Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:34:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/11_2022/7xiz_33213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/11_2022/7xiz_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_33213/11_2022/7xiz_33213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/11_2022/7xiz_33213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/11_2022/7xiz_33213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xiz_33213/11_2022/7xiz_33213.pdb" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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 chiralities: 2 Time building chain proxies: 1.83, per 1000 atoms: 0.85 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: 0.82 Conformation dependent library (CDL) restraints added in 305.2 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: 0.10 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: 0.48 Time building geometry restraints manager: 0.92 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=" 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 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.426 1.494 -0.068 3.20e-02 9.77e+02 4.53e+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 - 20.74: 1134 20.74 - 41.47: 151 41.47 - 62.20: 18 62.20 - 82.93: 6 82.93 - 103.66: 2 Dihedral angle restraints: 1311 sinusoidal: 530 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=" C3 NAG B 601 " pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sinusoidal sigma weight residual -50.00 53.66 -103.66 1 2.00e+01 2.50e-03 2.97e+01 dihedral pdb=" C2 NAG B 601 " pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " pdb=" C5 NAG B 601 " ideal model delta sinusoidal sigma weight residual -50.00 29.03 -79.03 1 2.00e+01 2.50e-03 1.94e+01 ... (remaining 1308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 193 0.039 - 0.078: 83 0.078 - 0.117: 40 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 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. 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: 1.250 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: 6.890 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 11.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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= 0.816 Angle : 1.101 24.653 3018 Z= 0.636 Chirality : 0.057 0.194 331 Planarity : 0.010 0.134 393 Dihedral : 18.153 103.662 802 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 % 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 *********************** 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 : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1178 time to fit residues: 3.2384 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.259 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3427 ------------------------------------------------------------------------------- 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: 0.9980 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: 8.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.7246 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 2219 Z= 0.248 Angle : 0.668 6.693 3018 Z= 0.350 Chirality : 0.048 0.153 331 Planarity : 0.007 0.058 393 Dihedral : 10.804 109.394 307 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer Outliers : 3.40 % 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: -3.48 (0.47), residues: 265 helix: -4.26 (0.52), residues: 25 sheet: -0.88 (0.67), residues: 50 loop : -2.64 (0.43), residues: 190 *********************** 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 : 0.265 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 24 average time/residue: 0.0824 time to fit residues: 2.8354 Evaluate side-chains 21 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 15 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0243 time to fit residues: 0.5950 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 0.0670 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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: 0.7287 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 2219 Z= 0.221 Angle : 0.636 5.526 3018 Z= 0.333 Chirality : 0.047 0.142 331 Planarity : 0.006 0.056 393 Dihedral : 10.762 109.318 307 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.23 % Favored : 83.02 % Rotamer Outliers : 4.68 % 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: -3.36 (0.47), residues: 265 helix: -4.19 (0.69), residues: 26 sheet: -0.46 (0.75), residues: 38 loop : -2.53 (0.41), residues: 201 *********************** 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 25 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 14 time to evaluate : 0.227 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 25 average time/residue: 0.0786 time to fit residues: 2.7885 Evaluate side-chains 18 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 13 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0263 time to fit residues: 0.5736 ------------------------------------------------------------------------------- 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: 3.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7222 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 2219 Z= 0.174 Angle : 0.619 7.132 3018 Z= 0.320 Chirality : 0.046 0.144 331 Planarity : 0.006 0.056 393 Dihedral : 10.532 108.708 307 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.85 % Favored : 83.40 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.48), residues: 265 helix: -4.76 (0.51), residues: 18 sheet: -0.45 (0.71), residues: 48 loop : -2.45 (0.42), residues: 199 *********************** 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 22 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 18 time to evaluate : 0.261 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 21 average time/residue: 0.0778 time to fit residues: 2.4090 Evaluate side-chains 17 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0249 time to fit residues: 0.4250 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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: 0.7337 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 2219 Z= 0.295 Angle : 0.698 6.979 3018 Z= 0.364 Chirality : 0.049 0.167 331 Planarity : 0.006 0.053 393 Dihedral : 11.025 109.792 307 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.75 % Allowed : 17.74 % Favored : 81.51 % Rotamer Outliers : 2.98 % 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: -3.33 (0.48), residues: 265 helix: -4.48 (0.54), residues: 26 sheet: -0.65 (0.76), residues: 48 loop : -2.49 (0.43), residues: 191 *********************** 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: 7 poor density : 17 time to evaluate : 0.253 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 24 average time/residue: 0.1134 time to fit residues: 3.5592 Evaluate side-chains 19 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 13 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0925 time to fit residues: 1.0040 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 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: 0.7249 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 2219 Z= 0.196 Angle : 0.654 6.156 3018 Z= 0.341 Chirality : 0.048 0.171 331 Planarity : 0.005 0.055 393 Dihedral : 10.586 108.704 307 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.47 % Favored : 83.77 % Rotamer Outliers : 2.98 % 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: -3.30 (0.48), residues: 265 helix: -4.80 (0.39), residues: 18 sheet: -0.81 (0.71), residues: 49 loop : -2.51 (0.42), residues: 198 *********************** 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 27 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 20 time to evaluate : 0.279 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 27 average time/residue: 0.0741 time to fit residues: 2.9279 Evaluate side-chains 17 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 15 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0259 time to fit residues: 0.4448 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.7254 moved from start: 0.3433 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= 0.198 Angle : 0.653 6.701 3018 Z= 0.340 Chirality : 0.049 0.157 331 Planarity : 0.005 0.055 393 Dihedral : 10.568 108.844 307 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.60 % Favored : 82.64 % Rotamer Outliers : 2.13 % 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: -3.43 (0.48), residues: 265 helix: -4.53 (0.49), residues: 31 sheet: -0.75 (0.71), residues: 49 loop : -2.47 (0.44), residues: 185 *********************** 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 23 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 18 time to evaluate : 0.268 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 23 average time/residue: 0.0779 time to fit residues: 2.6129 Evaluate side-chains 18 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 16 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0253 time to fit residues: 0.4394 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7221 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 2219 Z= 0.201 Angle : 0.659 7.462 3018 Z= 0.340 Chirality : 0.048 0.155 331 Planarity : 0.005 0.055 393 Dihedral : 10.451 108.533 307 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.85 % Favored : 83.40 % Rotamer Outliers : 0.43 % 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: -3.20 (0.48), residues: 265 helix: -5.10 (0.24), residues: 18 sheet: -0.69 (0.71), residues: 49 loop : -2.40 (0.43), residues: 198 *********************** 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 20 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.261 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.1006 time to fit residues: 2.7798 Evaluate side-chains 16 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.260 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.0770 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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: 0.7221 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 2219 Z= 0.199 Angle : 0.684 8.121 3018 Z= 0.349 Chirality : 0.048 0.153 331 Planarity : 0.005 0.057 393 Dihedral : 10.420 108.530 307 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.75 % Allowed : 15.09 % Favored : 84.15 % Rotamer Outliers : 0.00 % 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: -3.27 (0.48), residues: 265 helix: -4.87 (0.38), residues: 24 sheet: -0.56 (0.71), residues: 49 loop : -2.43 (0.44), residues: 192 *********************** 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 16 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0858 time to fit residues: 2.0736 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.261 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3488 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 23 optimal weight: 0.0470 chunk 13 optimal weight: 7.9990 overall best weight: 3.2084 ------------------------------------------------------------------------------- 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: 0.7309 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 2219 Z= 0.290 Angle : 0.740 7.657 3018 Z= 0.383 Chirality : 0.052 0.160 331 Planarity : 0.006 0.052 393 Dihedral : 10.888 109.468 307 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.98 % Favored : 82.26 % Rotamer Outliers : 0.43 % 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: -3.54 (0.48), residues: 265 helix: -4.75 (0.40), residues: 31 sheet: -0.69 (0.72), residues: 47 loop : -2.55 (0.44), residues: 187 ********************** 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 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.269 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.0796 time to fit residues: 1.8652 Evaluate side-chains 15 residues out of total 235 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0244 time to fit residues: 0.3902 ------------------------------------------------------------------------------- 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: 9.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.075800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064853 restraints weight = 10097.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.066081 restraints weight = 6245.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.066988 restraints weight = 4477.943| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 2219 Z= 0.273 Angle : 0.736 8.076 3018 Z= 0.379 Chirality : 0.051 0.156 331 Planarity : 0.006 0.050 393 Dihedral : 10.887 109.539 307 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.75 % Allowed : 16.60 % Favored : 82.64 % Rotamer Outliers : 0.43 % 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: -3.64 (0.47), residues: 265 helix: -4.75 (0.38), residues: 31 sheet: -0.82 (0.71), residues: 47 loop : -2.62 (0.44), residues: 187 =============================================================================== Job complete usr+sys time: 894.67 seconds wall clock time: 16 minutes 41.44 seconds (1001.44 seconds total)