Starting phenix.real_space_refine on Wed Jul 1 22:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lck_23276/07_2026/7lck_23276.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lck_23276/07_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_23276/07_2026/7lck_23276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lck_23276/07_2026/7lck_23276.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lck_23276/07_2026/7lck_23276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lck_23276/07_2026/7lck_23276.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lck_23276/07_2026/7lck_23276.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lck_23276/07_2026/7lck_23276.cif" } 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-6108/lib/python3.11/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: 0.88, per 1000 atoms: 0.27 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: 0.27 Conformation dependent library (CDL) restraints added in 111.8 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: 0.08 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: 0.44 Time building geometry restraints manager: 0.34 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: 1694 16.60 - 33.20: 168 33.20 - 49.80: 47 49.80 - 66.40: 7 66.40 - 83.00: 2 Dihedral angle restraints: 1918 sinusoidal: 762 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 1915 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.790 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 14.226 82.998 1158 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/Z covalent geometry : bond 0.00803 / 0.46 ( 3351) covalent geometry : angle 1.05042 / 0.66 ( 4571) SS BOND : bond 0.00425 / 0.22 ( 4) SS BOND : angle 1.48997 / 0.86 ( 8) hydrogen bonds : bond 0.18755 / 11.79 ( 189) hydrogen bonds : angle 6.17455 / 4.50 ( 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 : 0.135 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.0712 time to fit residues: 3.9602 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 : 0.126 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.132377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.108648 restraints weight = 5935.324| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.93 r_work: 0.3483 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3355 Z= 0.124 Angle : 0.622 11.221 4579 Z= 0.309 Chirality : 0.038 0.147 497 Planarity : 0.004 0.042 557 Dihedral : 5.219 34.805 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 0.13 (0.44), residues: 386 helix: 0.77 (0.33), residues: 267 sheet: 0.05 (1.91), residues: 10 loop : -1.54 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 102 TYR 0.031 0.002 TYR R 148 PHE 0.010 0.001 PHE R 367 TRP 0.011 0.001 TRP R 214 HIS 0.002 0.000 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 3351) covalent geometry : angle 0.62103 / 0.31 ( 4571) SS BOND : bond 0.00225 / 0.11 ( 4) SS BOND : angle 1.09664 / 0.59 ( 8) hydrogen bonds : bond 0.05043 / 3.26 ( 189) hydrogen bonds : angle 3.97110 / 2.89 ( 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 : 0.072 Fit side-chains REVERT: R 294 GLU cc_start: 0.7354 (pp20) cc_final: 0.6997 (pp20) outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0510 time to fit residues: 2.0016 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 : 0.126 ------------------------------------------------------------------------------- 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: 0.4980 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105942 restraints weight = 5944.061| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.91 r_work: 0.3433 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3355 Z= 0.124 Angle : 0.562 8.658 4579 Z= 0.286 Chirality : 0.038 0.131 497 Planarity : 0.004 0.050 557 Dihedral : 4.431 36.124 439 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.58 % Allowed : 11.34 % Favored : 88.08 % 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: 0.61 (0.44), residues: 386 helix: 1.17 (0.33), residues: 267 sheet: 0.07 (1.73), residues: 10 loop : -1.45 (0.57), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 102 TYR 0.029 0.001 TYR R 148 PHE 0.007 0.001 PHE R 156 TRP 0.012 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3351) covalent geometry : angle 0.55941 / 0.28 ( 4571) SS BOND : bond 0.00735 / 0.39 ( 4) SS BOND : angle 1.37179 / 0.81 ( 8) hydrogen bonds : bond 0.04955 / 3.21 ( 189) hydrogen bonds : angle 3.59085 / 2.66 ( 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 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.122 Fit side-chains REVERT: R 294 GLU cc_start: 0.7371 (pp20) cc_final: 0.6923 (pp20) REVERT: R 371 MET cc_start: 0.7821 (tpp) cc_final: 0.7609 (tpt) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.0450 time to fit residues: 1.7697 Evaluate side-chains 25 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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: 0.4980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.105223 restraints weight = 5941.617| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.92 r_work: 0.3437 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2532 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= 0.131 Angle : 0.562 8.126 4579 Z= 0.286 Chirality : 0.038 0.124 497 Planarity : 0.004 0.053 557 Dihedral : 4.451 36.879 439 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.16 % Allowed : 13.66 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.44), residues: 386 helix: 1.20 (0.33), residues: 272 sheet: 0.03 (1.52), residues: 10 loop : -1.37 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 102 TYR 0.028 0.001 TYR R 148 PHE 0.008 0.001 PHE R 156 TRP 0.009 0.001 TRP R 284 HIS 0.001 0.000 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 3351) covalent geometry : angle 0.55896 / 0.28 ( 4571) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 1.43976 / 0.88 ( 8) hydrogen bonds : bond 0.04947 / 3.20 ( 189) hydrogen bonds : angle 3.67480 / 2.69 ( 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: 4 poor density : 24 time to evaluate : 0.124 Fit side-chains REVERT: R 260 PHE cc_start: 0.5249 (OUTLIER) cc_final: 0.4303 (m-80) REVERT: R 294 GLU cc_start: 0.7567 (pp20) cc_final: 0.7082 (pp20) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0620 time to fit residues: 2.2021 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 : 0.124 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.128581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104141 restraints weight = 5958.959| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.91 r_work: 0.3409 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3355 Z= 0.135 Angle : 0.552 7.836 4579 Z= 0.282 Chirality : 0.038 0.124 497 Planarity : 0.004 0.054 557 Dihedral : 4.360 37.314 439 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.16 % Allowed : 14.53 % Favored : 84.30 % 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: 0.90 (0.44), residues: 386 helix: 1.40 (0.33), residues: 267 sheet: 0.13 (1.46), residues: 10 loop : -1.36 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 348 TYR 0.027 0.001 TYR R 148 PHE 0.009 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/Z covalent geometry : bond 0.00306 / 0.13 ( 3351) covalent geometry : angle 0.54853 / 0.28 ( 4571) SS BOND : bond 0.00435 / 0.23 ( 4) SS BOND : angle 1.54955 / 0.95 ( 8) hydrogen bonds : bond 0.04941 / 3.19 ( 189) hydrogen bonds : angle 3.45133 / 2.57 ( 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 31 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.122 Fit side-chains REVERT: R 60 LEU cc_start: 0.9336 (mp) cc_final: 0.9006 (tp) REVERT: R 260 PHE cc_start: 0.5201 (OUTLIER) cc_final: 0.4260 (m-80) outliers start: 4 outliers final: 2 residues processed: 30 average time/residue: 0.0777 time to fit residues: 2.9076 Evaluate side-chains 26 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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: 0.4980 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.0000 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105769 restraints weight = 5888.628| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.83 r_work: 0.3452 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3355 Z= 0.120 Angle : 0.564 7.834 4579 Z= 0.289 Chirality : 0.037 0.141 497 Planarity : 0.004 0.055 557 Dihedral : 4.357 36.432 439 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: 1.13 (0.44), residues: 386 helix: 1.61 (0.33), residues: 266 sheet: 0.18 (1.46), residues: 10 loop : -1.34 (0.57), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 44 TYR 0.025 0.001 TYR R 148 PHE 0.007 0.001 PHE R 156 TRP 0.008 0.001 TRP R 243 HIS 0.001 0.000 HIS R 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 3351) covalent geometry : angle 0.56017 / 0.29 ( 4571) SS BOND : bond 0.00376 / 0.20 ( 4) SS BOND : angle 1.75072 / 1.11 ( 8) hydrogen bonds : bond 0.04737 / 3.07 ( 189) hydrogen bonds : angle 3.54146 / 2.61 ( 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 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.142 Fit side-chains REVERT: R 60 LEU cc_start: 0.9329 (mp) cc_final: 0.9035 (tp) REVERT: R 260 PHE cc_start: 0.5214 (OUTLIER) cc_final: 0.4273 (m-80) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0814 time to fit residues: 2.7903 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 : 0.125 ------------------------------------------------------------------------------- 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 390 PHE 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: 0.5980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.129573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105402 restraints weight = 6024.782| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.86 r_work: 0.3443 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 0.027 3355 Z= 0.123 Angle : 0.574 7.825 4579 Z= 0.290 Chirality : 0.038 0.121 497 Planarity : 0.004 0.055 557 Dihedral : 4.284 36.538 439 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.16 % Allowed : 15.41 % Favored : 83.43 % 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: 1.11 (0.44), residues: 386 helix: 1.62 (0.33), residues: 269 sheet: 0.41 (1.48), residues: 10 loop : -1.55 (0.56), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 44 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/Z covalent geometry : bond 0.00277 / 0.12 ( 3351) covalent geometry : angle 0.57202 / 0.29 ( 4571) SS BOND : bond 0.00428 / 0.22 ( 4) SS BOND : angle 1.35990 / 0.82 ( 8) hydrogen bonds : bond 0.04710 / 3.03 ( 189) hydrogen bonds : angle 3.34347 / 2.50 ( 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 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.123 Fit side-chains REVERT: R 60 LEU cc_start: 0.9315 (mp) cc_final: 0.9039 (tp) REVERT: R 260 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4286 (m-80) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0683 time to fit residues: 2.3724 Evaluate side-chains 26 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.129903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.105378 restraints weight = 5934.816| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.86 r_work: 0.3447 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3355 Z= 0.119 Angle : 0.562 7.376 4579 Z= 0.286 Chirality : 0.038 0.122 497 Planarity : 0.004 0.054 557 Dihedral : 4.316 36.340 439 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % 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: 1.23 (0.44), residues: 386 helix: 1.69 (0.33), residues: 269 sheet: 0.79 (1.59), residues: 10 loop : -1.50 (0.57), residues: 107 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 0.008 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/Z covalent geometry : bond 0.00272 / 0.12 ( 3351) covalent geometry : angle 0.55976 / 0.29 ( 4571) SS BOND : bond 0.00363 / 0.19 ( 4) SS BOND : angle 1.41412 / 0.88 ( 8) hydrogen bonds : bond 0.04621 / 3.00 ( 189) hydrogen bonds : angle 3.45439 / 2.54 ( 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 29 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.121 Fit side-chains REVERT: R 60 LEU cc_start: 0.9283 (mp) cc_final: 0.9039 (tp) REVERT: R 260 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.4229 (m-80) outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.0698 time to fit residues: 2.4271 Evaluate side-chains 26 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.146 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 1 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 34 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105693 restraints weight = 5950.925| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.86 r_work: 0.3452 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3140 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= 0.115 Angle : 0.556 7.365 4579 Z= 0.284 Chirality : 0.037 0.121 497 Planarity : 0.004 0.055 557 Dihedral : 4.206 36.174 439 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.87 % Allowed : 15.70 % Favored : 83.43 % 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: 1.38 (0.44), residues: 386 helix: 1.89 (0.33), residues: 263 sheet: 0.91 (1.69), residues: 10 loop : -1.49 (0.54), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 44 TYR 0.025 0.001 TYR R 148 PHE 0.007 0.001 PHE R 156 TRP 0.016 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 3351) covalent geometry : angle 0.55391 / 0.28 ( 4571) SS BOND : bond 0.00473 / 0.25 ( 4) SS BOND : angle 1.23042 / 0.74 ( 8) hydrogen bonds : bond 0.04495 / 2.90 ( 189) hydrogen bonds : angle 3.29141 / 2.46 ( 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: 3 poor density : 26 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: R 60 LEU cc_start: 0.9275 (mp) cc_final: 0.9028 (tp) REVERT: R 260 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.4329 (m-80) outliers start: 3 outliers final: 2 residues processed: 28 average time/residue: 0.0675 time to fit residues: 2.4349 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 : 0.121 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104234 restraints weight = 5933.806| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.84 r_work: 0.3428 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3214 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= 0.145 Angle : 0.579 7.404 4579 Z= 0.297 Chirality : 0.039 0.138 497 Planarity : 0.005 0.055 557 Dihedral : 4.395 37.088 439 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.90 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: 1.28 (0.44), residues: 386 helix: 1.74 (0.33), residues: 264 sheet: 1.07 (1.75), residues: 10 loop : -1.39 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 44 TYR 0.026 0.002 TYR R 148 PHE 0.010 0.001 PHE R 156 TRP 0.009 0.001 TRP R 243 HIS 0.002 0.000 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 3351) covalent geometry : angle 0.57777 / 0.30 ( 4571) SS BOND : bond 0.00413 / 0.22 ( 4) SS BOND : angle 1.13228 / 0.66 ( 8) hydrogen bonds : bond 0.04907 / 3.19 ( 189) hydrogen bonds : angle 3.48295 / 2.56 ( 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 28 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.121 Fit side-chains REVERT: R 60 LEU cc_start: 0.9264 (mp) cc_final: 0.9028 (tp) REVERT: R 260 PHE cc_start: 0.5165 (OUTLIER) cc_final: 0.4249 (m-80) outliers start: 4 outliers final: 2 residues processed: 26 average time/residue: 0.0710 time to fit residues: 2.3529 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 : 0.133 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.0030 chunk 4 optimal weight: 0.0070 overall best weight: 0.2806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.131370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.107159 restraints weight = 5922.672| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.87 r_work: 0.3475 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3355 Z= 0.109 Angle : 0.550 7.328 4579 Z= 0.281 Chirality : 0.037 0.122 497 Planarity : 0.004 0.055 557 Dihedral : 4.141 35.673 439 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: 1.42 (0.45), residues: 386 helix: 2.01 (0.33), residues: 262 sheet: -0.73 (1.08), residues: 20 loop : -1.59 (0.57), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 44 TYR 0.024 0.001 TYR R 148 PHE 0.007 0.001 PHE R 367 TRP 0.011 0.001 TRP R 72 HIS 0.001 0.000 HIS R 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 3351) covalent geometry : angle 0.54796 / 0.28 ( 4571) SS BOND : bond 0.00504 / 0.27 ( 4) SS BOND : angle 1.19677 / 0.71 ( 8) hydrogen bonds : bond 0.04331 / 2.80 ( 189) hydrogen bonds : angle 3.24493 / 2.43 ( 570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 949.31 seconds wall clock time: 16 minutes 57.69 seconds (1017.69 seconds total)