Starting phenix.real_space_refine on Tue Feb 13 04:54:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/02_2024/7lck_23276_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/02_2024/7lck_23276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/02_2024/7lck_23276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/02_2024/7lck_23276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/02_2024/7lck_23276_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/02_2024/7lck_23276_updated.pdb" } resolution = 3.24 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 565 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 52": "OE1" <-> "OE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ASP 372": "OD1" <-> "OD2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R GLU 387": "OE1" <-> "OE2" Residue "R GLU 412": "OE1" <-> "OE2" Residue "R GLU 418": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3258 Unusual residues: {'UK4': 1} Classifications: {'peptide': 390, 'undetermined': 1, 'water': 11} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375, None: 12} Not linked: pdbres="GLU R 423 " pdbres="UK4 R 501 " Not linked: pdbres="UK4 R 501 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " Not linked: pdbres="HOH R 602 " pdbres="HOH R 603 " Not linked: pdbres="HOH R 603 " pdbres="HOH R 604 " ... (remaining 7 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.48, per 1000 atoms: 0.76 Number of scatterers: 3258 At special positions: 0 Unit cell: (60.8, 115.9, 69.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 F 1 9.00 O 565 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.04 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 622.6 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 1 sheets defined 62.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.690A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 Processing helix chain 'R' and resid 176 through 200 removed outlier: 3.923A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 221 removed outlier: 5.230A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 217 " --> pdb=" O TRP R 214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R 218 " --> pdb=" O ASP R 215 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER R 219 " --> pdb=" O GLY R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 255 removed outlier: 3.610A pdb=" N MET R 233 " --> pdb=" O VAL R 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 244 " --> pdb=" O ASN R 240 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 274 Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 281 through 291 removed outlier: 3.616A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 336 removed outlier: 3.538A pdb=" N ILE R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG R 310 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 4.005A pdb=" N VAL R 332 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 removed outlier: 4.280A pdb=" N LYS R 346 " --> pdb=" O LYS R 342 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 369 removed outlier: 3.502A pdb=" N VAL R 365 " --> pdb=" O THR R 362 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 390 removed outlier: 3.552A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 401 Processing helix chain 'R' and resid 407 through 422 removed outlier: 4.099A pdb=" N LEU R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.611A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 408 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: 0.77 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 487 1.27 - 1.41: 980 1.41 - 1.54: 1857 1.54 - 1.68: 4 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.417 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.448 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CA SER R 392 " pdb=" CB SER R 392 " ideal model delta sigma weight residual 1.531 1.480 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" C GLU R 387 " pdb=" O GLU R 387 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.05e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 89.16 - 107.30: 126 107.30 - 125.44: 4348 125.44 - 143.57: 96 143.57 - 161.71: 0 161.71 - 179.85: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.97 104.88 9.09 1.28e+00 6.10e-01 5.04e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.85 121.54 -10.69 1.70e+00 3.46e-01 3.95e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 112.23 104.36 7.87 1.26e+00 6.30e-01 3.90e+01 angle pdb=" N TYR R 152 " pdb=" CA TYR R 152 " pdb=" C TYR R 152 " ideal model delta sigma weight residual 113.01 106.26 6.75 1.20e+00 6.94e-01 3.16e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 93.70 16.56 3.00e+00 1.11e-01 3.05e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 1701 16.60 - 33.20: 171 33.20 - 49.80: 51 49.80 - 66.40: 7 66.40 - 83.00: 2 Dihedral angle restraints: 1932 sinusoidal: 776 harmonic: 1156 Sorted by residual: dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -144.20 21.60 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual 122.80 141.04 -18.24 0 2.50e+00 1.60e-01 5.32e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -44.74 -41.26 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 1929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 480 0.165 - 0.329: 14 0.329 - 0.493: 2 0.493 - 0.658: 0 0.658 - 0.822: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA PHE R 385 " pdb=" N PHE R 385 " pdb=" C PHE R 385 " pdb=" CB PHE R 385 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PHE R 367 " pdb=" N PHE R 367 " pdb=" C PHE R 367 " pdb=" CB PHE R 367 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 144 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU R 144 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU R 144 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR R 145 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ILE R 146 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 368 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ALA R 368 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA R 368 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE R 369 " 0.016 2.00e-02 2.50e+03 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 89 2.71 - 3.26: 3219 3.26 - 3.80: 4981 3.80 - 4.35: 6333 4.35 - 4.90: 10748 Nonbonded interactions: 25370 Sorted by model distance: nonbonded pdb=" NE2 GLN R 112 " pdb=" O SER R 117 " model vdw 2.160 2.520 nonbonded pdb=" O LEU R 244 " pdb=" ND2 ASN R 320 " model vdw 2.204 2.520 nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.278 2.520 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH2 ARG R 102 " model vdw 2.315 2.520 nonbonded pdb=" OG SER R 31 " pdb=" N LEU R 32 " model vdw 2.422 2.520 ... (remaining 25365 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.430 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.330 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 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 : 0.008 0.118 3351 Z= 0.488 Angle : 1.050 16.557 4571 Z= 0.664 Chirality : 0.075 0.822 497 Planarity : 0.006 0.040 557 Dihedral : 14.388 82.998 1172 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.16 % Allowed : 2.62 % Favored : 96.22 % Cbeta Deviations : 1.07 % 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: -0.93 (0.42), residues: 386 helix: -0.15 (0.32), residues: 265 sheet: 0.36 (2.04), residues: 10 loop : -1.62 (0.58), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 243 HIS 0.005 0.001 HIS R 180 PHE 0.020 0.002 PHE R 393 TYR 0.019 0.002 TYR R 242 ARG 0.003 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.412 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1740 time to fit residues: 9.6792 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3351 Z= 0.207 Angle : 0.614 11.107 4571 Z= 0.311 Chirality : 0.038 0.136 497 Planarity : 0.005 0.040 557 Dihedral : 6.378 37.683 458 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.87 % Allowed : 8.72 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.44), residues: 386 helix: 0.27 (0.33), residues: 262 sheet: 0.38 (2.01), residues: 10 loop : -1.51 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 284 HIS 0.002 0.000 HIS R 363 PHE 0.012 0.001 PHE R 324 TYR 0.032 0.002 TYR R 148 ARG 0.002 0.000 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 28 time to evaluate : 0.364 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.1718 time to fit residues: 6.4787 Evaluate side-chains 26 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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: 0.7701 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3351 Z= 0.153 Angle : 0.528 7.370 4571 Z= 0.271 Chirality : 0.037 0.122 497 Planarity : 0.004 0.047 557 Dihedral : 5.653 33.900 457 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.29 % Allowed : 11.92 % Favored : 87.79 % 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: -0.07 (0.44), residues: 386 helix: 0.62 (0.33), residues: 261 sheet: 0.41 (1.87), residues: 10 loop : -1.52 (0.56), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 72 HIS 0.001 0.000 HIS R 363 PHE 0.009 0.001 PHE R 324 TYR 0.028 0.001 TYR R 148 ARG 0.001 0.000 ARG R 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.359 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.1522 time to fit residues: 5.4651 Evaluate side-chains 24 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 23 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.200 Angle : 0.563 12.219 4571 Z= 0.281 Chirality : 0.037 0.123 497 Planarity : 0.005 0.051 557 Dihedral : 5.595 34.265 455 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.45 % Allowed : 13.66 % Favored : 84.88 % 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: 0.10 (0.44), residues: 386 helix: 0.76 (0.34), residues: 262 sheet: 0.39 (1.64), residues: 10 loop : -1.49 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 284 HIS 0.002 0.000 HIS R 363 PHE 0.009 0.001 PHE R 156 TYR 0.028 0.001 TYR R 148 ARG 0.002 0.000 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.324 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1261 time to fit residues: 4.5276 Evaluate side-chains 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.0020 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3351 Z= 0.197 Angle : 0.553 12.401 4571 Z= 0.277 Chirality : 0.037 0.124 497 Planarity : 0.005 0.051 557 Dihedral : 5.531 34.268 455 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.16 % Allowed : 14.83 % Favored : 84.01 % 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: 0.24 (0.44), residues: 386 helix: 0.95 (0.34), residues: 256 sheet: 0.17 (1.48), residues: 10 loop : -1.53 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 72 HIS 0.002 0.000 HIS R 363 PHE 0.009 0.001 PHE R 156 TYR 0.027 0.001 TYR R 148 ARG 0.001 0.000 ARG R 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.410 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.1436 time to fit residues: 5.6166 Evaluate side-chains 26 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 22 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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: 0.7781 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3351 Z= 0.231 Angle : 0.580 12.851 4571 Z= 0.291 Chirality : 0.038 0.125 497 Planarity : 0.005 0.052 557 Dihedral : 5.665 34.781 455 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.74 % Allowed : 15.41 % Favored : 82.85 % 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: 0.23 (0.44), residues: 386 helix: 0.94 (0.34), residues: 256 sheet: 0.13 (1.45), residues: 10 loop : -1.50 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 243 HIS 0.002 0.001 HIS R 363 PHE 0.010 0.001 PHE R 156 TYR 0.027 0.001 TYR R 148 ARG 0.002 0.000 ARG R 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 24 time to evaluate : 0.388 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.1378 time to fit residues: 5.1782 Evaluate side-chains 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3351 Z= 0.190 Angle : 0.560 13.229 4571 Z= 0.280 Chirality : 0.037 0.124 497 Planarity : 0.005 0.053 557 Dihedral : 5.510 34.133 455 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.16 % Allowed : 16.28 % Favored : 82.56 % 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: 0.31 (0.44), residues: 386 helix: 1.03 (0.34), residues: 254 sheet: 0.43 (1.45), residues: 10 loop : -1.53 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 72 HIS 0.001 0.000 HIS R 363 PHE 0.009 0.001 PHE R 156 TYR 0.026 0.001 TYR R 148 ARG 0.001 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.381 Fit side-chains REVERT: R 260 PHE cc_start: 0.4663 (OUTLIER) cc_final: 0.3555 (m-80) outliers start: 4 outliers final: 3 residues processed: 26 average time/residue: 0.1418 time to fit residues: 4.9303 Evaluate side-chains 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 260 PHE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.0010 chunk 23 optimal weight: 0.9980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3351 Z= 0.156 Angle : 0.551 13.827 4571 Z= 0.274 Chirality : 0.037 0.130 497 Planarity : 0.005 0.054 557 Dihedral : 5.392 32.761 455 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.45 % Allowed : 16.86 % Favored : 81.69 % 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: 0.41 (0.44), residues: 386 helix: 1.10 (0.34), residues: 258 sheet: 0.60 (1.46), residues: 10 loop : -1.61 (0.55), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 PHE 0.007 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.001 0.000 ARG R 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.402 Fit side-chains REVERT: R 260 PHE cc_start: 0.4583 (OUTLIER) cc_final: 0.3483 (m-80) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.1584 time to fit residues: 5.9676 Evaluate side-chains 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 260 PHE Chi-restraints excluded: chain R residue 329 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 chunk 26 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.181 Angle : 0.560 13.947 4571 Z= 0.278 Chirality : 0.037 0.123 497 Planarity : 0.005 0.054 557 Dihedral : 5.354 32.706 455 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.45 % Allowed : 16.57 % Favored : 81.98 % 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: 0.48 (0.44), residues: 386 helix: 1.16 (0.34), residues: 256 sheet: 0.89 (1.51), residues: 10 loop : -1.56 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 72 HIS 0.001 0.000 HIS R 363 PHE 0.008 0.001 PHE R 156 TYR 0.026 0.001 TYR R 148 ARG 0.003 0.000 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.417 Fit side-chains REVERT: R 260 PHE cc_start: 0.4579 (OUTLIER) cc_final: 0.3499 (m-80) outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.1489 time to fit residues: 5.8296 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 260 PHE Chi-restraints excluded: chain R residue 329 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.203 Angle : 0.572 14.179 4571 Z= 0.285 Chirality : 0.037 0.134 497 Planarity : 0.005 0.054 557 Dihedral : 5.450 32.879 455 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.03 % Allowed : 16.28 % Favored : 81.69 % 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: 0.48 (0.44), residues: 386 helix: 1.14 (0.34), residues: 255 sheet: 0.86 (1.51), residues: 10 loop : -1.47 (0.55), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 420 HIS 0.001 0.001 HIS R 180 PHE 0.009 0.001 PHE R 156 TYR 0.026 0.001 TYR R 148 ARG 0.002 0.000 ARG R 419 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.395 Fit side-chains REVERT: R 260 PHE cc_start: 0.4478 (OUTLIER) cc_final: 0.3434 (m-80) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.1442 time to fit residues: 5.4154 Evaluate side-chains 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 260 PHE Chi-restraints excluded: chain R residue 329 CYS Chi-restraints excluded: chain R residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0870 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.128846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104890 restraints weight = 6023.679| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.98 r_work: 0.3446 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3351 Z= 0.153 Angle : 0.555 13.815 4571 Z= 0.274 Chirality : 0.036 0.122 497 Planarity : 0.005 0.054 557 Dihedral : 5.231 31.663 455 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 15.99 % Favored : 82.27 % 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: 0.67 (0.44), residues: 386 helix: 1.28 (0.34), residues: 256 sheet: 1.34 (1.67), residues: 10 loop : -1.48 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 420 HIS 0.001 0.000 HIS R 180 PHE 0.008 0.001 PHE R 156 TYR 0.025 0.001 TYR R 148 ARG 0.002 0.000 ARG R 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.14 seconds wall clock time: 21 minutes 13.26 seconds (1273.26 seconds total)