5172/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: 0.93 Conformation dependent library (CDL) restraints added in 354.7 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: 0.45 Time building geometry restraints manager: 0.96 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.060 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: 22.510 ------------------------------------------------------------------------------- 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 : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1114 time to fit residues: 3.0684 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3531 ------------------------------------------------------------------------------- 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 : 0.195 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.0692 time to fit residues: 2.4159 Evaluate side-chains 20 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 14 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0234 time to fit residues: 0.5203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 1.9990 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: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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: 0.7314 moved from start: 0.2314 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= 0.173 Angle : 0.642 5.763 3018 Z= 0.323 Chirality : 0.047 0.159 331 Planarity : 0.006 0.056 393 Dihedral : 12.263 91.289 337 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.34 % Favored : 84.91 % Rotamer: Outliers : 3.83 % Allowed : 36.17 % 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: -3.21 (0.47), residues: 265 helix: -4.61 (0.56), residues: 19 sheet: -0.50 (0.72), residues: 45 loop : -2.49 (0.41), residues: 201 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 0.011 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 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 15 time to evaluate : 0.251 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 24 average time/residue: 0.0777 time to fit residues: 2.7194 Evaluate side-chains 17 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 12 time to evaluate : 0.253 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0266 time to fit residues: 0.5524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.7297 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2219 Z= 0.158 Angle : 0.645 7.253 3018 Z= 0.321 Chirality : 0.048 0.167 331 Planarity : 0.006 0.057 393 Dihedral : 12.041 89.204 337 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer: Outliers : 2.55 % Allowed : 37.02 % Favored : 60.43 % 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: -3.09 (0.48), residues: 265 helix: -4.78 (0.47), residues: 19 sheet: -0.30 (0.74), residues: 45 loop : -2.40 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 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 23 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 17 time to evaluate : 0.220 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 22 average time/residue: 0.0765 time to fit residues: 2.4057 Evaluate side-chains 20 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 16 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0281 time to fit residues: 0.5331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 chunk 11 optimal weight: 3.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- 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: 0.7310 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2219 Z= 0.160 Angle : 0.645 6.554 3018 Z= 0.319 Chirality : 0.047 0.166 331 Planarity : 0.006 0.056 393 Dihedral : 11.863 87.120 337 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer: Outliers : 2.13 % Allowed : 35.74 % Favored : 62.13 % 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: -2.97 (0.49), residues: 265 helix: -4.84 (0.50), residues: 18 sheet: -0.22 (0.71), residues: 48 loop : -2.34 (0.43), residues: 199 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 0.006 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 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.250 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 24 average time/residue: 0.1171 time to fit residues: 3.6180 Evaluate side-chains 19 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 15 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1328 time to fit residues: 0.9393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.0060 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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: 0.7246 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 2219 Z= 0.172 Angle : 0.661 6.093 3018 Z= 0.329 Chirality : 0.049 0.168 331 Planarity : 0.005 0.057 393 Dihedral : 11.300 82.794 337 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.75 % Allowed : 13.96 % Favored : 85.28 % Rotamer: Outliers : 1.28 % Allowed : 36.17 % Favored : 62.55 % 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: -2.92 (0.49), residues: 265 helix: -4.94 (0.46), residues: 18 sheet: -0.29 (0.71), residues: 49 loop : -2.27 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.008 0.001 PHE B 456 TYR 0.010 0.001 TYR B 365 ARG 0.001 0.000 ARG B 577 *********************** 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 24 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.257 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 24 average time/residue: 0.1086 time to fit residues: 3.4448 Evaluate side-chains 17 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.256 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0245 time to fit residues: 0.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7259 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 2219 Z= 0.173 Angle : 0.683 6.471 3018 Z= 0.335 Chirality : 0.049 0.161 331 Planarity : 0.005 0.056 393 Dihedral : 10.922 79.136 337 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.72 % Favored : 84.53 % Rotamer: Outliers : 1.28 % Allowed : 36.17 % Favored : 62.55 % 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: -3.08 (0.48), residues: 265 helix: -4.76 (0.35), residues: 25 sheet: -0.28 (0.70), residues: 49 loop : -2.33 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.009 0.001 PHE B 456 TYR 0.006 0.001 TYR B 365 ARG 0.002 0.000 ARG B 457 *********************** 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 20 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 17 time to evaluate : 0.268 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 20 average time/residue: 0.0724 time to fit residues: 2.2049 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0246 time to fit residues: 0.3838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 2219 Z= 0.185 Angle : 0.714 8.701 3018 Z= 0.348 Chirality : 0.051 0.154 331 Planarity : 0.005 0.055 393 Dihedral : 10.837 76.811 337 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer: Outliers : 0.85 % Allowed : 36.60 % Favored : 62.55 % 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: -3.08 (0.49), residues: 265 helix: -4.87 (0.33), residues: 25 sheet: -0.42 (0.76), residues: 44 loop : -2.22 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.009 0.001 PHE B 456 TYR 0.015 0.001 TYR B 365 ARG 0.002 0.000 ARG B 328 *********************** 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 18 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.253 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0732 time to fit residues: 2.0321 Evaluate side-chains 16 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 15 time to evaluate : 0.254 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0247 time to fit residues: 0.3884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 2219 Z= 0.162 Angle : 0.703 8.325 3018 Z= 0.340 Chirality : 0.050 0.152 331 Planarity : 0.005 0.055 393 Dihedral : 10.057 71.170 337 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.34 % Favored : 84.91 % Rotamer: Outliers : 0.00 % Allowed : 37.45 % Favored : 62.55 % 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: -3.00 (0.50), residues: 265 helix: -4.88 (0.34), residues: 25 sheet: -0.09 (0.73), residues: 49 loop : -2.28 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS B 505 PHE 0.008 0.001 PHE B 456 TYR 0.013 0.001 TYR B 365 ARG 0.001 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 17 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.255 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0767 time to fit residues: 2.0697 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.272 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 5 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 0.2980 chunk 13 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 2219 Z= 0.256 Angle : 0.760 8.369 3018 Z= 0.377 Chirality : 0.053 0.168 331 Planarity : 0.006 0.053 393 Dihedral : 10.293 67.729 337 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.98 % Favored : 82.26 % Rotamer: Outliers : 0.43 % Allowed : 37.45 % Favored : 62.13 % 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: -3.13 (0.51), residues: 265 helix: -4.40 (0.55), residues: 32 sheet: -0.38 (0.80), residues: 42 loop : -2.22 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.012 0.002 PHE B 456 TYR 0.018 0.002 TYR B 365 ARG 0.003 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 14 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.260 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 14 average time/residue: 0.0783 time to fit residues: 1.7453 Evaluate side-chains 13 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.256 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0542 time to fit residues: 0.4531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.078745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.067998 restraints weight = 9758.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069365 restraints weight = 5974.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.070396 restraints weight = 4188.981| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2219 Z= 0.179 Angle : 0.723 8.436 3018 Z= 0.354 Chirality : 0.050 0.149 331 Planarity : 0.005 0.054 393 Dihedral : 9.107 60.715 337 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.75 % Allowed : 14.34 % Favored : 84.91 % Rotamer: Outliers : 0.00 % Allowed : 37.45 % Favored : 62.55 % 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: -3.14 (0.50), residues: 265 helix: -4.92 (0.36), residues: 24 sheet: -0.22 (0.75), residues: 49 loop : -2.40 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 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 0.002 0.000 ARG B 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 942.50 seconds wall clock time: 17 minutes 34.96 seconds (1054.96 seconds total)