Starting phenix.real_space_refine on Tue Feb 13 15:30:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2024/7x8w_33059_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2024/7x8w_33059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2024/7x8w_33059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2024/7x8w_33059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2024/7x8w_33059_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x8w_33059/02_2024/7x8w_33059_trim.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2186 2.51 5 N 574 2.21 5 O 682 1.98 5 H 3214 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 28": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6674 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 3065 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 11, 'TRANS': 186} Chain: "H" Number of atoms: 1883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1883 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 1627 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "B" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 3.87, per 1000 atoms: 0.58 Number of scatterers: 6674 At special positions: 0 Unit cell: (94.506, 63.004, 99.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 O 682 8.00 N 574 7.00 C 2186 6.00 H 3214 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " NAG C 1 " - " FUC C 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG B 1 " - " ASN A 343 " " NAG C 1 " - " ASN H 59 " Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 770.2 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.1% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.329A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.694A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.059A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.044A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.906A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.871A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.697A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.697A pdb=" N ALA L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 18 through 23 109 hydrogen bonds defined for protein. 258 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: 2.25 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3214 1.04 - 1.23: 82 1.23 - 1.43: 1488 1.43 - 1.62: 1954 1.62 - 1.82: 24 Bond restraints: 6762 Sorted by residual: bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 MAN C 5 " pdb=" C2 MAN C 5 " ideal model delta sigma weight residual 1.526 1.562 -0.036 2.00e-02 2.50e+03 3.33e+00 bond pdb=" N GLN L 1 " pdb=" CA GLN L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 bond pdb=" N GLN L 1 " pdb=" H GLN L 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.81: 121 106.81 - 113.60: 7661 113.60 - 120.40: 2248 120.40 - 127.19: 2010 127.19 - 133.99: 40 Bond angle restraints: 12080 Sorted by residual: angle pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" O2 BMA C 3 " ideal model delta sigma weight residual 112.95 106.35 6.60 3.00e+00 1.11e-01 4.85e+00 angle pdb=" C3 MAN C 5 " pdb=" C2 MAN C 5 " pdb=" O2 MAN C 5 " ideal model delta sigma weight residual 111.77 105.37 6.40 3.00e+00 1.11e-01 4.55e+00 angle pdb=" C3 MAN C 4 " pdb=" C2 MAN C 4 " pdb=" O2 MAN C 4 " ideal model delta sigma weight residual 111.77 105.65 6.12 3.00e+00 1.11e-01 4.16e+00 angle pdb=" C4 FUC C 6 " pdb=" C3 FUC C 6 " pdb=" O3 FUC C 6 " ideal model delta sigma weight residual 113.24 107.38 5.86 3.00e+00 1.11e-01 3.82e+00 angle pdb=" C1 BMA C 3 " pdb=" O5 BMA C 3 " pdb=" C5 BMA C 3 " ideal model delta sigma weight residual 118.82 113.51 5.31 3.00e+00 1.11e-01 3.14e+00 ... (remaining 12075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 3140 21.68 - 43.35: 166 43.35 - 65.03: 54 65.03 - 86.71: 16 86.71 - 108.39: 5 Dihedral angle restraints: 3381 sinusoidal: 1856 harmonic: 1525 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.68 108.39 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.69 106.31 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" C6 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O4 BMA C 3 " ideal model delta sinusoidal sigma weight residual -163.34 -60.53 -102.81 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 3378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 459 0.055 - 0.110: 68 0.110 - 0.164: 12 0.164 - 0.219: 0 0.219 - 0.273: 2 Chirality restraints: 541 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN H 59 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 538 not shown) Planarity restraints: 1023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 106 " -0.128 9.50e-02 1.11e+02 4.30e-02 2.23e+00 pdb=" NE ARG H 106 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG H 106 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG H 106 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG H 106 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG H 106 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG H 106 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 521 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " -0.004 2.00e-02 2.50e+03 7.44e-03 5.54e-01 pdb=" C PHE A 400 " 0.013 2.00e-02 2.50e+03 pdb=" O PHE A 400 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL A 401 " -0.004 2.00e-02 2.50e+03 ... (remaining 1020 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 616 2.22 - 2.81: 13564 2.81 - 3.41: 16199 3.41 - 4.00: 23473 4.00 - 4.60: 35091 Nonbonded interactions: 88943 Sorted by model distance: nonbonded pdb=" O GLY H 31 " pdb=" H SER H 103 " model vdw 1.624 1.850 nonbonded pdb=" O THR A 345 " pdb="HH22 ARG A 509 " model vdw 1.651 1.850 nonbonded pdb=" OD1 ASN A 360 " pdb=" HG1 THR A 523 " model vdw 1.655 1.850 nonbonded pdb="HH21 ARG A 454 " pdb=" O ASP A 467 " model vdw 1.674 1.850 nonbonded pdb="HH11 ARG A 457 " pdb=" O SER A 459 " model vdw 1.704 1.850 ... (remaining 88938 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: 0.220 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: 0.100 Extract box with map and model: 1.210 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.650 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 0.041 3548 Z= 0.264 Angle : 0.601 6.605 4825 Z= 0.280 Chirality : 0.045 0.273 541 Planarity : 0.004 0.056 611 Dihedral : 16.079 108.387 1376 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.40), residues: 429 helix: -3.61 (0.73), residues: 27 sheet: 0.25 (0.44), residues: 146 loop : -1.32 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 36 HIS 0.001 0.001 HIS L 41 PHE 0.009 0.001 PHE A 347 TYR 0.008 0.001 TYR L 51 ARG 0.008 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.4712 time to fit residues: 37.4783 Evaluate side-chains 58 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.0000 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3548 Z= 0.161 Angle : 0.507 5.574 4825 Z= 0.248 Chirality : 0.042 0.148 541 Planarity : 0.003 0.036 611 Dihedral : 10.040 68.685 637 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.27 % Allowed : 6.03 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.40), residues: 429 helix: -3.81 (0.68), residues: 32 sheet: 0.49 (0.45), residues: 136 loop : -1.27 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.001 HIS L 41 PHE 0.005 0.001 PHE L 101 TYR 0.009 0.001 TYR A 369 ARG 0.006 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 60 average time/residue: 0.4579 time to fit residues: 31.9553 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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: 0.8404 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3548 Z= 0.131 Angle : 0.486 6.184 4825 Z= 0.237 Chirality : 0.041 0.182 541 Planarity : 0.003 0.043 611 Dihedral : 8.858 56.669 637 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.43 % Favored : 95.34 % Rotamer: Outliers : 0.27 % Allowed : 7.67 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.40), residues: 429 helix: -3.78 (0.69), residues: 32 sheet: 0.48 (0.45), residues: 142 loop : -1.21 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.001 0.001 HIS L 41 PHE 0.005 0.001 PHE L 101 TYR 0.010 0.001 TYR A 369 ARG 0.005 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7480 (t0) cc_final: 0.7230 (t0) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.4745 time to fit residues: 33.4633 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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: 0.8421 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3548 Z= 0.203 Angle : 0.492 6.420 4825 Z= 0.240 Chirality : 0.042 0.212 541 Planarity : 0.003 0.041 611 Dihedral : 7.958 58.189 637 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.36 % Favored : 94.41 % Rotamer: Outliers : 0.27 % Allowed : 8.77 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.41), residues: 429 helix: -3.75 (0.71), residues: 32 sheet: 0.48 (0.45), residues: 142 loop : -1.23 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 50 HIS 0.001 0.001 HIS L 41 PHE 0.006 0.001 PHE A 347 TYR 0.009 0.001 TYR A 369 ARG 0.007 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7532 (t0) cc_final: 0.7239 (t0) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.4629 time to fit residues: 32.7713 Evaluate side-chains 59 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8402 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3548 Z= 0.121 Angle : 0.473 6.322 4825 Z= 0.231 Chirality : 0.042 0.205 541 Planarity : 0.003 0.046 611 Dihedral : 7.383 57.856 637 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.27 % Allowed : 9.32 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.41), residues: 429 helix: -3.75 (0.70), residues: 32 sheet: 0.54 (0.45), residues: 142 loop : -1.14 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.001 0.000 HIS L 41 PHE 0.005 0.000 PHE L 101 TYR 0.009 0.001 TYR A 369 ARG 0.005 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 73 ASP cc_start: 0.7534 (t0) cc_final: 0.7308 (t0) REVERT: L 89 TYR cc_start: 0.8799 (m-80) cc_final: 0.8509 (m-80) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.4574 time to fit residues: 33.0175 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3548 Z= 0.193 Angle : 0.481 5.878 4825 Z= 0.235 Chirality : 0.041 0.197 541 Planarity : 0.003 0.048 611 Dihedral : 7.136 59.183 637 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.36 % Favored : 94.41 % Rotamer: Outliers : 0.55 % Allowed : 10.96 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.41), residues: 429 helix: -3.70 (0.72), residues: 32 sheet: 0.50 (0.45), residues: 142 loop : -1.17 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.001 0.001 HIS L 41 PHE 0.006 0.001 PHE A 347 TYR 0.009 0.001 TYR A 369 ARG 0.005 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8897 (OUTLIER) cc_final: 0.7898 (m-10) REVERT: H 73 ASP cc_start: 0.7592 (t0) cc_final: 0.7279 (t0) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.4456 time to fit residues: 31.1212 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8402 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3548 Z= 0.132 Angle : 0.468 5.203 4825 Z= 0.230 Chirality : 0.041 0.175 541 Planarity : 0.003 0.052 611 Dihedral : 6.856 59.222 637 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.96 % Favored : 95.80 % Rotamer: Outliers : 0.55 % Allowed : 11.23 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.41), residues: 429 helix: -3.67 (0.72), residues: 32 sheet: 0.57 (0.45), residues: 142 loop : -1.09 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS L 41 PHE 0.005 0.001 PHE A 338 TYR 0.009 0.001 TYR A 369 ARG 0.006 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: L 89 TYR cc_start: 0.8821 (m-80) cc_final: 0.8573 (m-80) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 0.4841 time to fit residues: 34.1230 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8398 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3548 Z= 0.132 Angle : 0.460 4.679 4825 Z= 0.227 Chirality : 0.041 0.154 541 Planarity : 0.003 0.054 611 Dihedral : 6.665 59.895 637 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.43 % Favored : 95.34 % Rotamer: Outliers : 0.82 % Allowed : 10.96 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.41), residues: 429 helix: -3.67 (0.72), residues: 32 sheet: 0.60 (0.45), residues: 142 loop : -1.10 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS H 35 PHE 0.005 0.001 PHE L 101 TYR 0.009 0.001 TYR A 369 ARG 0.009 0.001 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: H 73 ASP cc_start: 0.7507 (t0) cc_final: 0.7259 (t0) outliers start: 3 outliers final: 1 residues processed: 59 average time/residue: 0.4691 time to fit residues: 32.4803 Evaluate side-chains 60 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.0040 chunk 25 optimal weight: 0.2980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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: 0.8387 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3548 Z= 0.118 Angle : 0.460 4.337 4825 Z= 0.229 Chirality : 0.041 0.151 541 Planarity : 0.003 0.056 611 Dihedral : 6.558 59.945 637 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.26 % Favored : 96.50 % Rotamer: Outliers : 1.10 % Allowed : 11.23 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.41), residues: 429 helix: -3.64 (0.73), residues: 32 sheet: 0.60 (0.45), residues: 142 loop : -1.08 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS L 41 PHE 0.005 0.000 PHE A 338 TYR 0.009 0.001 TYR A 369 ARG 0.008 0.000 ARG H 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8109 (m-80) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 0.4626 time to fit residues: 32.3622 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3548 Z= 0.131 Angle : 0.463 4.409 4825 Z= 0.229 Chirality : 0.041 0.153 541 Planarity : 0.004 0.058 611 Dihedral : 6.510 59.926 637 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.96 % Favored : 95.80 % Rotamer: Outliers : 0.82 % Allowed : 12.60 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.41), residues: 429 helix: -3.66 (0.72), residues: 32 sheet: 0.60 (0.45), residues: 142 loop : -1.05 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS H 35 PHE 0.004 0.000 PHE L 101 TYR 0.009 0.001 TYR A 369 ARG 0.009 0.001 ARG H 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8125 (m-80) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.4653 time to fit residues: 31.9302 Evaluate side-chains 62 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain H residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071370 restraints weight = 18200.069| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.40 r_work: 0.2788 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3548 Z= 0.129 Angle : 0.462 3.745 4825 Z= 0.230 Chirality : 0.041 0.152 541 Planarity : 0.004 0.065 611 Dihedral : 6.447 59.801 637 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.82 % Allowed : 12.88 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.41), residues: 429 helix: -3.63 (0.73), residues: 32 sheet: 0.63 (0.45), residues: 142 loop : -1.04 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.000 HIS H 35 PHE 0.004 0.000 PHE A 338 TYR 0.009 0.001 TYR A 369 ARG 0.009 0.001 ARG H 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.14 seconds wall clock time: 47 minutes 38.87 seconds (2858.87 seconds total)