Starting phenix.real_space_refine on Mon Jun 24 14:21:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/06_2024/9fgt_50424.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/06_2024/9fgt_50424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/06_2024/9fgt_50424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/06_2024/9fgt_50424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/06_2024/9fgt_50424.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fgt_50424/06_2024/9fgt_50424.pdb" } resolution = 3.8 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= -0.006 sd= 0.052 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 10 5.16 5 C 1863 2.51 5 N 496 2.21 5 O 552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 2921 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1280 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 2 Chain: "E" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.27, per 1000 atoms: 1.12 Number of scatterers: 2921 At special positions: 0 Unit cell: (78.232, 65.786, 79.121, 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 10 16.00 O 552 8.00 N 496 7.00 C 1863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 627.4 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 676 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 9 sheets defined 8.0% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.523A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.211A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.589A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.884A pdb=" N GLY C 482 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.586A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.761A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 18 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 77 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.921A pdb=" N ALA E 96 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.668A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 172 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.668A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 221 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN E 172 " --> pdb=" O VAL E 219 " (cutoff:3.500A) 77 hydrogen bonds defined for protein. 183 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: 0.75 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 925 1.34 - 1.46: 657 1.46 - 1.57: 1399 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2993 Sorted by residual: bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.487 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.413 1.446 -0.033 2.00e-02 2.50e+03 2.64e+00 bond pdb=" CA VAL C 395 " pdb=" C VAL C 395 " ideal model delta sigma weight residual 1.525 1.502 0.023 2.10e-02 2.27e+03 1.21e+00 bond pdb=" C SER E 100 " pdb=" O SER E 100 " ideal model delta sigma weight residual 1.235 1.222 0.013 1.26e-02 6.30e+03 1.12e+00 bond pdb=" CB TRP E 47 " pdb=" CG TRP E 47 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.04e+00 ... (remaining 2988 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 79 107.09 - 113.82: 1582 113.82 - 120.55: 1134 120.55 - 127.28: 1236 127.28 - 134.01: 27 Bond angle restraints: 4058 Sorted by residual: angle pdb=" C ASN C 343 " pdb=" CA ASN C 343 " pdb=" CB ASN C 343 " ideal model delta sigma weight residual 109.80 115.12 -5.32 1.70e+00 3.46e-01 9.80e+00 angle pdb=" C PRO C 479 " pdb=" N CYS C 480 " pdb=" CA CYS C 480 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.18e+00 angle pdb=" C LEU E 99 " pdb=" N SER E 100 " pdb=" CA SER E 100 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.98e+00 angle pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C5 NAG C1301 " ideal model delta sigma weight residual 113.21 120.77 -7.56 3.00e+00 1.11e-01 6.36e+00 angle pdb=" CA ASP C 428 " pdb=" CB ASP C 428 " pdb=" CG ASP C 428 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.05e+00 ... (remaining 4053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 1640 22.35 - 44.69: 96 44.69 - 67.04: 21 67.04 - 89.39: 0 89.39 - 111.73: 3 Dihedral angle restraints: 1760 sinusoidal: 691 harmonic: 1069 Sorted by residual: dihedral pdb=" CB CYS E 156 " pdb=" SG CYS E 156 " pdb=" SG CYS E 222 " pdb=" CB CYS E 222 " ideal model delta sinusoidal sigma weight residual 93.00 145.53 -52.53 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" C1 NAG C1301 " pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C4 NAG C1301 " ideal model delta sinusoidal sigma weight residual -64.11 47.62 -111.73 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" C1 NAG C1301 " pdb=" C5 NAG C1301 " pdb=" O5 NAG C1301 " pdb=" C6 NAG C1301 " ideal model delta sinusoidal sigma weight residual 171.16 -78.54 -110.30 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 1757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 319 0.047 - 0.094: 84 0.094 - 0.141: 29 0.141 - 0.188: 1 0.188 - 0.236: 2 Chirality restraints: 435 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU E 167 " pdb=" CB LEU E 167 " pdb=" CD1 LEU E 167 " pdb=" CD2 LEU E 167 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 432 not shown) Planarity restraints: 522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 13 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO E 14 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 225 " -0.012 2.00e-02 2.50e+03 1.31e-02 3.44e+00 pdb=" CG TYR E 225 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 225 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR E 225 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 225 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 225 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 225 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " 0.016 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 453 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " 0.002 2.00e-02 2.50e+03 ... (remaining 519 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 44 2.66 - 3.22: 2668 3.22 - 3.78: 3965 3.78 - 4.34: 5381 4.34 - 4.90: 9059 Nonbonded interactions: 21117 Sorted by model distance: nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.094 2.440 nonbonded pdb=" O GLY E 142 " pdb=" OG1 THR E 236 " model vdw 2.186 2.440 nonbonded pdb=" OG1 THR C 376 " pdb=" O ALA C 435 " model vdw 2.218 2.440 nonbonded pdb=" OH TYR C 473 " pdb=" O ALA E 31 " model vdw 2.303 2.440 nonbonded pdb=" NH1 ARG E 188 " pdb=" O PHE E 196 " model vdw 2.315 2.520 ... (remaining 21112 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 12.790 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.400 Find NCS groups from input model: 0.070 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: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.005 0.081 2993 Z= 0.339 Angle : 0.703 7.564 4058 Z= 0.370 Chirality : 0.049 0.236 435 Planarity : 0.005 0.050 521 Dihedral : 14.859 111.732 1072 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.43), residues: 361 helix: -3.41 (1.05), residues: 13 sheet: -0.18 (0.51), residues: 117 loop : -1.41 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 169 HIS 0.002 0.001 HIS C 505 PHE 0.017 0.002 PHE E 205 TYR 0.029 0.002 TYR E 225 ARG 0.004 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.333 Fit side-chains REVERT: C 458 LYS cc_start: 0.8502 (mttt) cc_final: 0.8291 (mttp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1162 time to fit residues: 8.2724 Evaluate side-chains 49 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 0.043 2993 Z= 0.253 Angle : 0.692 12.815 4058 Z= 0.346 Chirality : 0.047 0.143 435 Planarity : 0.005 0.052 521 Dihedral : 9.032 69.445 436 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.57 % Allowed : 9.65 % Favored : 87.78 % 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: -1.52 (0.43), residues: 361 helix: -3.25 (1.16), residues: 13 sheet: -0.03 (0.54), residues: 108 loop : -1.42 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.008 0.001 PHE E 205 TYR 0.015 0.001 TYR E 225 ARG 0.003 0.001 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.315 Fit side-chains REVERT: C 406 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7741 (mt-10) outliers start: 8 outliers final: 7 residues processed: 57 average time/residue: 0.1043 time to fit residues: 7.8362 Evaluate side-chains 58 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.0270 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.0970 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 0.0000 chunk 11 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.1778 ------------------------------------------------------------------------------- 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: 0.7864 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 2993 Z= 0.144 Angle : 0.566 7.411 4058 Z= 0.282 Chirality : 0.044 0.143 435 Planarity : 0.004 0.051 521 Dihedral : 6.851 59.410 436 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.29 % Allowed : 15.76 % Favored : 82.96 % 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: -1.31 (0.44), residues: 361 helix: -3.18 (1.18), residues: 13 sheet: 0.16 (0.56), residues: 106 loop : -1.28 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.000 0.000 HIS C 505 PHE 0.022 0.001 PHE C 486 TYR 0.018 0.001 TYR E 225 ARG 0.003 0.000 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.318 Fit side-chains REVERT: C 406 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7719 (mt-10) REVERT: E 83 ASN cc_start: 0.7941 (m110) cc_final: 0.7557 (m-40) outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 0.1078 time to fit residues: 8.1161 Evaluate side-chains 56 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.7943 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2993 Z= 0.232 Angle : 0.587 7.103 4058 Z= 0.299 Chirality : 0.044 0.141 435 Planarity : 0.004 0.051 521 Dihedral : 6.915 59.991 436 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.22 % Allowed : 15.76 % Favored : 81.03 % 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: -1.42 (0.44), residues: 361 helix: -3.19 (1.14), residues: 13 sheet: 0.14 (0.56), residues: 106 loop : -1.39 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.028 0.001 PHE E 205 TYR 0.012 0.001 TYR E 225 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.325 Fit side-chains REVERT: C 406 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7749 (mt-10) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.1119 time to fit residues: 8.0126 Evaluate side-chains 57 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2993 Z= 0.236 Angle : 0.597 7.288 4058 Z= 0.304 Chirality : 0.045 0.140 435 Planarity : 0.004 0.051 521 Dihedral : 6.858 59.951 436 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.89 % Allowed : 17.36 % Favored : 79.74 % 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: -1.56 (0.43), residues: 361 helix: -3.11 (1.19), residues: 13 sheet: 0.05 (0.55), residues: 106 loop : -1.50 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 108 HIS 0.001 0.001 HIS C 505 PHE 0.028 0.002 PHE C 486 TYR 0.012 0.001 TYR E 225 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 52 time to evaluate : 0.321 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 57 average time/residue: 0.1256 time to fit residues: 9.0459 Evaluate side-chains 58 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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: 0.7934 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2993 Z= 0.188 Angle : 0.573 7.570 4058 Z= 0.289 Chirality : 0.044 0.138 435 Planarity : 0.004 0.051 521 Dihedral : 6.603 56.729 436 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.89 % Allowed : 18.65 % Favored : 78.46 % 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: -1.55 (0.43), residues: 361 helix: -3.07 (1.19), residues: 13 sheet: 0.05 (0.55), residues: 106 loop : -1.49 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.016 0.001 PHE E 205 TYR 0.012 0.001 TYR E 225 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.335 Fit side-chains REVERT: E 83 ASN cc_start: 0.7932 (m110) cc_final: 0.7538 (m-40) outliers start: 9 outliers final: 8 residues processed: 55 average time/residue: 0.1053 time to fit residues: 7.5654 Evaluate side-chains 58 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7966 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2993 Z= 0.248 Angle : 0.612 8.473 4058 Z= 0.308 Chirality : 0.045 0.141 435 Planarity : 0.004 0.051 521 Dihedral : 6.631 56.441 436 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.89 % Allowed : 18.97 % Favored : 78.14 % 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: -1.73 (0.43), residues: 361 helix: -2.96 (1.38), residues: 13 sheet: -0.23 (0.52), residues: 118 loop : -1.61 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.029 0.002 PHE C 486 TYR 0.011 0.001 TYR E 225 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.330 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 54 average time/residue: 0.1124 time to fit residues: 7.9107 Evaluate side-chains 57 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 31 optimal weight: 0.0070 chunk 33 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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: 0.7940 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2993 Z= 0.198 Angle : 0.590 8.123 4058 Z= 0.297 Chirality : 0.044 0.140 435 Planarity : 0.004 0.052 521 Dihedral : 6.336 53.209 436 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.89 % Allowed : 19.94 % Favored : 77.17 % 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: -1.73 (0.43), residues: 361 helix: -2.89 (1.43), residues: 13 sheet: -0.24 (0.52), residues: 116 loop : -1.59 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 169 HIS 0.001 0.001 HIS C 505 PHE 0.029 0.002 PHE C 486 TYR 0.013 0.001 TYR E 225 ARG 0.002 0.000 ARG E 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.320 Fit side-chains REVERT: E 83 ASN cc_start: 0.7972 (m110) cc_final: 0.7558 (m-40) outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.1084 time to fit residues: 7.7759 Evaluate side-chains 58 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2993 Z= 0.249 Angle : 0.633 8.428 4058 Z= 0.317 Chirality : 0.045 0.137 435 Planarity : 0.004 0.052 521 Dihedral : 6.214 51.909 436 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.54 % Allowed : 19.94 % Favored : 76.53 % 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: -1.84 (0.43), residues: 361 helix: -2.93 (1.44), residues: 13 sheet: -0.36 (0.51), residues: 118 loop : -1.66 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 108 HIS 0.001 0.001 HIS C 505 PHE 0.033 0.002 PHE C 486 TYR 0.012 0.001 TYR E 225 ARG 0.002 0.000 ARG E 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.328 Fit side-chains REVERT: E 83 ASN cc_start: 0.7937 (m110) cc_final: 0.7556 (m-40) outliers start: 11 outliers final: 10 residues processed: 56 average time/residue: 0.1112 time to fit residues: 8.1180 Evaluate side-chains 58 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.0040 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 overall best weight: 0.2942 ------------------------------------------------------------------------------- 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: 0.7893 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2993 Z= 0.171 Angle : 0.615 8.704 4058 Z= 0.307 Chirality : 0.044 0.137 435 Planarity : 0.004 0.054 521 Dihedral : 5.597 54.668 436 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.22 % Allowed : 20.90 % Favored : 75.88 % 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: -1.64 (0.43), residues: 361 helix: -3.12 (1.26), residues: 13 sheet: -0.00 (0.56), residues: 105 loop : -1.56 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 108 HIS 0.001 0.000 HIS C 505 PHE 0.012 0.001 PHE E 205 TYR 0.015 0.001 TYR E 225 ARG 0.002 0.000 ARG E 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.333 Fit side-chains REVERT: E 83 ASN cc_start: 0.7842 (m110) cc_final: 0.7600 (m-40) outliers start: 10 outliers final: 10 residues processed: 55 average time/residue: 0.1117 time to fit residues: 7.9845 Evaluate side-chains 59 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 225 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.150634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132326 restraints weight = 5134.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135006 restraints weight = 3172.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136959 restraints weight = 2246.227| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2993 Z= 0.208 Angle : 0.617 8.282 4058 Z= 0.305 Chirality : 0.045 0.136 435 Planarity : 0.004 0.055 521 Dihedral : 5.465 52.327 436 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 3.22 % Allowed : 21.22 % Favored : 75.56 % 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: -1.60 (0.43), residues: 361 helix: -3.17 (1.27), residues: 13 sheet: 0.03 (0.56), residues: 105 loop : -1.53 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 108 HIS 0.001 0.000 HIS C 505 PHE 0.014 0.001 PHE E 205 TYR 0.012 0.001 TYR E 225 ARG 0.002 0.000 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.79 seconds wall clock time: 22 minutes 54.26 seconds (1374.26 seconds total)