Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 00:22:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/04_2023/7wrz_32738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/04_2023/7wrz_32738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/04_2023/7wrz_32738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/04_2023/7wrz_32738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/04_2023/7wrz_32738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/04_2023/7wrz_32738.pdb" } resolution = 3.26 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= 0.001 sd= 0.055 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 14 5.16 5 C 2077 2.51 5 N 553 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 406": "OE1" <-> "OE2" Residue "R ASP 427": "OD1" <-> "OD2" Residue "R ASP 428": "OD1" <-> "OD2" Residue "R ASP 442": "OD1" <-> "OD2" Residue "R TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.31, per 1000 atoms: 0.71 Number of scatterers: 3270 At special positions: 0 Unit cell: (84.24, 64.8, 71.28, 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 14 16.00 O 626 8.00 N 553 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 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 BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 481.1 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 12.8% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.795A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.506A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.567A pdb=" N TYR R 369 " --> pdb=" O TYR R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 390 removed outlier: 3.550A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.622A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS H 96 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.539A pdb=" N ILE H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.596A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.343A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 356 through 358 Processing sheet with id=AA7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'R' and resid 473 through 474 103 hydrogen bonds defined for protein. 243 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: 0.87 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 834 1.46 - 1.57: 1460 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3355 Sorted by residual: bond pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" N ILE R 410 " pdb=" CA ILE R 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 3350 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.11: 76 106.11 - 113.07: 1714 113.07 - 120.04: 1168 120.04 - 127.01: 1564 127.01 - 133.97: 37 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta sigma weight residual 121.72 132.63 -10.91 1.54e+00 4.22e-01 5.02e+01 angle pdb=" C VAL R 382 " pdb=" N SER R 383 " pdb=" CA SER R 383 " ideal model delta sigma weight residual 120.49 114.45 6.04 1.42e+00 4.96e-01 1.81e+01 angle pdb=" N PHE R 374 " pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 110.79 114.90 -4.11 1.63e+00 3.76e-01 6.35e+00 angle pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " pdb=" CG PHE R 374 " ideal model delta sigma weight residual 113.80 116.26 -2.46 1.00e+00 1.00e+00 6.06e+00 angle pdb=" N TRP L 96 " pdb=" CA TRP L 96 " pdb=" C TRP L 96 " ideal model delta sigma weight residual 109.81 114.95 -5.14 2.21e+00 2.05e-01 5.42e+00 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1738 15.87 - 31.74: 164 31.74 - 47.61: 31 47.61 - 63.48: 9 63.48 - 79.34: 6 Dihedral angle restraints: 1948 sinusoidal: 752 harmonic: 1196 Sorted by residual: dihedral pdb=" CA TRP L 96 " pdb=" C TRP L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 134.00 46.00 0 5.00e+00 4.00e-02 8.47e+01 dihedral pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASP H 104 " pdb=" C ASP H 104 " pdb=" N TYR H 105 " pdb=" CA TYR H 105 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 310 0.034 - 0.067: 124 0.067 - 0.101: 36 0.101 - 0.134: 21 0.134 - 0.168: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 96 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO L 97 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 41 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO L 42 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO L 46 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.018 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 243 2.74 - 3.28: 3077 3.28 - 3.82: 5219 3.82 - 4.36: 6717 4.36 - 4.90: 11797 Nonbonded interactions: 27053 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.201 2.440 nonbonded pdb=" NH1 ARG L 56 " pdb=" O ILE L 60 " model vdw 2.301 2.520 nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR R 369 " pdb=" O PRO R 384 " model vdw 2.314 2.440 nonbonded pdb=" O ASP R 442 " pdb=" ND2 ASN R 448 " model vdw 2.367 2.520 ... (remaining 27048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 9.820 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.920 Find NCS groups from input model: 0.090 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.004 0.029 3355 Z= 0.229 Angle : 0.618 10.910 4559 Z= 0.356 Chirality : 0.044 0.168 492 Planarity : 0.005 0.066 587 Dihedral : 13.698 79.345 1170 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.40), residues: 406 helix: -3.69 (0.60), residues: 27 sheet: -0.30 (0.41), residues: 152 loop : -0.47 (0.41), residues: 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2218 time to fit residues: 18.7963 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3355 Z= 0.243 Angle : 0.544 5.871 4559 Z= 0.288 Chirality : 0.044 0.152 492 Planarity : 0.005 0.066 587 Dihedral : 4.930 44.764 460 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.39), residues: 406 helix: -3.38 (0.63), residues: 33 sheet: -0.36 (0.39), residues: 154 loop : -0.59 (0.41), residues: 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.2123 time to fit residues: 15.3229 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0331 time to fit residues: 0.7542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3355 Z= 0.232 Angle : 0.520 5.961 4559 Z= 0.271 Chirality : 0.044 0.147 492 Planarity : 0.005 0.068 587 Dihedral : 4.937 44.740 460 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.40), residues: 406 helix: -3.46 (0.59), residues: 33 sheet: -0.42 (0.39), residues: 153 loop : -0.50 (0.41), residues: 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.387 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.2469 time to fit residues: 18.5819 Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.492 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0313 time to fit residues: 0.7402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 21 optimal weight: 0.0870 chunk 0 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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: 0.8244 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3355 Z= 0.239 Angle : 0.523 6.001 4559 Z= 0.270 Chirality : 0.044 0.143 492 Planarity : 0.005 0.068 587 Dihedral : 4.886 44.127 460 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.40), residues: 406 helix: -3.55 (0.57), residues: 33 sheet: -0.45 (0.40), residues: 153 loop : -0.50 (0.42), residues: 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.397 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 65 average time/residue: 0.2690 time to fit residues: 19.9679 Evaluate side-chains 65 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0357 time to fit residues: 0.8007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3355 Z= 0.247 Angle : 0.521 6.200 4559 Z= 0.270 Chirality : 0.044 0.179 492 Planarity : 0.005 0.068 587 Dihedral : 4.912 44.148 460 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.40), residues: 406 helix: -3.53 (0.59), residues: 33 sheet: -0.37 (0.40), residues: 152 loop : -0.50 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.405 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.2387 time to fit residues: 19.2556 Evaluate side-chains 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0358 time to fit residues: 0.7160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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: 0.8242 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3355 Z= 0.224 Angle : 0.533 9.180 4559 Z= 0.272 Chirality : 0.044 0.153 492 Planarity : 0.005 0.068 587 Dihedral : 4.878 43.984 460 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.09 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.41), residues: 406 helix: -3.46 (0.61), residues: 33 sheet: -0.33 (0.41), residues: 152 loop : -0.45 (0.42), residues: 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 64 time to evaluate : 0.404 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 0.2285 time to fit residues: 17.7051 Evaluate side-chains 63 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0484 time to fit residues: 0.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 3355 Z= 0.294 Angle : 0.566 10.931 4559 Z= 0.287 Chirality : 0.045 0.146 492 Planarity : 0.005 0.068 587 Dihedral : 4.987 44.652 460 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.40), residues: 406 helix: -3.47 (0.59), residues: 33 sheet: -0.22 (0.41), residues: 149 loop : -0.57 (0.42), residues: 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.402 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.2445 time to fit residues: 17.7862 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0350 time to fit residues: 0.7125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 3355 Z= 0.217 Angle : 0.518 7.178 4559 Z= 0.269 Chirality : 0.044 0.151 492 Planarity : 0.005 0.068 587 Dihedral : 4.876 44.161 460 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.41), residues: 406 helix: -3.68 (0.68), residues: 27 sheet: -0.34 (0.41), residues: 152 loop : -0.30 (0.42), residues: 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.406 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.2313 time to fit residues: 17.0567 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0365 time to fit residues: 0.6689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 0.0870 chunk 22 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.8215 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3355 Z= 0.183 Angle : 0.499 6.023 4559 Z= 0.259 Chirality : 0.043 0.155 492 Planarity : 0.005 0.068 587 Dihedral : 4.762 43.984 460 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.42), residues: 406 helix: -3.62 (0.69), residues: 27 sheet: -0.27 (0.42), residues: 152 loop : -0.24 (0.42), residues: 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 67 average time/residue: 0.2142 time to fit residues: 16.7572 Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0628 time to fit residues: 0.6331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8240 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 3355 Z= 0.252 Angle : 0.527 6.446 4559 Z= 0.273 Chirality : 0.044 0.159 492 Planarity : 0.005 0.068 587 Dihedral : 4.833 44.673 460 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.42), residues: 406 helix: -3.63 (0.71), residues: 27 sheet: -0.27 (0.42), residues: 152 loop : -0.28 (0.42), residues: 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.411 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.2158 time to fit residues: 15.5344 Evaluate side-chains 60 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0339 time to fit residues: 0.6095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.0370 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.0570 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 354 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.091419 restraints weight = 4577.125| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.74 r_work: 0.2822 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3355 Z= 0.189 Angle : 0.506 6.670 4559 Z= 0.261 Chirality : 0.043 0.157 492 Planarity : 0.005 0.068 587 Dihedral : 4.733 44.041 460 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.42), residues: 406 helix: -3.59 (0.70), residues: 27 sheet: -0.22 (0.43), residues: 152 loop : -0.23 (0.42), residues: 227 =============================================================================== Job complete usr+sys time: 1359.40 seconds wall clock time: 25 minutes 10.11 seconds (1510.11 seconds total)