Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:24:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/11_2022/7wrz_32738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/11_2022/7wrz_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_32738/11_2022/7wrz_32738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/11_2022/7wrz_32738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/11_2022/7wrz_32738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrz_32738/11_2022/7wrz_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 Convert atoms to be neutral 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-dev-4778/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: 2.40, per 1000 atoms: 0.73 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: 1.36 Conformation dependent library (CDL) restraints added in 487.0 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: 0.22 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: 0.83 Time building geometry restraints manager: 1.44 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=" 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=" C ALA R 372 " pdb=" N PRO R 373 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.94e-01 bond pdb=" CB TRP L 96 " pdb=" CG TRP L 96 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.75e-01 bond pdb=" CB MET L 4 " pdb=" CG MET L 4 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.84e-01 ... (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: 1750 15.87 - 31.74: 164 31.74 - 47.61: 31 47.61 - 63.48: 9 63.48 - 79.34: 6 Dihedral angle restraints: 1960 sinusoidal: 764 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 1957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 314 0.034 - 0.067: 122 0.067 - 0.101: 34 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 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. 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.670 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 14.500 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.003 0.029 3355 Z= 0.217 Angle : 0.606 10.910 4559 Z= 0.354 Chirality : 0.043 0.168 492 Planarity : 0.005 0.066 587 Dihedral : 13.652 79.345 1182 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.05 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 : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1999 time to fit residues: 17.2539 Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5232 ------------------------------------------------------------------------------- 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: 0.0980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 35 optimal weight: 2.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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: 0.8449 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3355 Z= 0.165 Angle : 0.511 5.837 4559 Z= 0.272 Chirality : 0.044 0.169 492 Planarity : 0.005 0.065 587 Dihedral : 4.900 43.752 472 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % 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: -1.14 (0.40), residues: 406 helix: -3.40 (0.62), residues: 33 sheet: -0.30 (0.40), residues: 154 loop : -0.56 (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 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 65 average time/residue: 0.2037 time to fit residues: 15.6335 Evaluate side-chains 66 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0345 time to fit residues: 0.7595 ------------------------------------------------------------------------------- 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: 0.4980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3355 Z= 0.183 Angle : 0.493 5.803 4559 Z= 0.260 Chirality : 0.043 0.158 492 Planarity : 0.005 0.068 587 Dihedral : 4.887 44.710 472 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % 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: -1.08 (0.40), residues: 406 helix: -3.39 (0.61), residues: 33 sheet: -0.32 (0.40), residues: 153 loop : -0.46 (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 65 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.367 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 63 average time/residue: 0.2077 time to fit residues: 15.5260 Evaluate side-chains 60 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0344 time to fit residues: 0.5713 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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: 0.8512 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 3355 Z= 0.292 Angle : 0.541 5.839 4559 Z= 0.281 Chirality : 0.045 0.186 492 Planarity : 0.005 0.068 587 Dihedral : 5.054 45.388 472 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.16 % Favored : 93.60 % Rotamer Outliers : 1.72 % 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: -1.14 (0.40), residues: 406 helix: -3.55 (0.57), residues: 33 sheet: -0.40 (0.40), residues: 152 loop : -0.45 (0.42), residues: 221 *********************** 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 72 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.383 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.2377 time to fit residues: 18.5387 Evaluate side-chains 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0334 time to fit residues: 0.8130 ------------------------------------------------------------------------------- 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: 0.0770 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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: 0.8489 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3355 Z= 0.208 Angle : 0.525 8.736 4559 Z= 0.269 Chirality : 0.044 0.151 492 Planarity : 0.005 0.068 587 Dihedral : 4.958 43.817 472 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.43 % Favored : 95.32 % 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: -1.10 (0.41), residues: 406 helix: -3.43 (0.61), residues: 33 sheet: -0.34 (0.40), residues: 152 loop : -0.46 (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 75 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.392 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 0.2141 time to fit residues: 18.0770 Evaluate side-chains 70 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0636 time to fit residues: 0.6009 ------------------------------------------------------------------------------- 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: 0.0040 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 overall best weight: 0.3602 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.1902 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= 0.169 Angle : 0.506 8.628 4559 Z= 0.261 Chirality : 0.043 0.153 492 Planarity : 0.005 0.068 587 Dihedral : 4.841 43.321 472 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % 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: -0.76 (0.42), residues: 406 helix: -3.61 (0.69), residues: 27 sheet: -0.07 (0.42), residues: 149 loop : -0.30 (0.42), residues: 230 *********************** 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 75 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.436 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 73 average time/residue: 0.2187 time to fit residues: 19.0846 Evaluate side-chains 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0427 time to fit residues: 0.7382 ------------------------------------------------------------------------------- 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: 0.6980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3355 Z= 0.263 Angle : 0.537 6.978 4559 Z= 0.278 Chirality : 0.044 0.142 492 Planarity : 0.005 0.068 587 Dihedral : 4.974 44.782 472 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.65 % Favored : 93.10 % Rotamer Outliers : 1.72 % 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: -3.64 (0.68), residues: 27 sheet: -0.21 (0.42), residues: 152 loop : -0.29 (0.42), residues: 227 *********************** 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 69 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.396 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.2192 time to fit residues: 16.6634 Evaluate side-chains 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0343 time to fit residues: 0.7665 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8512 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 3355 Z= 0.278 Angle : 0.545 7.004 4559 Z= 0.282 Chirality : 0.045 0.160 492 Planarity : 0.005 0.068 587 Dihedral : 5.027 45.009 472 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.65 % Favored : 93.10 % Rotamer Outliers : 1.72 % 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: -0.85 (0.42), residues: 406 helix: -3.71 (0.64), residues: 27 sheet: -0.24 (0.42), residues: 152 loop : -0.27 (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 69 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.398 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.2090 time to fit residues: 16.0193 Evaluate side-chains 65 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0434 time to fit residues: 0.8084 ------------------------------------------------------------------------------- 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: 0.4980 chunk 34 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 3355 Z= 0.243 Angle : 0.526 6.542 4559 Z= 0.273 Chirality : 0.044 0.168 492 Planarity : 0.005 0.068 587 Dihedral : 4.982 44.625 472 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % 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: -3.64 (0.67), residues: 27 sheet: -0.28 (0.42), residues: 152 loop : -0.27 (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 66 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 65 average time/residue: 0.2077 time to fit residues: 15.8616 Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0389 time to fit residues: 0.6014 ------------------------------------------------------------------------------- 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: 0.0980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3355 Z= 0.214 Angle : 0.516 6.525 4559 Z= 0.268 Chirality : 0.044 0.156 492 Planarity : 0.005 0.068 587 Dihedral : 4.925 44.375 472 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % 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: -3.53 (0.72), residues: 27 sheet: -0.23 (0.43), residues: 152 loop : -0.23 (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 63 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.354 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2043 time to fit residues: 15.1463 Evaluate side-chains 63 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5307 ------------------------------------------------------------------------------- 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: 0.7980 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 22 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.0070 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.108529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.091789 restraints weight = 4575.413| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.81 r_work: 0.2940 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 1.61 restraints_weight: 0.2500 r_work: 0.2918 rms_B_bonded: 1.65 restraints_weight: 0.1250 r_work: 0.2907 rms_B_bonded: 1.73 restraints_weight: 0.0625 r_work: 0.2894 rms_B_bonded: 1.84 restraints_weight: 0.0312 r_work: 0.2881 rms_B_bonded: 1.98 restraints_weight: 0.0156 r_work: 0.2866 rms_B_bonded: 2.15 restraints_weight: 0.0078 r_work: 0.2850 rms_B_bonded: 2.35 restraints_weight: 0.0039 r_work: 0.2833 rms_B_bonded: 2.59 restraints_weight: 0.0020 r_work: 0.2815 rms_B_bonded: 2.86 restraints_weight: 0.0010 r_work: 0.2794 rms_B_bonded: 3.18 restraints_weight: 0.0005 r_work: 0.2772 rms_B_bonded: 3.54 restraints_weight: 0.0002 r_work: 0.2746 rms_B_bonded: 3.96 restraints_weight: 0.0001 r_work: 0.2719 rms_B_bonded: 4.45 restraints_weight: 0.0001 r_work: 0.2688 rms_B_bonded: 5.00 restraints_weight: 0.0000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 3355 Z= 0.152 Angle : 0.500 8.871 4559 Z= 0.256 Chirality : 0.043 0.147 492 Planarity : 0.005 0.068 587 Dihedral : 4.726 43.010 472 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % 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: -0.79 (0.42), residues: 406 helix: -4.11 (0.64), residues: 21 sheet: -0.10 (0.43), residues: 150 loop : -0.37 (0.41), residues: 235 =============================================================================== Job complete usr+sys time: 1304.09 seconds wall clock time: 24 minutes 24.11 seconds (1464.11 seconds total)