Starting phenix.real_space_refine on Sun Mar 10 16:18:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wry_32737/03_2024/7wry_32737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wry_32737/03_2024/7wry_32737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wry_32737/03_2024/7wry_32737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wry_32737/03_2024/7wry_32737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wry_32737/03_2024/7wry_32737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wry_32737/03_2024/7wry_32737.pdb" } resolution = 3.28 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2078 2.51 5 N 549 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 357": "NH1" <-> "NH2" Residue "R ASP 364": "OD1" <-> "OD2" Residue "R TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 13": "NH1" <-> "NH2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 105": "NH1" <-> "NH2" Residue "H ASP 108": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3267 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1496 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 930 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.35, per 1000 atoms: 0.72 Number of scatterers: 3267 At special positions: 0 Unit cell: (76.68, 81, 73.44, 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 549 7.00 C 2078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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=2.06 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 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 584.6 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'R' and resid 337 through 341 removed outlier: 3.706A pdb=" N GLU R 340 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 Processing helix chain 'R' and resid 405 through 410 removed outlier: 5.153A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 removed outlier: 3.787A pdb=" N TYR R 421 " --> pdb=" O LYS R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.910A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.677A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.541A pdb=" N ASP H 90 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR H 91 " --> pdb=" O ILE H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'R' and resid 356 through 358 removed outlier: 3.636A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 361 through 362 removed outlier: 6.702A pdb=" N CYS R 361 " --> pdb=" O CYS R 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.540A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.273A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.685A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.628A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.948A pdb=" N ALA H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.948A pdb=" N ALA H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 201 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: 0.80 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 1042 1.36 - 1.49: 972 1.49 - 1.62: 1320 1.62 - 1.75: 0 1.75 - 1.88: 16 Bond restraints: 3350 Sorted by residual: bond pdb=" C LYS R 478 " pdb=" N PRO R 479 " ideal model delta sigma weight residual 1.332 1.360 -0.029 1.26e-02 6.30e+03 5.21e+00 bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.882 -0.074 3.30e-02 9.18e+02 5.05e+00 bond pdb=" N ASN R 487 " pdb=" CA ASN R 487 " ideal model delta sigma weight residual 1.462 1.486 -0.025 1.48e-02 4.57e+03 2.81e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.08e+00 ... (remaining 3345 not shown) Histogram of bond angle deviations from ideal: 99.89 - 106.71: 98 106.71 - 113.53: 1740 113.53 - 120.36: 1245 120.36 - 127.18: 1436 127.18 - 134.01: 37 Bond angle restraints: 4556 Sorted by residual: angle pdb=" C TYR R 473 " pdb=" N GLN R 474 " pdb=" CA GLN R 474 " ideal model delta sigma weight residual 120.82 130.37 -9.55 1.50e+00 4.44e-01 4.05e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 128.28 -13.88 2.30e+00 1.89e-01 3.64e+01 angle pdb=" C PHE R 486 " pdb=" N ASN R 487 " pdb=" CA ASN R 487 " ideal model delta sigma weight residual 122.61 131.45 -8.84 1.56e+00 4.11e-01 3.21e+01 angle pdb=" N GLY L 50 " pdb=" CA GLY L 50 " pdb=" C GLY L 50 " ideal model delta sigma weight residual 111.14 103.18 7.96 1.46e+00 4.69e-01 2.97e+01 angle pdb=" N GLN R 474 " pdb=" CA GLN R 474 " pdb=" C GLN R 474 " ideal model delta sigma weight residual 111.37 118.99 -7.62 1.65e+00 3.67e-01 2.13e+01 ... (remaining 4551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 1831 21.36 - 42.72: 136 42.72 - 64.08: 14 64.08 - 85.44: 12 85.44 - 106.80: 5 Dihedral angle restraints: 1998 sinusoidal: 808 harmonic: 1190 Sorted by residual: dihedral pdb=" CA TYR R 473 " pdb=" C TYR R 473 " pdb=" N GLN R 474 " pdb=" CA GLN R 474 " ideal model delta harmonic sigma weight residual 180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.29 48.71 1 1.00e+01 1.00e-02 3.26e+01 dihedral pdb=" CA GLY L 50 " pdb=" C GLY L 50 " pdb=" N VAL L 51 " pdb=" CA VAL L 51 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 1995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 394 0.058 - 0.115: 82 0.115 - 0.172: 16 0.172 - 0.229: 4 0.229 - 0.287: 3 Chirality restraints: 499 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ASN R 487 " pdb=" N ASN R 487 " pdb=" C ASN R 487 " pdb=" CB ASN R 487 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN R 474 " pdb=" N GLN R 474 " pdb=" C GLN R 474 " pdb=" CB GLN R 474 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 496 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.044 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO L 59 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO L 15 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 486 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C PHE R 486 " -0.033 2.00e-02 2.50e+03 pdb=" O PHE R 486 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN R 487 " 0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1026 2.83 - 3.35: 2557 3.35 - 3.87: 5385 3.87 - 4.38: 6325 4.38 - 4.90: 10971 Nonbonded interactions: 26264 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR H 103 " model vdw 2.313 2.440 nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.323 2.440 nonbonded pdb=" OG SER L 63 " pdb=" OG1 THR L 74 " model vdw 2.333 2.440 nonbonded pdb=" OG SER L 65 " pdb=" OG1 THR L 72 " model vdw 2.342 2.440 nonbonded pdb=" OE1 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.356 2.440 ... (remaining 26259 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.620 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 : 0.006 0.074 3350 Z= 0.359 Angle : 0.915 13.884 4556 Z= 0.512 Chirality : 0.056 0.287 499 Planarity : 0.007 0.068 584 Dihedral : 16.465 106.799 1226 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.29 % Allowed : 0.00 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.38), residues: 405 helix: -4.91 (0.29), residues: 27 sheet: -1.33 (0.40), residues: 152 loop : -1.77 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS L 49 PHE 0.029 0.002 PHE R 377 TYR 0.024 0.002 TYR H 27 ARG 0.020 0.001 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.397 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.1528 time to fit residues: 13.7785 Evaluate side-chains 70 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3350 Z= 0.247 Angle : 0.607 7.588 4556 Z= 0.318 Chirality : 0.045 0.145 499 Planarity : 0.005 0.050 584 Dihedral : 8.982 61.858 517 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.86 % Allowed : 10.92 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.39), residues: 405 helix: -4.46 (0.49), residues: 27 sheet: -1.02 (0.42), residues: 149 loop : -1.57 (0.37), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.001 0.001 HIS H 35 PHE 0.010 0.001 PHE R 377 TYR 0.021 0.001 TYR H 27 ARG 0.008 0.001 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.348 Fit side-chains REVERT: H 23 LYS cc_start: 0.8446 (tttp) cc_final: 0.8200 (tttp) REVERT: H 95 TYR cc_start: 0.8822 (m-80) cc_final: 0.8542 (m-80) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 0.1563 time to fit residues: 14.1183 Evaluate side-chains 74 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3350 Z= 0.186 Angle : 0.537 6.252 4556 Z= 0.284 Chirality : 0.044 0.145 499 Planarity : 0.004 0.045 584 Dihedral : 5.662 27.159 517 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.44 % Allowed : 12.36 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.39), residues: 405 helix: -4.26 (0.58), residues: 27 sheet: -0.81 (0.41), residues: 149 loop : -1.31 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.002 0.001 HIS L 49 PHE 0.009 0.001 PHE R 456 TYR 0.009 0.001 TYR L 91 ARG 0.008 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.369 Fit side-chains REVERT: L 48 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8111 (mp) REVERT: H 23 LYS cc_start: 0.8538 (tttp) cc_final: 0.8283 (tttp) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.1569 time to fit residues: 14.5897 Evaluate side-chains 73 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.0040 chunk 35 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3350 Z= 0.142 Angle : 0.498 5.581 4556 Z= 0.265 Chirality : 0.042 0.145 499 Planarity : 0.004 0.043 584 Dihedral : 4.446 18.881 517 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.72 % Allowed : 13.51 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.61 (0.40), residues: 405 helix: -4.51 (0.54), residues: 21 sheet: -0.61 (0.43), residues: 149 loop : -1.00 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 HIS 0.002 0.001 HIS L 49 PHE 0.008 0.001 PHE R 456 TYR 0.017 0.001 TYR H 27 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.401 Fit side-chains REVERT: H 23 LYS cc_start: 0.8465 (tttp) cc_final: 0.8209 (tttp) REVERT: H 101 ASP cc_start: 0.7659 (t70) cc_final: 0.7430 (t70) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.1454 time to fit residues: 14.2746 Evaluate side-chains 75 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 0.0000 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3350 Z= 0.174 Angle : 0.495 5.862 4556 Z= 0.264 Chirality : 0.042 0.146 499 Planarity : 0.004 0.040 584 Dihedral : 4.475 18.720 517 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.59 % Allowed : 14.37 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.50 (0.41), residues: 405 helix: -4.11 (0.62), residues: 27 sheet: -0.48 (0.43), residues: 149 loop : -0.89 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.002 0.001 HIS L 49 PHE 0.005 0.001 PHE R 456 TYR 0.009 0.001 TYR L 91 ARG 0.003 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.380 Fit side-chains REVERT: L 48 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8039 (mp) REVERT: H 23 LYS cc_start: 0.8515 (tttp) cc_final: 0.8246 (tttm) outliers start: 9 outliers final: 6 residues processed: 77 average time/residue: 0.1530 time to fit residues: 14.4070 Evaluate side-chains 78 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3350 Z= 0.220 Angle : 0.524 6.447 4556 Z= 0.278 Chirality : 0.043 0.141 499 Planarity : 0.004 0.039 584 Dihedral : 4.530 20.309 517 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.30 % Allowed : 14.94 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.37 (0.41), residues: 405 helix: -4.07 (0.62), residues: 27 sheet: -0.41 (0.43), residues: 149 loop : -0.78 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.003 0.001 HIS L 49 PHE 0.006 0.001 PHE R 456 TYR 0.018 0.001 TYR H 27 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.374 Fit side-chains REVERT: L 48 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7980 (mp) REVERT: H 23 LYS cc_start: 0.8526 (tttp) cc_final: 0.8227 (tttp) outliers start: 8 outliers final: 7 residues processed: 75 average time/residue: 0.1598 time to fit residues: 14.7056 Evaluate side-chains 78 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.0770 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3350 Z= 0.150 Angle : 0.488 5.695 4556 Z= 0.260 Chirality : 0.042 0.148 499 Planarity : 0.003 0.040 584 Dihedral : 4.354 19.754 517 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.87 % Allowed : 14.66 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.32 (0.41), residues: 405 helix: -4.07 (0.61), residues: 27 sheet: -0.40 (0.43), residues: 149 loop : -0.71 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 436 HIS 0.002 0.001 HIS L 49 PHE 0.004 0.001 PHE R 456 TYR 0.008 0.001 TYR L 91 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.377 Fit side-chains REVERT: L 48 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7918 (mp) REVERT: H 23 LYS cc_start: 0.8499 (tttp) cc_final: 0.8244 (tttm) REVERT: H 101 ASP cc_start: 0.7714 (t70) cc_final: 0.7508 (t70) outliers start: 10 outliers final: 8 residues processed: 79 average time/residue: 0.1518 time to fit residues: 14.7112 Evaluate side-chains 82 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3350 Z= 0.172 Angle : 0.493 5.819 4556 Z= 0.263 Chirality : 0.042 0.146 499 Planarity : 0.003 0.039 584 Dihedral : 4.346 17.809 517 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.45 % Allowed : 14.94 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.41), residues: 405 helix: -4.00 (0.64), residues: 27 sheet: -0.39 (0.43), residues: 149 loop : -0.73 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.003 0.001 HIS L 49 PHE 0.004 0.001 PHE R 456 TYR 0.018 0.001 TYR H 27 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.401 Fit side-chains REVERT: L 48 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7937 (mp) REVERT: H 23 LYS cc_start: 0.8468 (tttp) cc_final: 0.8224 (tttm) REVERT: H 101 ASP cc_start: 0.7729 (t70) cc_final: 0.7513 (t70) outliers start: 12 outliers final: 11 residues processed: 78 average time/residue: 0.1520 time to fit residues: 14.5428 Evaluate side-chains 85 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3350 Z= 0.277 Angle : 0.541 6.594 4556 Z= 0.286 Chirality : 0.044 0.145 499 Planarity : 0.004 0.037 584 Dihedral : 4.632 20.663 517 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.87 % Allowed : 15.52 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.41), residues: 405 helix: -4.00 (0.64), residues: 27 sheet: -0.37 (0.44), residues: 147 loop : -0.79 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS L 49 PHE 0.005 0.001 PHE H 64 TYR 0.008 0.001 TYR R 473 ARG 0.002 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.382 Fit side-chains REVERT: L 36 TYR cc_start: 0.9028 (m-80) cc_final: 0.8784 (m-80) REVERT: L 48 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8079 (mp) REVERT: H 23 LYS cc_start: 0.8514 (tttp) cc_final: 0.8197 (tttp) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.1616 time to fit residues: 15.3602 Evaluate side-chains 83 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0000 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 9 optimal weight: 0.7980 chunk 28 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3350 Z= 0.164 Angle : 0.495 5.518 4556 Z= 0.264 Chirality : 0.042 0.147 499 Planarity : 0.003 0.039 584 Dihedral : 4.401 18.449 517 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.16 % Allowed : 15.80 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.33 (0.41), residues: 405 helix: -3.99 (0.64), residues: 27 sheet: -0.39 (0.43), residues: 148 loop : -0.75 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.003 0.001 PHE R 456 TYR 0.016 0.001 TYR H 27 ARG 0.002 0.000 ARG H 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.335 Fit side-chains REVERT: L 48 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7995 (mp) REVERT: H 23 LYS cc_start: 0.8427 (tttp) cc_final: 0.8189 (tttm) REVERT: H 101 ASP cc_start: 0.7636 (t70) cc_final: 0.7385 (t70) outliers start: 11 outliers final: 10 residues processed: 78 average time/residue: 0.1527 time to fit residues: 14.5470 Evaluate side-chains 83 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 340 GLU Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.107239 restraints weight = 4695.124| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.15 r_work: 0.3049 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3350 Z= 0.180 Angle : 0.500 5.649 4556 Z= 0.267 Chirality : 0.043 0.146 499 Planarity : 0.003 0.038 584 Dihedral : 4.367 18.952 517 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.87 % Allowed : 15.80 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.38 (0.42), residues: 405 helix: -4.22 (0.54), residues: 33 sheet: -0.37 (0.44), residues: 148 loop : -0.68 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.004 0.001 PHE R 456 TYR 0.008 0.001 TYR L 91 ARG 0.002 0.000 ARG H 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.42 seconds wall clock time: 25 minutes 28.19 seconds (1528.19 seconds total)