Starting phenix.real_space_refine on Tue Mar 3 12:06:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zh0_14716/03_2026/7zh0_14716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zh0_14716/03_2026/7zh0_14716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2026/7zh0_14716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2026/7zh0_14716.map" model { file = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2026/7zh0_14716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zh0_14716/03_2026/7zh0_14716.cif" } resolution = 3.2 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 2557 2.51 5 N 640 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 3869 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3869 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 3 Time building chain proxies: 1.02, per 1000 atoms: 0.26 Number of scatterers: 3869 At special positions: 0 Unit cell: (102.3, 63.36, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 650 8.00 N 640 7.00 C 2557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " 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: 0.28 Conformation dependent library (CDL) restraints added in 145.1 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 80.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.620A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.162A pdb=" N ALA A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.614A pdb=" N TRP A 152 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 179 removed outlier: 3.835A pdb=" N THR A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.629A pdb=" N ILE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.970A pdb=" N GLY A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.776A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.575A pdb=" N VAL A 288 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.577A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.641A pdb=" N VAL A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 373 removed outlier: 3.655A pdb=" N GLY A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 389 through 405 removed outlier: 4.637A pdb=" N GLY A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 Processing helix chain 'A' and resid 433 through 461 removed outlier: 4.268A pdb=" N THR A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 471 through 495 Proline residue: A 485 - end of helix removed outlier: 3.669A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.859A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 93 262 hydrogen bonds defined for protein. 768 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: 0.60 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1196 1.34 - 1.46: 633 1.46 - 1.57: 2106 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3965 Sorted by residual: bond pdb=" N PHE A 450 " pdb=" CA PHE A 450 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.35e+00 bond pdb=" N MET A 448 " pdb=" CA MET A 448 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 bond pdb=" N GLU A 451 " pdb=" CA GLU A 451 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.96e+00 bond pdb=" N ALA A 449 " pdb=" CA ALA A 449 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.67e+00 bond pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.24e+00 ... (remaining 3960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 5075 1.31 - 2.61: 234 2.61 - 3.92: 64 3.92 - 5.22: 15 5.22 - 6.53: 9 Bond angle restraints: 5397 Sorted by residual: angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.28 107.52 3.76 1.09e+00 8.42e-01 1.19e+01 angle pdb=" C VAL A 470 " pdb=" N SER A 471 " pdb=" CA SER A 471 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N VAL A 529 " pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 112.80 109.18 3.62 1.15e+00 7.56e-01 9.90e+00 angle pdb=" C GLU A 13 " pdb=" CA GLU A 13 " pdb=" CB GLU A 13 " ideal model delta sigma weight residual 110.42 116.48 -6.06 1.99e+00 2.53e-01 9.27e+00 angle pdb=" C THR A 297 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " ideal model delta sigma weight residual 123.91 128.84 -4.93 1.66e+00 3.63e-01 8.82e+00 ... (remaining 5392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2089 17.90 - 35.79: 161 35.79 - 53.69: 39 53.69 - 71.58: 5 71.58 - 89.48: 4 Dihedral angle restraints: 2298 sinusoidal: 895 harmonic: 1403 Sorted by residual: dihedral pdb=" CA VAL A 532 " pdb=" C VAL A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" N PHE A 450 " pdb=" CA PHE A 450 " pdb=" CB PHE A 450 " pdb=" CG PHE A 450 " ideal model delta sinusoidal sigma weight residual -60.00 -118.37 58.37 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET A 448 " pdb=" CG MET A 448 " pdb=" SD MET A 448 " pdb=" CE MET A 448 " ideal model delta sinusoidal sigma weight residual 60.00 1.88 58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 427 0.038 - 0.076: 149 0.076 - 0.114: 46 0.114 - 0.151: 3 0.151 - 0.189: 4 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA PHE A 450 " pdb=" N PHE A 450 " pdb=" C PHE A 450 " pdb=" CB PHE A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA MET A 448 " pdb=" N MET A 448 " pdb=" C MET A 448 " pdb=" CB MET A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB ILE A 523 " pdb=" CA ILE A 523 " pdb=" CG1 ILE A 523 " pdb=" CG2 ILE A 523 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 626 not shown) Planarity restraints: 669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 292 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C GLU A 519 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU A 519 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 520 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 131 " 0.010 2.00e-02 2.50e+03 9.61e-03 2.31e+00 pdb=" CG TRP A 131 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 131 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 131 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 131 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 131 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 131 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 131 " 0.000 2.00e-02 2.50e+03 ... (remaining 666 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 240 2.73 - 3.27: 4304 3.27 - 3.82: 6583 3.82 - 4.36: 7315 4.36 - 4.90: 12549 Nonbonded interactions: 30991 Sorted by model distance: nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.191 3.040 nonbonded pdb=" O CYS A 189 " pdb=" OG SER A 278 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.254 3.120 nonbonded pdb=" N ARG A 406 " pdb=" OE2 GLU A 519 " model vdw 2.293 3.120 nonbonded pdb=" NE ARG A 178 " pdb=" OD1 ASN A 335 " model vdw 2.296 3.120 ... (remaining 30986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.600 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.004 0.035 3967 Z= 0.188 Angle : 0.719 6.530 5401 Z= 0.394 Chirality : 0.043 0.189 629 Planarity : 0.005 0.082 669 Dihedral : 13.972 89.476 1394 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.51 % 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: 1.08 (0.39), residues: 487 helix: 1.50 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 212 TYR 0.009 0.001 TYR A 133 PHE 0.025 0.002 PHE A 410 TRP 0.025 0.002 TRP A 131 HIS 0.002 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 3965) covalent geometry : angle 0.71911 ( 5397) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.45525 ( 4) hydrogen bonds : bond 0.13569 ( 262) hydrogen bonds : angle 5.65391 ( 768) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.166 Fit side-chains REVERT: A 306 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 478 ASP cc_start: 0.7986 (m-30) cc_final: 0.7611 (m-30) REVERT: A 515 MET cc_start: 0.6320 (ttm) cc_final: 0.5736 (mmp) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0712 time to fit residues: 7.2864 Evaluate side-chains 59 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.140959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.120621 restraints weight = 6816.124| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.06 r_work: 0.3680 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3967 Z= 0.153 Angle : 0.637 5.863 5401 Z= 0.327 Chirality : 0.041 0.136 629 Planarity : 0.005 0.067 669 Dihedral : 4.417 16.764 536 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.47 % Allowed : 13.45 % Favored : 85.09 % 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: 1.34 (0.39), residues: 487 helix: 1.74 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.37 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.014 0.001 TYR A 185 PHE 0.013 0.001 PHE A 450 TRP 0.014 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3965) covalent geometry : angle 0.63725 ( 5397) SS BOND : bond 0.00258 ( 2) SS BOND : angle 0.52526 ( 4) hydrogen bonds : bond 0.04868 ( 262) hydrogen bonds : angle 4.76227 ( 768) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.146 Fit side-chains REVERT: A 179 TYR cc_start: 0.7446 (m-10) cc_final: 0.7185 (m-10) REVERT: A 478 ASP cc_start: 0.8074 (m-30) cc_final: 0.7648 (m-30) REVERT: A 515 MET cc_start: 0.6665 (ttm) cc_final: 0.6020 (mmp) outliers start: 6 outliers final: 5 residues processed: 73 average time/residue: 0.0546 time to fit residues: 5.2260 Evaluate side-chains 65 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.139483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119189 restraints weight = 6759.463| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.04 r_work: 0.3661 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3967 Z= 0.163 Angle : 0.633 7.163 5401 Z= 0.325 Chirality : 0.041 0.123 629 Planarity : 0.005 0.061 669 Dihedral : 4.408 17.829 536 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.44 % Allowed : 17.11 % Favored : 80.44 % 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: 1.24 (0.39), residues: 487 helix: 1.57 (0.28), residues: 352 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.007 0.001 TYR A 133 PHE 0.014 0.002 PHE A 384 TRP 0.009 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 3965) covalent geometry : angle 0.63307 ( 5397) SS BOND : bond 0.00308 ( 2) SS BOND : angle 0.55405 ( 4) hydrogen bonds : bond 0.04775 ( 262) hydrogen bonds : angle 4.69098 ( 768) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.134 Fit side-chains REVERT: A 14 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: A 459 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 478 ASP cc_start: 0.8124 (m-30) cc_final: 0.7746 (m-30) REVERT: A 515 MET cc_start: 0.6735 (ttm) cc_final: 0.6132 (mmp) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0443 time to fit residues: 4.6176 Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 13 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 = 0.4061 r_free = 0.4061 target = 0.140205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119885 restraints weight = 6767.235| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.07 r_work: 0.3675 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3967 Z= 0.150 Angle : 0.620 6.783 5401 Z= 0.317 Chirality : 0.040 0.124 629 Planarity : 0.005 0.059 669 Dihedral : 4.336 17.016 536 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.40 % Allowed : 18.34 % Favored : 77.26 % 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: 1.22 (0.39), residues: 487 helix: 1.60 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.22 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.005 0.001 TYR A 49 PHE 0.022 0.002 PHE A 356 TRP 0.009 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3965) covalent geometry : angle 0.62058 ( 5397) SS BOND : bond 0.00243 ( 2) SS BOND : angle 0.46990 ( 4) hydrogen bonds : bond 0.04518 ( 262) hydrogen bonds : angle 4.60310 ( 768) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.153 Fit side-chains REVERT: A 14 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: A 140 ILE cc_start: 0.7873 (pt) cc_final: 0.7514 (pt) REVERT: A 435 ARG cc_start: 0.7393 (tpt-90) cc_final: 0.7067 (tpt-90) REVERT: A 459 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: A 478 ASP cc_start: 0.8118 (m-30) cc_final: 0.7749 (m-30) REVERT: A 515 MET cc_start: 0.6737 (ttm) cc_final: 0.6228 (mmp) outliers start: 18 outliers final: 11 residues processed: 81 average time/residue: 0.0541 time to fit residues: 5.8588 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 9 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.139416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119194 restraints weight = 6751.427| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.05 r_work: 0.3663 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3967 Z= 0.151 Angle : 0.617 8.220 5401 Z= 0.317 Chirality : 0.040 0.124 629 Planarity : 0.005 0.053 669 Dihedral : 4.353 16.756 536 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.65 % Allowed : 19.56 % Favored : 75.79 % 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: 1.21 (0.38), residues: 487 helix: 1.60 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.25 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.006 0.001 TYR A 179 PHE 0.011 0.001 PHE A 356 TRP 0.009 0.001 TRP A 358 HIS 0.005 0.002 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3965) covalent geometry : angle 0.61750 ( 5397) SS BOND : bond 0.00282 ( 2) SS BOND : angle 0.49395 ( 4) hydrogen bonds : bond 0.04520 ( 262) hydrogen bonds : angle 4.61896 ( 768) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.166 Fit side-chains REVERT: A 14 PHE cc_start: 0.9124 (OUTLIER) cc_final: 0.8860 (m-80) REVERT: A 384 PHE cc_start: 0.7882 (t80) cc_final: 0.7319 (t80) REVERT: A 435 ARG cc_start: 0.7382 (tpt-90) cc_final: 0.7079 (tpt-90) REVERT: A 459 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: A 478 ASP cc_start: 0.8115 (m-30) cc_final: 0.7747 (m-30) REVERT: A 515 MET cc_start: 0.6722 (ttm) cc_final: 0.6178 (mmp) outliers start: 19 outliers final: 13 residues processed: 87 average time/residue: 0.0515 time to fit residues: 6.0188 Evaluate side-chains 81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.0270 chunk 40 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.140768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.120280 restraints weight = 6906.474| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.10 r_work: 0.3678 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3967 Z= 0.140 Angle : 0.614 7.306 5401 Z= 0.314 Chirality : 0.040 0.170 629 Planarity : 0.005 0.052 669 Dihedral : 4.296 16.361 536 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.16 % Allowed : 20.78 % Favored : 75.06 % 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: 1.15 (0.39), residues: 487 helix: 1.57 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.32 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.006 0.001 TYR A 49 PHE 0.011 0.001 PHE A 356 TRP 0.010 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3965) covalent geometry : angle 0.61399 ( 5397) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.42804 ( 4) hydrogen bonds : bond 0.04383 ( 262) hydrogen bonds : angle 4.56957 ( 768) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.147 Fit side-chains REVERT: A 14 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: A 384 PHE cc_start: 0.7913 (t80) cc_final: 0.7333 (t80) REVERT: A 435 ARG cc_start: 0.7385 (tpt-90) cc_final: 0.7093 (tpt-90) REVERT: A 459 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: A 478 ASP cc_start: 0.8163 (m-30) cc_final: 0.7777 (m-30) REVERT: A 515 MET cc_start: 0.6670 (ttm) cc_final: 0.6166 (mmp) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 0.0585 time to fit residues: 6.2086 Evaluate side-chains 81 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.0000 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.141641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121271 restraints weight = 6845.356| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.06 r_work: 0.3696 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3967 Z= 0.137 Angle : 0.621 9.003 5401 Z= 0.317 Chirality : 0.040 0.165 629 Planarity : 0.005 0.051 669 Dihedral : 4.256 15.795 536 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.16 % Allowed : 22.74 % Favored : 73.11 % 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: 1.15 (0.39), residues: 487 helix: 1.57 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.31 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.012 0.001 TYR A 179 PHE 0.033 0.001 PHE A 356 TRP 0.015 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3965) covalent geometry : angle 0.62129 ( 5397) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.44521 ( 4) hydrogen bonds : bond 0.04306 ( 262) hydrogen bonds : angle 4.50261 ( 768) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.143 Fit side-chains REVERT: A 14 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8889 (m-80) REVERT: A 384 PHE cc_start: 0.7885 (t80) cc_final: 0.7297 (t80) REVERT: A 456 VAL cc_start: 0.8751 (p) cc_final: 0.8521 (t) REVERT: A 459 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 478 ASP cc_start: 0.8197 (m-30) cc_final: 0.7804 (m-30) REVERT: A 515 MET cc_start: 0.6623 (ttm) cc_final: 0.6129 (mmp) outliers start: 17 outliers final: 12 residues processed: 85 average time/residue: 0.0472 time to fit residues: 5.3113 Evaluate side-chains 85 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.141044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.120812 restraints weight = 6791.832| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.03 r_work: 0.3686 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3967 Z= 0.145 Angle : 0.643 10.862 5401 Z= 0.328 Chirality : 0.041 0.156 629 Planarity : 0.005 0.051 669 Dihedral : 4.283 15.716 536 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.40 % Allowed : 22.74 % Favored : 72.86 % 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: 1.07 (0.38), residues: 487 helix: 1.48 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.23 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 73 TYR 0.006 0.001 TYR A 285 PHE 0.019 0.001 PHE A 356 TRP 0.041 0.002 TRP A 65 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3965) covalent geometry : angle 0.64267 ( 5397) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.48010 ( 4) hydrogen bonds : bond 0.04481 ( 262) hydrogen bonds : angle 4.52137 ( 768) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.143 Fit side-chains REVERT: A 14 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: A 384 PHE cc_start: 0.7840 (t80) cc_final: 0.7250 (t80) REVERT: A 435 ARG cc_start: 0.7322 (tpt-90) cc_final: 0.6974 (tpp80) REVERT: A 459 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: A 478 ASP cc_start: 0.8189 (m-30) cc_final: 0.7801 (m-30) REVERT: A 515 MET cc_start: 0.6630 (ttm) cc_final: 0.6141 (mmp) outliers start: 18 outliers final: 14 residues processed: 80 average time/residue: 0.0587 time to fit residues: 6.1534 Evaluate side-chains 80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.139479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.119683 restraints weight = 6778.814| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.02 r_work: 0.3663 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3967 Z= 0.159 Angle : 0.663 11.676 5401 Z= 0.338 Chirality : 0.042 0.154 629 Planarity : 0.005 0.052 669 Dihedral : 4.386 15.913 536 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.16 % Allowed : 22.98 % Favored : 72.86 % 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: 0.99 (0.38), residues: 487 helix: 1.40 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.23 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.014 0.001 TYR A 179 PHE 0.022 0.002 PHE A 356 TRP 0.033 0.002 TRP A 65 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3965) covalent geometry : angle 0.66311 ( 5397) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.52867 ( 4) hydrogen bonds : bond 0.04670 ( 262) hydrogen bonds : angle 4.61122 ( 768) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.161 Fit side-chains REVERT: A 14 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: A 384 PHE cc_start: 0.7869 (t80) cc_final: 0.7306 (t80) REVERT: A 435 ARG cc_start: 0.7393 (tpt-90) cc_final: 0.7055 (tpp80) REVERT: A 459 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: A 478 ASP cc_start: 0.8190 (m-30) cc_final: 0.7832 (m-30) REVERT: A 515 MET cc_start: 0.6657 (ttm) cc_final: 0.6228 (mmp) outliers start: 17 outliers final: 15 residues processed: 80 average time/residue: 0.0522 time to fit residues: 5.5167 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 8 optimal weight: 0.0870 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.142557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122339 restraints weight = 6823.945| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.06 r_work: 0.3704 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3967 Z= 0.139 Angle : 0.651 11.840 5401 Z= 0.331 Chirality : 0.041 0.154 629 Planarity : 0.005 0.053 669 Dihedral : 4.291 15.348 536 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.16 % Allowed : 23.23 % Favored : 72.62 % 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: 0.98 (0.38), residues: 487 helix: 1.42 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.006 0.001 TYR A 49 PHE 0.019 0.001 PHE A 356 TRP 0.031 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3965) covalent geometry : angle 0.65139 ( 5397) SS BOND : bond 0.00192 ( 2) SS BOND : angle 0.42373 ( 4) hydrogen bonds : bond 0.04347 ( 262) hydrogen bonds : angle 4.50147 ( 768) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.159 Fit side-chains REVERT: A 14 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8860 (m-80) REVERT: A 306 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7738 (tm-30) REVERT: A 384 PHE cc_start: 0.7877 (t80) cc_final: 0.7313 (t80) REVERT: A 435 ARG cc_start: 0.7317 (tpt-90) cc_final: 0.6968 (tpp80) REVERT: A 459 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: A 478 ASP cc_start: 0.8227 (m-30) cc_final: 0.7840 (m-30) REVERT: A 515 MET cc_start: 0.6600 (ttm) cc_final: 0.6171 (mmp) outliers start: 17 outliers final: 14 residues processed: 79 average time/residue: 0.0512 time to fit residues: 5.4253 Evaluate side-chains 80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 48 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.141057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.120768 restraints weight = 6864.646| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.08 r_work: 0.3681 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3967 Z= 0.144 Angle : 0.645 12.184 5401 Z= 0.330 Chirality : 0.041 0.149 629 Planarity : 0.005 0.051 669 Dihedral : 4.275 15.190 536 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.16 % Allowed : 24.94 % Favored : 70.90 % 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: 0.95 (0.38), residues: 487 helix: 1.39 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 73 TYR 0.015 0.001 TYR A 179 PHE 0.023 0.001 PHE A 356 TRP 0.029 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3965) covalent geometry : angle 0.64469 ( 5397) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.48062 ( 4) hydrogen bonds : bond 0.04452 ( 262) hydrogen bonds : angle 4.47745 ( 768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1174.35 seconds wall clock time: 20 minutes 44.31 seconds (1244.31 seconds total)