Starting phenix.real_space_refine on Tue Mar 3 12:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bc7_12141/03_2026/7bc7_12141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc7_12141/03_2026/7bc7_12141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bc7_12141/03_2026/7bc7_12141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc7_12141/03_2026/7bc7_12141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bc7_12141/03_2026/7bc7_12141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc7_12141/03_2026/7bc7_12141.map" } resolution = 3.3 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= 0.053 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 2734 2.51 5 N 700 2.21 5 O 753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4209 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3269 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 17, 'TRANS': 414} Chain: "B" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 909 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LYA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.93, per 1000 atoms: 0.22 Number of scatterers: 4209 At special positions: 0 Unit cell: (104.832, 64.896, 66.56, 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 753 8.00 N 700 7.00 C 2734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 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 156.8 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 64.8% alpha, 7.3% 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 29 through 59 removed outlier: 3.731A pdb=" N LEU A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 80 through 120 removed outlier: 3.921A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.858A pdb=" N SER A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 146 removed outlier: 4.378A pdb=" N VAL A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.778A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 178 removed outlier: 3.633A pdb=" N ILE A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 211 removed outlier: 3.920A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 237 removed outlier: 4.014A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 223 " --> pdb=" O PRO A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 removed outlier: 3.616A pdb=" N TYR A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 300 removed outlier: 4.549A pdb=" N LYS A 274 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 334 removed outlier: 3.530A pdb=" N ILE A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 324 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 removed outlier: 4.042A pdb=" N ALA A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 373 removed outlier: 3.639A pdb=" N MET A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 391 removed outlier: 4.135A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 425 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.598A pdb=" N SER A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.855A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.801A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 82 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.778A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.778A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 798 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: 0.63 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: 1.18 - 1.31: 657 1.31 - 1.43: 1206 1.43 - 1.56: 2415 1.56 - 1.68: 0 1.68 - 1.81: 33 Bond restraints: 4311 Sorted by residual: bond pdb=" C20 LYA A 501 " pdb=" N22 LYA A 501 " ideal model delta sigma weight residual 1.340 1.468 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C17 LYA A 501 " pdb=" N19 LYA A 501 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C13 LYA A 501 " pdb=" C14 LYA A 501 " ideal model delta sigma weight residual 1.444 1.367 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.50e-03 1.11e+04 1.16e+01 bond pdb=" C13 LYA A 501 " pdb=" C9 LYA A 501 " ideal model delta sigma weight residual 1.434 1.366 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 4306 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 5788 3.21 - 6.42: 70 6.42 - 9.63: 12 9.63 - 12.84: 0 12.84 - 16.05: 3 Bond angle restraints: 5873 Sorted by residual: angle pdb=" C10 LYA A 501 " pdb=" C9 LYA A 501 " pdb=" C8 LYA A 501 " ideal model delta sigma weight residual 126.87 110.82 16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C13 LYA A 501 " pdb=" C9 LYA A 501 " pdb=" C8 LYA A 501 " ideal model delta sigma weight residual 126.91 141.38 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N18 LYA A 501 " pdb=" C17 LYA A 501 " pdb=" N19 LYA A 501 " ideal model delta sigma weight residual 116.30 129.65 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA VAL A 382 " pdb=" C VAL A 382 " pdb=" O VAL A 382 " ideal model delta sigma weight residual 121.27 117.50 3.77 1.04e+00 9.25e-01 1.31e+01 angle pdb=" N LEU A 387 " pdb=" CA LEU A 387 " pdb=" C LEU A 387 " ideal model delta sigma weight residual 111.28 107.84 3.44 1.09e+00 8.42e-01 9.95e+00 ... (remaining 5868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2197 17.17 - 34.34: 255 34.34 - 51.51: 35 51.51 - 68.68: 10 68.68 - 85.85: 8 Dihedral angle restraints: 2505 sinusoidal: 940 harmonic: 1565 Sorted by residual: dihedral pdb=" CA GLU A 267 " pdb=" C GLU A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CB CYS A 72 " pdb=" SG CYS A 72 " pdb=" SG CYS A 306 " pdb=" CB CYS A 306 " ideal model delta sinusoidal sigma weight residual 93.00 130.28 -37.28 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA TYR B 80 " pdb=" C TYR B 80 " pdb=" N LEU B 81 " pdb=" CA LEU B 81 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 2502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 398 0.041 - 0.082: 194 0.082 - 0.124: 64 0.124 - 0.165: 13 0.165 - 0.206: 3 Chirality restraints: 672 Sorted by residual: chirality pdb=" C23 LYA A 501 " pdb=" C24 LYA A 501 " pdb=" C29 LYA A 501 " pdb=" N22 LYA A 501 " both_signs ideal model delta sigma weight residual False -2.46 -2.67 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR A 363 " pdb=" N THR A 363 " pdb=" C THR A 363 " pdb=" CB THR A 363 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA LEU A 387 " pdb=" N LEU A 387 " pdb=" C LEU A 387 " pdb=" CB LEU A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 669 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 216 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C TYR A 216 " -0.031 2.00e-02 2.50e+03 pdb=" O TYR A 216 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 217 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 432 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 433 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 443 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 444 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.022 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 80 2.67 - 3.23: 4235 3.23 - 3.78: 6609 3.78 - 4.34: 8851 4.34 - 4.90: 14974 Nonbonded interactions: 34749 Sorted by model distance: nonbonded pdb=" O LYS A 249 " pdb=" OG1 THR A 252 " model vdw 2.110 3.040 nonbonded pdb=" O TYR A 299 " pdb=" NH2 ARG A 430 " model vdw 2.233 3.120 nonbonded pdb=" NH1 ARG A 156 " pdb=" OD2 ASP A 164 " model vdw 2.268 3.120 nonbonded pdb=" O SER A 28 " pdb=" OH TYR A 233 " model vdw 2.274 3.040 nonbonded pdb=" O GLY A 113 " pdb=" OG SER A 116 " model vdw 2.282 3.040 ... (remaining 34744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.010 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.009 0.128 4313 Z= 0.437 Angle : 0.977 16.055 5877 Z= 0.493 Chirality : 0.053 0.206 672 Planarity : 0.005 0.039 733 Dihedral : 15.119 85.854 1507 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.36 % Favored : 90.46 % Rotamer: Outliers : 0.23 % Allowed : 1.37 % Favored : 98.40 % 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: -1.48 (0.36), residues: 545 helix: 0.54 (0.29), residues: 325 sheet: -3.74 (0.63), residues: 54 loop : -3.06 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 430 TYR 0.024 0.002 TYR A 299 PHE 0.016 0.002 PHE A 103 TRP 0.012 0.002 TRP B 36 HIS 0.005 0.002 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00909 ( 4311) covalent geometry : angle 0.97771 ( 5873) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.48982 ( 4) hydrogen bonds : bond 0.17575 ( 269) hydrogen bonds : angle 6.53299 ( 798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.157 Fit side-chains REVERT: A 332 LEU cc_start: 0.8018 (tp) cc_final: 0.7815 (tp) REVERT: A 377 MET cc_start: 0.7508 (mtm) cc_final: 0.7273 (mtm) REVERT: B 57 ASP cc_start: 0.8199 (t70) cc_final: 0.7879 (t70) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.0507 time to fit residues: 7.1699 Evaluate side-chains 90 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 135 GLN ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.129110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120368 restraints weight = 5873.621| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.72 r_work: 0.3312 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4313 Z= 0.142 Angle : 0.671 8.473 5877 Z= 0.326 Chirality : 0.042 0.154 672 Planarity : 0.005 0.042 733 Dihedral : 8.801 89.789 612 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.69 % Allowed : 10.98 % Favored : 88.33 % 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: -0.69 (0.37), residues: 545 helix: 0.99 (0.28), residues: 340 sheet: -3.50 (0.74), residues: 40 loop : -2.78 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 430 TYR 0.016 0.001 TYR A 299 PHE 0.014 0.001 PHE A 436 TRP 0.012 0.001 TRP A 450 HIS 0.001 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4311) covalent geometry : angle 0.67137 ( 5873) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.39494 ( 4) hydrogen bonds : bond 0.04925 ( 269) hydrogen bonds : angle 4.59726 ( 798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8099 (tp) cc_final: 0.7858 (tp) REVERT: A 366 MET cc_start: 0.8779 (tpp) cc_final: 0.8317 (tpp) REVERT: B 57 ASP cc_start: 0.8592 (t70) cc_final: 0.8301 (t70) outliers start: 3 outliers final: 2 residues processed: 100 average time/residue: 0.0483 time to fit residues: 6.3492 Evaluate side-chains 82 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 80 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3486 r_free = 0.3486 target = 0.127110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118489 restraints weight = 5872.219| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.73 r_work: 0.3284 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4313 Z= 0.166 Angle : 0.656 8.952 5877 Z= 0.319 Chirality : 0.042 0.166 672 Planarity : 0.005 0.040 733 Dihedral : 8.204 87.027 612 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.06 % Allowed : 15.33 % Favored : 82.61 % 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: -0.34 (0.37), residues: 545 helix: 1.34 (0.29), residues: 337 sheet: -2.85 (0.66), residues: 49 loop : -2.82 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 430 TYR 0.018 0.001 TYR A 299 PHE 0.011 0.002 PHE A 283 TRP 0.010 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4311) covalent geometry : angle 0.65658 ( 5873) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.49070 ( 4) hydrogen bonds : bond 0.04839 ( 269) hydrogen bonds : angle 4.35852 ( 798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.132 Fit side-chains REVERT: A 46 LEU cc_start: 0.9416 (mt) cc_final: 0.9215 (mt) REVERT: A 220 PHE cc_start: 0.8807 (t80) cc_final: 0.8560 (t80) REVERT: A 332 LEU cc_start: 0.8145 (tp) cc_final: 0.7893 (tp) REVERT: A 366 MET cc_start: 0.8786 (tpp) cc_final: 0.8333 (tpp) REVERT: B 57 ASP cc_start: 0.8628 (t70) cc_final: 0.8245 (t0) REVERT: B 69 THR cc_start: 0.8116 (p) cc_final: 0.7882 (p) outliers start: 9 outliers final: 7 residues processed: 93 average time/residue: 0.0543 time to fit residues: 6.6483 Evaluate side-chains 91 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 427 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3499 r_free = 0.3499 target = 0.128164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119543 restraints weight = 5777.255| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.73 r_work: 0.3299 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4313 Z= 0.149 Angle : 0.633 8.834 5877 Z= 0.306 Chirality : 0.041 0.164 672 Planarity : 0.005 0.042 733 Dihedral : 7.876 84.503 612 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.06 % Allowed : 18.99 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.37), residues: 545 helix: 1.49 (0.29), residues: 338 sheet: -2.57 (0.66), residues: 49 loop : -2.71 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.017 0.001 TYR A 299 PHE 0.012 0.001 PHE A 283 TRP 0.011 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 4311) covalent geometry : angle 0.63357 ( 5873) SS BOND : bond 0.00210 ( 2) SS BOND : angle 0.46478 ( 4) hydrogen bonds : bond 0.04548 ( 269) hydrogen bonds : angle 4.20093 ( 798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.130 Fit side-chains REVERT: A 332 LEU cc_start: 0.8144 (tp) cc_final: 0.7881 (tp) REVERT: A 366 MET cc_start: 0.8751 (tpp) cc_final: 0.8308 (tpp) REVERT: B 57 ASP cc_start: 0.8588 (t70) cc_final: 0.8285 (t70) REVERT: B 69 THR cc_start: 0.8099 (p) cc_final: 0.7855 (p) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.0539 time to fit residues: 6.7787 Evaluate side-chains 93 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3503 r_free = 0.3503 target = 0.128440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119704 restraints weight = 5792.530| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.73 r_work: 0.3299 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4313 Z= 0.148 Angle : 0.643 8.102 5877 Z= 0.308 Chirality : 0.041 0.160 672 Planarity : 0.005 0.042 733 Dihedral : 7.826 84.072 612 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.97 % Allowed : 20.82 % Favored : 76.20 % 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: 0.04 (0.37), residues: 545 helix: 1.53 (0.29), residues: 340 sheet: -2.46 (0.68), residues: 49 loop : -2.58 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.016 0.001 TYR A 299 PHE 0.012 0.001 PHE A 283 TRP 0.009 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4311) covalent geometry : angle 0.64284 ( 5873) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.44733 ( 4) hydrogen bonds : bond 0.04493 ( 269) hydrogen bonds : angle 4.14181 ( 798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.094 Fit side-chains REVERT: A 332 LEU cc_start: 0.8165 (tp) cc_final: 0.7887 (tp) REVERT: A 366 MET cc_start: 0.8775 (tpp) cc_final: 0.8342 (tpp) REVERT: B 57 ASP cc_start: 0.8595 (t70) cc_final: 0.8280 (t70) REVERT: B 69 THR cc_start: 0.8082 (p) cc_final: 0.7848 (p) outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.0533 time to fit residues: 6.6383 Evaluate side-chains 94 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3533 r_free = 0.3533 target = 0.130673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121858 restraints weight = 5928.440| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.77 r_work: 0.3326 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4313 Z= 0.128 Angle : 0.619 7.707 5877 Z= 0.295 Chirality : 0.040 0.159 672 Planarity : 0.004 0.043 733 Dihedral : 7.673 83.363 612 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.20 % Allowed : 20.14 % Favored : 76.66 % 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: 0.21 (0.37), residues: 545 helix: 1.64 (0.29), residues: 341 sheet: -2.33 (0.68), residues: 49 loop : -2.50 (0.45), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.016 0.001 TYR A 299 PHE 0.012 0.001 PHE A 283 TRP 0.014 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4311) covalent geometry : angle 0.61873 ( 5873) SS BOND : bond 0.00247 ( 2) SS BOND : angle 0.48734 ( 4) hydrogen bonds : bond 0.04234 ( 269) hydrogen bonds : angle 4.03098 ( 798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.126 Fit side-chains REVERT: A 40 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7815 (tp) REVERT: A 332 LEU cc_start: 0.8125 (tp) cc_final: 0.7854 (tp) REVERT: A 366 MET cc_start: 0.8773 (tpp) cc_final: 0.8368 (tpp) REVERT: A 377 MET cc_start: 0.8055 (mtm) cc_final: 0.7810 (mtt) REVERT: B 69 THR cc_start: 0.7954 (p) cc_final: 0.7719 (p) outliers start: 14 outliers final: 12 residues processed: 100 average time/residue: 0.0523 time to fit residues: 7.0631 Evaluate side-chains 102 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3506 r_free = 0.3506 target = 0.128596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119825 restraints weight = 5908.344| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.76 r_work: 0.3297 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4313 Z= 0.161 Angle : 0.637 8.525 5877 Z= 0.307 Chirality : 0.041 0.166 672 Planarity : 0.005 0.041 733 Dihedral : 7.746 84.364 612 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.66 % Allowed : 20.37 % Favored : 75.97 % 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: 0.15 (0.37), residues: 545 helix: 1.64 (0.29), residues: 340 sheet: -2.33 (0.69), residues: 49 loop : -2.61 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 430 TYR 0.017 0.001 TYR A 299 PHE 0.013 0.002 PHE A 283 TRP 0.010 0.001 TRP A 307 HIS 0.005 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4311) covalent geometry : angle 0.63702 ( 5873) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.53387 ( 4) hydrogen bonds : bond 0.04484 ( 269) hydrogen bonds : angle 4.07463 ( 798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.130 Fit side-chains REVERT: A 217 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 332 LEU cc_start: 0.8185 (tp) cc_final: 0.7910 (tp) REVERT: A 366 MET cc_start: 0.8801 (tpp) cc_final: 0.8394 (tpp) REVERT: B 69 THR cc_start: 0.8158 (p) cc_final: 0.7919 (p) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.0542 time to fit residues: 7.0857 Evaluate side-chains 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3516 r_free = 0.3516 target = 0.129441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120718 restraints weight = 5876.829| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.75 r_work: 0.3314 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4313 Z= 0.143 Angle : 0.632 7.844 5877 Z= 0.305 Chirality : 0.041 0.157 672 Planarity : 0.004 0.041 733 Dihedral : 7.696 83.741 612 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.66 % Allowed : 20.82 % Favored : 75.51 % 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: 0.31 (0.37), residues: 545 helix: 1.74 (0.29), residues: 338 sheet: -2.16 (0.69), residues: 49 loop : -2.49 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 430 TYR 0.017 0.001 TYR A 299 PHE 0.013 0.001 PHE A 283 TRP 0.013 0.001 TRP A 307 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4311) covalent geometry : angle 0.63198 ( 5873) SS BOND : bond 0.00293 ( 2) SS BOND : angle 0.60876 ( 4) hydrogen bonds : bond 0.04354 ( 269) hydrogen bonds : angle 4.04728 ( 798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.136 Fit side-chains REVERT: A 217 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 332 LEU cc_start: 0.8172 (tp) cc_final: 0.7897 (tp) REVERT: A 366 MET cc_start: 0.8798 (tpp) cc_final: 0.8399 (tpp) REVERT: A 377 MET cc_start: 0.8032 (mtm) cc_final: 0.7787 (mtt) REVERT: B 54 SER cc_start: 0.9000 (t) cc_final: 0.8625 (p) REVERT: B 69 THR cc_start: 0.8066 (p) cc_final: 0.7824 (p) outliers start: 16 outliers final: 14 residues processed: 105 average time/residue: 0.0626 time to fit residues: 8.3531 Evaluate side-chains 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 370 TYR Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 96 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.0370 chunk 49 optimal weight: 0.8980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3535 r_free = 0.3535 target = 0.130936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.122167 restraints weight = 5912.211| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.77 r_work: 0.3334 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4313 Z= 0.125 Angle : 0.632 11.083 5877 Z= 0.301 Chirality : 0.041 0.147 672 Planarity : 0.004 0.043 733 Dihedral : 7.598 83.625 612 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.89 % Allowed : 21.05 % 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: 0.41 (0.37), residues: 545 helix: 1.87 (0.29), residues: 338 sheet: -2.65 (0.66), residues: 46 loop : -2.39 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 430 TYR 0.020 0.001 TYR A 299 PHE 0.013 0.001 PHE A 283 TRP 0.015 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4311) covalent geometry : angle 0.63155 ( 5873) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.66912 ( 4) hydrogen bonds : bond 0.04130 ( 269) hydrogen bonds : angle 4.00428 ( 798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.183 Fit side-chains REVERT: A 40 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7584 (tp) REVERT: A 217 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 332 LEU cc_start: 0.8130 (tp) cc_final: 0.7856 (tp) REVERT: A 377 MET cc_start: 0.7954 (mtm) cc_final: 0.7713 (mtt) REVERT: B 54 SER cc_start: 0.8929 (t) cc_final: 0.8546 (p) outliers start: 17 outliers final: 13 residues processed: 103 average time/residue: 0.0609 time to fit residues: 8.0005 Evaluate side-chains 104 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 370 TYR Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3514 r_free = 0.3514 target = 0.129351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120609 restraints weight = 5825.326| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.75 r_work: 0.3316 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4313 Z= 0.149 Angle : 0.651 10.755 5877 Z= 0.312 Chirality : 0.042 0.169 672 Planarity : 0.005 0.042 733 Dihedral : 7.650 84.810 612 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.43 % Allowed : 22.20 % Favored : 74.37 % 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: 0.45 (0.37), residues: 545 helix: 1.83 (0.29), residues: 338 sheet: -1.85 (0.71), residues: 49 loop : -2.47 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 430 TYR 0.023 0.001 TYR A 299 PHE 0.012 0.001 PHE A 283 TRP 0.013 0.001 TRP A 307 HIS 0.003 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 4311) covalent geometry : angle 0.65112 ( 5873) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.92111 ( 4) hydrogen bonds : bond 0.04282 ( 269) hydrogen bonds : angle 4.00689 ( 798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.099 Fit side-chains REVERT: A 40 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7629 (tp) REVERT: A 217 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 332 LEU cc_start: 0.8188 (tp) cc_final: 0.7913 (tp) REVERT: A 377 MET cc_start: 0.8024 (mtm) cc_final: 0.7777 (mtt) REVERT: B 54 SER cc_start: 0.8948 (t) cc_final: 0.8586 (p) REVERT: B 69 THR cc_start: 0.8007 (p) cc_final: 0.7760 (p) outliers start: 15 outliers final: 13 residues processed: 103 average time/residue: 0.0579 time to fit residues: 7.7965 Evaluate side-chains 108 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 370 TYR Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3505 r_free = 0.3505 target = 0.128653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120053 restraints weight = 5816.562| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.71 r_work: 0.3306 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4313 Z= 0.163 Angle : 0.661 9.926 5877 Z= 0.319 Chirality : 0.043 0.176 672 Planarity : 0.005 0.042 733 Dihedral : 7.697 85.305 612 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.43 % Allowed : 22.65 % Favored : 73.91 % 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: 0.46 (0.37), residues: 545 helix: 1.83 (0.29), residues: 336 sheet: -1.77 (0.73), residues: 49 loop : -2.42 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 430 TYR 0.022 0.001 TYR A 299 PHE 0.013 0.002 PHE A 283 TRP 0.011 0.001 TRP A 307 HIS 0.004 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4311) covalent geometry : angle 0.66030 ( 5873) SS BOND : bond 0.00232 ( 2) SS BOND : angle 1.09753 ( 4) hydrogen bonds : bond 0.04466 ( 269) hydrogen bonds : angle 4.07388 ( 798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1074.18 seconds wall clock time: 19 minutes 0.89 seconds (1140.89 seconds total)