Starting phenix.real_space_refine on Tue Feb 11 02:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7srq_25401/02_2025/7srq_25401.cif Found real_map, /net/cci-nas-00/data/ceres_data/7srq_25401/02_2025/7srq_25401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7srq_25401/02_2025/7srq_25401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7srq_25401/02_2025/7srq_25401.map" model { file = "/net/cci-nas-00/data/ceres_data/7srq_25401/02_2025/7srq_25401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7srq_25401/02_2025/7srq_25401.cif" } resolution = 2.7 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1855 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1323 2.51 5 N 295 2.21 5 O 328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1960 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1922 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'7LD': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 2.88, per 1000 atoms: 1.47 Number of scatterers: 1960 At special positions: 0 Unit cell: (51.1943, 56.4005, 75.4899, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 328 8.00 N 295 7.00 C 1323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 207 " distance=2.03 Simple disulfide: pdb=" SG CYS R 350 " - pdb=" SG CYS R 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 R 501 " - " ASN R 204 " Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 221.3 milliseconds 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 486 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 56 through 82 removed outlier: 3.894A pdb=" N LEU R 60 " --> pdb=" O TRP R 56 " (cutoff:3.500A) Proline residue: R 67 - end of helix removed outlier: 3.686A pdb=" N ASN R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 removed outlier: 4.005A pdb=" N TYR R 91 " --> pdb=" O TYR R 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE R 92 " --> pdb=" O ALA R 88 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Proline residue: R 109 - end of helix Processing helix chain 'R' and resid 126 through 159 removed outlier: 4.110A pdb=" N ALA R 130 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER R 139 " --> pdb=" O ASP R 135 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR R 140 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS R 145 " --> pdb=" O ALA R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 188 Processing helix chain 'R' and resid 188 through 193 removed outlier: 4.095A pdb=" N ILE R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS R 193 " --> pdb=" O PRO R 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 188 through 193' Processing helix chain 'R' and resid 201 through 205 removed outlier: 3.579A pdb=" N ILE R 205 " --> pdb=" O PRO R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 226 removed outlier: 3.726A pdb=" N LEU R 219 " --> pdb=" O GLY R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 242 removed outlier: 3.616A pdb=" N PHE R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 333 removed outlier: 3.590A pdb=" N GLY R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE R 333 " --> pdb=" O VAL R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 336 No H-bonds generated for 'chain 'R' and resid 334 through 336' Processing helix chain 'R' and resid 337 through 350 removed outlier: 3.616A pdb=" N PHE R 341 " --> pdb=" O TRP R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 382 removed outlier: 3.543A pdb=" N MET R 360 " --> pdb=" O THR R 356 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU R 361 " --> pdb=" O THR R 357 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP R 367 " --> pdb=" O GLU R 363 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE R 368 " --> pdb=" O ILE R 364 " (cutoff:3.500A) Proline residue: R 377 - end of helix Processing helix chain 'R' and resid 384 through 394 removed outlier: 3.645A pdb=" N ARG R 388 " --> pdb=" O ASN R 384 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY R 392 " --> pdb=" O ARG R 388 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG R 393 " --> pdb=" O ASP R 389 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR R 394 " --> pdb=" O ALA R 390 " (cutoff:3.500A) 131 hydrogen bonds defined for protein. 390 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: 0.53 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 567 1.34 - 1.46: 441 1.46 - 1.58: 984 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 2014 Sorted by residual: bond pdb=" C14 7LD R 502 " pdb=" C16 7LD R 502 " ideal model delta sigma weight residual 1.525 1.402 0.123 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C11 7LD R 502 " pdb=" C9 7LD R 502 " ideal model delta sigma weight residual 1.525 1.406 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C10 7LD R 502 " pdb=" C14 7LD R 502 " ideal model delta sigma weight residual 1.501 1.397 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C15 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.491 1.396 0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C3 7LD R 502 " pdb=" C7 7LD R 502 " ideal model delta sigma weight residual 1.414 1.322 0.092 2.00e-02 2.50e+03 2.11e+01 ... (remaining 2009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 2616 1.56 - 3.13: 113 3.13 - 4.69: 24 4.69 - 6.26: 13 6.26 - 7.82: 1 Bond angle restraints: 2767 Sorted by residual: angle pdb=" CA LEU R 334 " pdb=" C LEU R 334 " pdb=" O LEU R 334 " ideal model delta sigma weight residual 120.90 116.80 4.10 1.07e+00 8.73e-01 1.47e+01 angle pdb=" CA PHE R 331 " pdb=" CB PHE R 331 " pdb=" CG PHE R 331 " ideal model delta sigma weight residual 113.80 117.51 -3.71 1.00e+00 1.00e+00 1.37e+01 angle pdb=" CA LEU R 326 " pdb=" C LEU R 326 " pdb=" O LEU R 326 " ideal model delta sigma weight residual 120.80 117.09 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" N TRP R 337 " pdb=" CA TRP R 337 " pdb=" C TRP R 337 " ideal model delta sigma weight residual 113.50 109.42 4.08 1.23e+00 6.61e-01 1.10e+01 angle pdb=" CA PHE R 330 " pdb=" CB PHE R 330 " pdb=" CG PHE R 330 " ideal model delta sigma weight residual 113.80 116.95 -3.15 1.00e+00 1.00e+00 9.92e+00 ... (remaining 2762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 1153 30.36 - 60.72: 24 60.72 - 91.08: 4 91.08 - 121.45: 0 121.45 - 151.81: 1 Dihedral angle restraints: 1182 sinusoidal: 438 harmonic: 744 Sorted by residual: dihedral pdb=" CB CYS R 128 " pdb=" SG CYS R 128 " pdb=" SG CYS R 207 " pdb=" CB CYS R 207 " ideal model delta sinusoidal sigma weight residual -86.00 -150.42 64.42 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" C16 7LD R 502 " pdb=" C17 7LD R 502 " pdb=" N3 7LD R 502 " pdb=" C18 7LD R 502 " ideal model delta sinusoidal sigma weight residual 91.75 -116.44 -151.81 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" CA PHE R 117 " pdb=" C PHE R 117 " pdb=" N GLU R 118 " pdb=" CA GLU R 118 " ideal model delta harmonic sigma weight residual -180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 303 0.066 - 0.132: 37 0.132 - 0.198: 6 0.198 - 0.263: 0 0.263 - 0.329: 2 Chirality restraints: 348 Sorted by residual: chirality pdb=" C14 7LD R 502 " pdb=" C10 7LD R 502 " pdb=" C13 7LD R 502 " pdb=" C16 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.63 2.30 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C11 7LD R 502 " pdb=" C15 7LD R 502 " pdb=" C9 7LD R 502 " pdb=" N2 7LD R 502 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CA PHE R 333 " pdb=" N PHE R 333 " pdb=" C PHE R 333 " pdb=" CB PHE R 333 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 345 not shown) Planarity restraints: 326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 188 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO R 189 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 189 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 189 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 370 " 0.014 2.00e-02 2.50e+03 1.24e-02 3.08e+00 pdb=" CG TYR R 370 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 370 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR R 370 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 370 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 370 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR R 370 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR R 370 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 337 " 0.016 2.00e-02 2.50e+03 1.09e-02 2.99e+00 pdb=" CG TRP R 337 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP R 337 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP R 337 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 337 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 337 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP R 337 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 337 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 337 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 337 " -0.002 2.00e-02 2.50e+03 ... (remaining 323 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 560 2.82 - 3.34: 2081 3.34 - 3.86: 3106 3.86 - 4.38: 3379 4.38 - 4.90: 5925 Nonbonded interactions: 15051 Sorted by model distance: nonbonded pdb=" O CYS R 147 " pdb=" OG SER R 150 " model vdw 2.296 3.040 nonbonded pdb=" O PHE R 92 " pdb=" OG SER R 95 " model vdw 2.416 3.040 nonbonded pdb=" O ILE R 174 " pdb=" OG1 THR R 177 " model vdw 2.572 3.040 nonbonded pdb=" C10 7LD R 502 " pdb=" O1 7LD R 502 " model vdw 2.580 2.672 nonbonded pdb=" O GLY R 369 " pdb=" OG SER R 372 " model vdw 2.633 3.040 ... (remaining 15046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.360 Find NCS groups from input model: 0.020 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 0.123 2014 Z= 0.459 Angle : 0.801 7.824 2767 Z= 0.467 Chirality : 0.051 0.329 348 Planarity : 0.006 0.064 325 Dihedral : 14.144 151.807 690 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.50 % Allowed : 0.00 % Favored : 98.50 % 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: 0.29 (0.52), residues: 248 helix: 0.73 (0.37), residues: 189 sheet: None (None), residues: 0 loop : -1.36 (0.76), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 337 HIS 0.005 0.002 HIS R 145 PHE 0.020 0.001 PHE R 331 TYR 0.030 0.002 TYR R 370 ARG 0.000 0.000 ARG R 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: R 331 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6771 (p90) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.4306 time to fit residues: 24.9156 Evaluate side-chains 46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 330 PHE Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.0670 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 chunk 7 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 15 optimal weight: 0.4980 overall best weight: 0.1916 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.157029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.144336 restraints weight = 2629.933| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.56 r_work: 0.3845 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2014 Z= 0.225 Angle : 0.658 10.067 2767 Z= 0.320 Chirality : 0.043 0.197 348 Planarity : 0.005 0.045 325 Dihedral : 11.254 134.105 312 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.00 % Allowed : 14.00 % Favored : 82.00 % 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: 1.51 (0.53), residues: 248 helix: 1.63 (0.37), residues: 190 sheet: None (None), residues: 0 loop : -1.05 (0.79), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 144 HIS 0.004 0.001 HIS R 145 PHE 0.017 0.001 PHE R 331 TYR 0.026 0.002 TYR R 370 ARG 0.005 0.001 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.192 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 46 average time/residue: 0.4830 time to fit residues: 23.2662 Evaluate side-chains 42 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 7 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 overall best weight: 0.2236 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.156131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.143296 restraints weight = 2609.245| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.54 r_work: 0.3840 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2014 Z= 0.231 Angle : 0.658 7.324 2767 Z= 0.318 Chirality : 0.044 0.204 348 Planarity : 0.004 0.040 325 Dihedral : 9.005 105.762 306 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.50 % Allowed : 16.00 % Favored : 79.50 % 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: 1.97 (0.54), residues: 248 helix: 1.69 (0.37), residues: 198 sheet: None (None), residues: 0 loop : -0.10 (0.91), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 144 HIS 0.004 0.002 HIS R 145 PHE 0.014 0.002 PHE R 92 TYR 0.011 0.002 TYR R 154 ARG 0.003 0.001 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.206 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 52 average time/residue: 0.4714 time to fit residues: 25.7046 Evaluate side-chains 44 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.0970 chunk 20 optimal weight: 0.1980 chunk 10 optimal weight: 0.0050 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1570 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.157084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.143723 restraints weight = 2589.557| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.58 r_work: 0.3849 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2014 Z= 0.210 Angle : 0.648 6.839 2767 Z= 0.309 Chirality : 0.042 0.193 348 Planarity : 0.004 0.039 325 Dihedral : 7.467 76.360 306 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.50 % Allowed : 19.50 % Favored : 75.00 % 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: 2.29 (0.54), residues: 248 helix: 1.90 (0.37), residues: 199 sheet: None (None), residues: 0 loop : 0.05 (0.93), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 144 HIS 0.004 0.002 HIS R 145 PHE 0.010 0.001 PHE R 217 TYR 0.022 0.002 TYR R 370 ARG 0.002 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5313 (tmm) outliers start: 11 outliers final: 5 residues processed: 48 average time/residue: 0.4931 time to fit residues: 24.7842 Evaluate side-chains 46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 6 optimal weight: 0.4980 chunk 22 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.3178 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.153957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140378 restraints weight = 2680.889| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.63 r_work: 0.3800 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 2014 Z= 0.305 Angle : 0.675 7.266 2767 Z= 0.331 Chirality : 0.044 0.209 348 Planarity : 0.004 0.036 325 Dihedral : 6.930 60.015 306 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.50 % Allowed : 23.50 % Favored : 72.00 % 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: 1.96 (0.53), residues: 248 helix: 1.74 (0.37), residues: 199 sheet: None (None), residues: 0 loop : -0.45 (0.85), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 144 HIS 0.004 0.002 HIS R 145 PHE 0.013 0.002 PHE R 217 TYR 0.011 0.002 TYR R 154 ARG 0.002 0.001 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.185 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 43 average time/residue: 0.5744 time to fit residues: 25.7880 Evaluate side-chains 45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 335 LEU Chi-restraints excluded: chain R residue 347 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.0980 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0970 chunk 1 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.0870 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.1954 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.155798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.142512 restraints weight = 2635.482| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.59 r_work: 0.3831 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2014 Z= 0.228 Angle : 0.643 6.914 2767 Z= 0.313 Chirality : 0.042 0.199 348 Planarity : 0.004 0.036 325 Dihedral : 5.898 35.343 306 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 6.50 % Allowed : 19.50 % Favored : 74.00 % 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: 2.08 (0.54), residues: 248 helix: 1.84 (0.37), residues: 199 sheet: None (None), residues: 0 loop : -0.44 (0.85), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 144 HIS 0.003 0.001 HIS R 145 PHE 0.009 0.001 PHE R 217 TYR 0.010 0.001 TYR R 154 ARG 0.002 0.001 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5300 (tmm) outliers start: 13 outliers final: 7 residues processed: 44 average time/residue: 0.5549 time to fit residues: 25.4889 Evaluate side-chains 46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 20 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 overall best weight: 0.1516 ------------------------------------------------------------------------------- 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 = 0.4085 r_free = 0.4085 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144008 restraints weight = 2584.236| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.56 r_work: 0.3849 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2014 Z= 0.208 Angle : 0.640 6.945 2767 Z= 0.307 Chirality : 0.042 0.189 348 Planarity : 0.004 0.037 325 Dihedral : 5.528 40.176 306 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 6.00 % Allowed : 20.00 % Favored : 74.00 % 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: 2.16 (0.54), residues: 248 helix: 1.90 (0.37), residues: 199 sheet: None (None), residues: 0 loop : -0.42 (0.85), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 121 HIS 0.003 0.001 HIS R 145 PHE 0.010 0.001 PHE R 217 TYR 0.023 0.002 TYR R 370 ARG 0.002 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.207 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 48 average time/residue: 0.5133 time to fit residues: 25.7327 Evaluate side-chains 47 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 6 optimal weight: 0.7980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.154986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.141614 restraints weight = 2631.863| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.61 r_work: 0.3812 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 2014 Z= 0.282 Angle : 0.681 7.122 2767 Z= 0.329 Chirality : 0.044 0.194 348 Planarity : 0.004 0.036 325 Dihedral : 5.861 42.564 306 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.00 % Allowed : 22.00 % Favored : 74.00 % 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: 1.88 (0.53), residues: 248 helix: 1.78 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -0.78 (0.78), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 144 HIS 0.004 0.002 HIS R 145 PHE 0.011 0.001 PHE R 217 TYR 0.009 0.002 TYR R 154 ARG 0.002 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5335 (tmm) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.5479 time to fit residues: 25.1285 Evaluate side-chains 45 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.0870 chunk 1 optimal weight: 0.0980 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.0670 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.0370 overall best weight: 0.0732 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.159713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146436 restraints weight = 2685.552| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.62 r_work: 0.3876 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2014 Z= 0.180 Angle : 0.651 7.004 2767 Z= 0.306 Chirality : 0.041 0.167 348 Planarity : 0.004 0.038 325 Dihedral : 5.472 42.024 306 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.50 % Allowed : 22.50 % Favored : 74.00 % 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: 2.26 (0.53), residues: 248 helix: 2.02 (0.37), residues: 197 sheet: None (None), residues: 0 loop : -0.54 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 144 HIS 0.003 0.001 HIS R 145 PHE 0.010 0.001 PHE R 330 TYR 0.023 0.002 TYR R 370 ARG 0.002 0.000 ARG R 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6072 (ttm) cc_final: 0.5148 (tmm) outliers start: 7 outliers final: 7 residues processed: 44 average time/residue: 0.5413 time to fit residues: 24.8761 Evaluate side-chains 46 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 331 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 7 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.156943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144274 restraints weight = 2582.259| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.49 r_work: 0.3855 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 2014 Z= 0.247 Angle : 0.684 8.634 2767 Z= 0.322 Chirality : 0.043 0.189 348 Planarity : 0.004 0.033 325 Dihedral : 5.664 42.491 306 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.00 % Allowed : 23.50 % Favored : 72.50 % 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: 2.15 (0.53), residues: 248 helix: 2.01 (0.38), residues: 196 sheet: None (None), residues: 0 loop : -0.82 (0.74), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 144 HIS 0.003 0.001 HIS R 145 PHE 0.013 0.001 PHE R 217 TYR 0.008 0.001 TYR R 87 ARG 0.002 0.000 ARG R 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 496 Ramachandran restraints generated. 248 Oldfield, 0 Emsley, 248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: R 63 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5260 (tmm) REVERT: R 386 THR cc_start: 0.5149 (OUTLIER) cc_final: 0.4362 (m) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.5276 time to fit residues: 24.7513 Evaluate side-chains 47 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 94 MET Chi-restraints excluded: chain R residue 171 THR Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 331 PHE Chi-restraints excluded: chain R residue 386 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 17 optimal weight: 0.0070 chunk 1 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 chunk 22 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 chunk 11 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.160149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147895 restraints weight = 2617.523| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.46 r_work: 0.3898 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2014 Z= 0.186 Angle : 0.660 8.327 2767 Z= 0.309 Chirality : 0.041 0.173 348 Planarity : 0.004 0.035 325 Dihedral : 5.432 42.473 306 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.50 % Allowed : 25.00 % Favored : 71.50 % 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: 2.38 (0.54), residues: 248 helix: 2.14 (0.38), residues: 196 sheet: None (None), residues: 0 loop : -0.64 (0.77), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 144 HIS 0.002 0.001 HIS R 145 PHE 0.011 0.001 PHE R 217 TYR 0.028 0.002 TYR R 370 ARG 0.002 0.000 ARG R 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1851.51 seconds wall clock time: 33 minutes 31.55 seconds (2011.55 seconds total)