Starting phenix.real_space_refine on Tue Mar 3 11:44:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lck_23276/03_2026/7lck_23276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lck_23276/03_2026/7lck_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 { model { file = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2026/7lck_23276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2026/7lck_23276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2026/7lck_23276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lck_23276/03_2026/7lck_23276.map" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3206 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375} 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 Chain: "R" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 52 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 11} Link IDs: {None: 11} Time building chain proxies: 0.72, per 1000 atoms: 0.22 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 - 3.00 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 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 119.3 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... Secondary structure from input PDB file: 15 helices and 3 sheets defined 67.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'R' and resid 31 through 53 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 136 through 169 removed outlier: 3.791A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 201 removed outlier: 3.923A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 212 No H-bonds generated for 'chain 'R' and resid 210 through 212' Processing helix chain 'R' and resid 213 through 222 Processing helix chain 'R' and resid 224 through 256 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 261 through 276 removed outlier: 4.025A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) 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 280 through 292 removed outlier: 3.933A pdb=" N TRP R 284 " --> pdb=" O PHE R 280 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 337 Proline residue: R 312 - end of helix removed outlier: 3.764A pdb=" N SER R 333 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 361 removed outlier: 4.317A pdb=" N ILE R 345 " --> pdb=" O CYS R 341 " (cutoff:3.500A) 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 363 through 370 removed outlier: 3.578A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 391 removed outlier: 3.552A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.615A pdb=" N GLN R 410 " --> pdb=" O ASN R 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AA2, 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) removed outlier: 3.738A pdb=" N LEU R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AA3, 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) 191 hydrogen bonds defined for protein. 570 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: 0.47 Time building geometry restraints manager: 0.32 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: 0.00 - 3.31: 4492 3.31 - 6.62: 64 6.62 - 9.93: 12 9.93 - 13.25: 2 13.25 - 16.56: 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: 87 2.71 - 3.26: 3191 3.26 - 3.80: 4981 3.80 - 4.35: 6279 4.35 - 4.90: 10736 Nonbonded interactions: 25274 Sorted by model distance: nonbonded pdb=" NE2 GLN R 112 " pdb=" O SER R 117 " model vdw 2.160 3.120 nonbonded pdb=" O LEU R 244 " pdb=" ND2 ASN R 320 " model vdw 2.204 3.120 nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.278 3.120 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH2 ARG R 102 " model vdw 2.315 3.120 nonbonded pdb=" OG SER R 31 " pdb=" N LEU R 32 " model vdw 2.422 3.120 ... (remaining 25269 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: 1.040 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: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.410 Find NCS groups from input model: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.610 ------------------------------------------------------------------------------- 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 3355 Z= 0.459 Angle : 1.051 16.557 4579 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG R 40 TYR 0.019 0.002 TYR R 242 PHE 0.020 0.002 PHE R 393 TRP 0.013 0.002 TRP R 243 HIS 0.005 0.001 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00803 ( 3351) covalent geometry : angle 1.05042 ( 4571) SS BOND : bond 0.00425 ( 4) SS BOND : angle 1.48997 ( 8) hydrogen bonds : bond 0.18755 ( 189) hydrogen bonds : angle 6.17455 ( 570) *********************** 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 to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.074 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.0672 time to fit residues: 3.6709 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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: 39 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.0170 chunk 22 optimal weight: 0.0770 chunk 37 optimal weight: 3.9990 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.132169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108431 restraints weight = 5947.353| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.94 r_work: 0.3478 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3355 Z= 0.129 Angle : 0.631 11.278 4579 Z= 0.314 Chirality : 0.037 0.130 497 Planarity : 0.004 0.042 557 Dihedral : 6.061 35.795 458 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.29 % Allowed : 8.14 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.44), residues: 386 helix: 0.74 (0.33), residues: 267 sheet: 0.11 (1.92), residues: 10 loop : -1.53 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 102 TYR 0.030 0.002 TYR R 148 PHE 0.011 0.001 PHE R 393 TRP 0.010 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3351) covalent geometry : angle 0.62973 ( 4571) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.20791 ( 8) hydrogen bonds : bond 0.05201 ( 189) hydrogen bonds : angle 3.96749 ( 570) *********************** 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 to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.118 Fit side-chains REVERT: R 294 GLU cc_start: 0.7362 (pp20) cc_final: 0.7002 (pp20) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0750 time to fit residues: 2.7857 Evaluate side-chains 26 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103702 restraints weight = 5988.276| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.94 r_work: 0.3406 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3355 Z= 0.143 Angle : 0.583 8.873 4579 Z= 0.297 Chirality : 0.038 0.128 497 Planarity : 0.004 0.050 557 Dihedral : 5.429 34.382 453 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.58 % Allowed : 11.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.44), residues: 386 helix: 1.06 (0.33), residues: 267 sheet: 0.05 (1.70), residues: 10 loop : -1.48 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 419 TYR 0.029 0.002 TYR R 148 PHE 0.009 0.001 PHE R 230 TRP 0.016 0.001 TRP R 72 HIS 0.001 0.000 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3351) covalent geometry : angle 0.57935 ( 4571) SS BOND : bond 0.00659 ( 4) SS BOND : angle 1.58406 ( 8) hydrogen bonds : bond 0.05302 ( 189) hydrogen bonds : angle 3.66342 ( 570) *********************** 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 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.121 Fit side-chains REVERT: R 294 GLU cc_start: 0.7399 (pp20) cc_final: 0.7003 (pp20) outliers start: 2 outliers final: 1 residues processed: 25 average time/residue: 0.0646 time to fit residues: 2.0723 Evaluate side-chains 23 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.128364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103867 restraints weight = 5972.459| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.93 r_work: 0.3410 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3355 Z= 0.142 Angle : 0.564 8.331 4579 Z= 0.290 Chirality : 0.038 0.124 497 Planarity : 0.004 0.053 557 Dihedral : 5.436 34.590 453 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.87 % Allowed : 13.66 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.44), residues: 386 helix: 1.09 (0.33), residues: 273 sheet: 0.03 (1.55), residues: 10 loop : -1.39 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 44 TYR 0.027 0.001 TYR R 148 PHE 0.008 0.001 PHE R 230 TRP 0.009 0.001 TRP R 284 HIS 0.001 0.000 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3351) covalent geometry : angle 0.56137 ( 4571) SS BOND : bond 0.00357 ( 4) SS BOND : angle 1.48790 ( 8) hydrogen bonds : bond 0.05191 ( 189) hydrogen bonds : angle 3.71660 ( 570) *********************** 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 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.099 Fit side-chains REVERT: R 294 GLU cc_start: 0.7624 (pp20) cc_final: 0.7202 (pp20) REVERT: R 421 ARG cc_start: 0.4844 (tpm170) cc_final: 0.4621 (tpp-160) outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.0600 time to fit residues: 2.0324 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 6 optimal weight: 0.0030 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.129215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104621 restraints weight = 5967.308| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.96 r_work: 0.3425 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3355 Z= 0.119 Angle : 0.541 7.922 4579 Z= 0.276 Chirality : 0.037 0.123 497 Planarity : 0.004 0.054 557 Dihedral : 5.239 33.713 453 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.87 % Allowed : 15.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.44), residues: 386 helix: 1.41 (0.33), residues: 267 sheet: 0.29 (1.50), residues: 10 loop : -1.36 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 419 TYR 0.026 0.001 TYR R 148 PHE 0.008 0.001 PHE R 156 TRP 0.016 0.001 TRP R 72 HIS 0.001 0.000 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3351) covalent geometry : angle 0.53677 ( 4571) SS BOND : bond 0.00499 ( 4) SS BOND : angle 1.68998 ( 8) hydrogen bonds : bond 0.04812 ( 189) hydrogen bonds : angle 3.42404 ( 570) *********************** 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 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.130 Fit side-chains REVERT: R 60 LEU cc_start: 0.9331 (mp) cc_final: 0.8990 (tp) REVERT: R 260 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4245 (m-80) REVERT: R 294 GLU cc_start: 0.7631 (pp20) cc_final: 0.7135 (pp20) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.0829 time to fit residues: 2.9254 Evaluate side-chains 27 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.129650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.105008 restraints weight = 5946.720| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.86 r_work: 0.3438 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3355 Z= 0.128 Angle : 0.556 7.687 4579 Z= 0.285 Chirality : 0.038 0.123 497 Planarity : 0.004 0.055 557 Dihedral : 5.272 33.540 453 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.16 % Allowed : 15.70 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.44), residues: 386 helix: 1.47 (0.33), residues: 267 sheet: 0.35 (1.49), residues: 10 loop : -1.33 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 419 TYR 0.026 0.001 TYR R 148 PHE 0.008 0.001 PHE R 156 TRP 0.008 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3351) covalent geometry : angle 0.55061 ( 4571) SS BOND : bond 0.00131 ( 4) SS BOND : angle 2.00627 ( 8) hydrogen bonds : bond 0.04852 ( 189) hydrogen bonds : angle 3.52871 ( 570) *********************** 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 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.127 Fit side-chains REVERT: R 60 LEU cc_start: 0.9329 (mp) cc_final: 0.9035 (tp) REVERT: R 260 PHE cc_start: 0.5244 (OUTLIER) cc_final: 0.4319 (m-80) REVERT: R 294 GLU cc_start: 0.7648 (pp20) cc_final: 0.7142 (pp20) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0610 time to fit residues: 2.1351 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.101 ------------------------------------------------------------------------------- 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 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.128956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104447 restraints weight = 5996.632| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.88 r_work: 0.3438 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3355 Z= 0.127 Angle : 0.548 7.566 4579 Z= 0.280 Chirality : 0.037 0.123 497 Planarity : 0.004 0.055 557 Dihedral : 5.191 33.267 453 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.87 % Allowed : 15.99 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.44), residues: 386 helix: 1.53 (0.33), residues: 269 sheet: 0.72 (1.58), residues: 10 loop : -1.48 (0.57), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 419 TYR 0.026 0.001 TYR R 148 PHE 0.008 0.001 PHE R 156 TRP 0.016 0.001 TRP R 72 HIS 0.001 0.000 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3351) covalent geometry : angle 0.54422 ( 4571) SS BOND : bond 0.00630 ( 4) SS BOND : angle 1.69229 ( 8) hydrogen bonds : bond 0.04804 ( 189) hydrogen bonds : angle 3.38151 ( 570) *********************** 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 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.145 Fit side-chains REVERT: R 60 LEU cc_start: 0.9306 (mp) cc_final: 0.9031 (tp) REVERT: R 260 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4295 (m-80) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.0583 time to fit residues: 2.2015 Evaluate side-chains 27 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.129421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104727 restraints weight = 5977.890| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.92 r_work: 0.3431 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.122 Angle : 0.590 8.949 4579 Z= 0.298 Chirality : 0.038 0.140 497 Planarity : 0.005 0.058 557 Dihedral : 5.214 32.642 453 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.45 % Allowed : 15.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.44), residues: 386 helix: 1.65 (0.33), residues: 269 sheet: 0.96 (1.69), residues: 10 loop : -1.46 (0.57), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 44 TYR 0.025 0.001 TYR R 148 PHE 0.008 0.001 PHE R 156 TRP 0.009 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3351) covalent geometry : angle 0.58576 ( 4571) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.74372 ( 8) hydrogen bonds : bond 0.04795 ( 189) hydrogen bonds : angle 3.51540 ( 570) *********************** 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 31 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.131 Fit side-chains REVERT: R 60 LEU cc_start: 0.9309 (mp) cc_final: 0.9046 (tp) REVERT: R 260 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4274 (m-80) outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.0643 time to fit residues: 2.4562 Evaluate side-chains 27 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.128726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104239 restraints weight = 6026.872| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.89 r_work: 0.3432 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3355 Z= 0.129 Angle : 0.587 8.017 4579 Z= 0.299 Chirality : 0.038 0.122 497 Planarity : 0.004 0.055 557 Dihedral : 5.164 32.565 453 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.16 % Allowed : 15.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.44), residues: 386 helix: 1.66 (0.33), residues: 266 sheet: 0.96 (1.73), residues: 10 loop : -1.39 (0.56), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 44 TYR 0.025 0.001 TYR R 148 PHE 0.008 0.001 PHE R 156 TRP 0.017 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3351) covalent geometry : angle 0.58298 ( 4571) SS BOND : bond 0.00622 ( 4) SS BOND : angle 1.80381 ( 8) hydrogen bonds : bond 0.04814 ( 189) hydrogen bonds : angle 3.41080 ( 570) *********************** 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 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: R 60 LEU cc_start: 0.9288 (mp) cc_final: 0.9051 (tp) REVERT: R 260 PHE cc_start: 0.5048 (OUTLIER) cc_final: 0.4152 (m-80) outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.0602 time to fit residues: 2.1784 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.128994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104344 restraints weight = 5957.589| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.91 r_work: 0.3425 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3355 Z= 0.129 Angle : 0.577 7.718 4579 Z= 0.296 Chirality : 0.038 0.124 497 Planarity : 0.005 0.055 557 Dihedral : 5.212 32.494 453 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.45 % Allowed : 15.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.44), residues: 386 helix: 1.79 (0.33), residues: 264 sheet: 1.13 (1.80), residues: 10 loop : -1.48 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 44 TYR 0.025 0.001 TYR R 148 PHE 0.009 0.001 PHE R 156 TRP 0.009 0.001 TRP R 243 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3351) covalent geometry : angle 0.57421 ( 4571) SS BOND : bond 0.00667 ( 4) SS BOND : angle 1.40001 ( 8) hydrogen bonds : bond 0.04826 ( 189) hydrogen bonds : angle 3.49952 ( 570) ********************** 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 30 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: R 60 LEU cc_start: 0.9278 (mp) cc_final: 0.9052 (tp) REVERT: R 260 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.4213 (m-80) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.0634 time to fit residues: 2.2776 Evaluate side-chains 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 0.0670 chunk 4 optimal weight: 0.1980 overall best weight: 0.3526 ------------------------------------------------------------------------------- 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 = 0.3888 r_free = 0.3888 target = 0.130382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.106066 restraints weight = 5986.798| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.88 r_work: 0.3458 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3355 Z= 0.114 Angle : 0.572 7.686 4579 Z= 0.293 Chirality : 0.037 0.122 497 Planarity : 0.004 0.055 557 Dihedral : 5.031 31.418 453 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.87 % Allowed : 15.99 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.44), residues: 386 helix: 1.76 (0.33), residues: 267 sheet: 1.02 (1.76), residues: 10 loop : -1.40 (0.56), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 44 TYR 0.024 0.001 TYR R 148 PHE 0.007 0.001 PHE R 156 TRP 0.015 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3351) covalent geometry : angle 0.56804 ( 4571) SS BOND : bond 0.00669 ( 4) SS BOND : angle 1.68340 ( 8) hydrogen bonds : bond 0.04512 ( 189) hydrogen bonds : angle 3.33320 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 836.48 seconds wall clock time: 14 minutes 56.27 seconds (896.27 seconds total)