Starting phenix.real_space_refine on Wed Jul 23 21:11:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bc7_12141/07_2025/7bc7_12141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bc7_12141/07_2025/7bc7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bc7_12141/07_2025/7bc7_12141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bc7_12141/07_2025/7bc7_12141.map" model { file = "/net/cci-nas-00/data/ceres_data/7bc7_12141/07_2025/7bc7_12141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bc7_12141/07_2025/7bc7_12141.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.57, per 1000 atoms: 0.85 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: 1.04 Conformation dependent library (CDL) restraints added in 504.8 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: 0.38 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: 1.36 Time building geometry restraints manager: 1.24 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: 0.010 Normalize map: mean=0, sd=1: 1.940 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- 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 : 12.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (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 TRP 0.012 0.002 TRP B 36 HIS 0.005 0.002 HIS A 427 PHE 0.016 0.002 PHE A 103 TYR 0.024 0.002 TYR A 299 ARG 0.010 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.17575 ( 269) hydrogen bonds : angle 6.53299 ( 798) SS BOND : bond 0.00404 ( 2) SS BOND : angle 0.48982 ( 4) covalent geometry : bond 0.00909 ( 4311) covalent geometry : angle 0.97771 ( 5873) *********************** 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 : 0.466 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: 0.7274 (mtm) REVERT: B 57 ASP cc_start: 0.8199 (t70) cc_final: 0.7880 (t70) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1337 time to fit residues: 18.2526 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 : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3494 r_free = 0.3494 target = 0.127876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119199 restraints weight = 5757.054| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.69 r_work: 0.3293 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1356 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= 0.157 Angle : 0.686 8.482 5877 Z= 0.334 Chirality : 0.042 0.162 672 Planarity : 0.005 0.042 733 Dihedral : 8.850 89.955 612 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.69 % Allowed : 11.67 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.37), residues: 545 helix: 0.95 (0.29), residues: 340 sheet: -3.51 (0.74), residues: 40 loop : -2.83 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 450 HIS 0.002 0.001 HIS B 50 PHE 0.013 0.001 PHE A 436 TYR 0.017 0.001 TYR A 299 ARG 0.006 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.05122 ( 269) hydrogen bonds : angle 4.63967 ( 798) SS BOND : bond 0.00198 ( 2) SS BOND : angle 0.39793 ( 4) covalent geometry : bond 0.00350 ( 4311) covalent geometry : angle 0.68643 ( 5873) *********************** 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 102 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 332 LEU cc_start: 0.8118 (tp) cc_final: 0.7872 (tp) REVERT: A 377 MET cc_start: 0.8310 (mtm) cc_final: 0.7975 (mtm) REVERT: B 57 ASP cc_start: 0.8629 (t70) cc_final: 0.8320 (t70) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.1406 time to fit residues: 18.5140 Evaluate side-chains 85 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.128556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119989 restraints weight = 5760.019| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.71 r_work: 0.3303 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1757 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= 0.145 Angle : 0.638 8.750 5877 Z= 0.310 Chirality : 0.041 0.159 672 Planarity : 0.005 0.042 733 Dihedral : 8.128 86.428 612 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.83 % Allowed : 15.79 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.37), residues: 545 helix: 1.38 (0.29), residues: 337 sheet: -3.08 (0.71), residues: 39 loop : -2.73 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 PHE 0.012 0.001 PHE A 283 TYR 0.018 0.001 TYR A 299 ARG 0.005 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04629 ( 269) hydrogen bonds : angle 4.29636 ( 798) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.41014 ( 4) covalent geometry : bond 0.00325 ( 4311) covalent geometry : angle 0.63791 ( 5873) *********************** 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: 8 poor density : 90 time to evaluate : 0.435 Fit side-chains REVERT: A 46 LEU cc_start: 0.9404 (mt) cc_final: 0.9199 (mt) REVERT: A 332 LEU cc_start: 0.8124 (tp) cc_final: 0.7871 (tp) REVERT: A 366 MET cc_start: 0.8727 (tpp) cc_final: 0.8316 (tpp) REVERT: A 377 MET cc_start: 0.8404 (mtm) cc_final: 0.8051 (mtm) REVERT: B 57 ASP cc_start: 0.8628 (t70) cc_final: 0.8255 (t0) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.1359 time to fit residues: 16.8435 Evaluate side-chains 86 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 0.0170 chunk 9 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3510 r_free = 0.3510 target = 0.129033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120333 restraints weight = 5821.279| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.75 r_work: 0.3307 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1961 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= 0.137 Angle : 0.614 8.714 5877 Z= 0.299 Chirality : 0.041 0.162 672 Planarity : 0.005 0.044 733 Dihedral : 7.832 84.460 612 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.75 % Allowed : 18.08 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.37), residues: 545 helix: 1.53 (0.29), residues: 339 sheet: -2.73 (0.72), residues: 39 loop : -2.59 (0.42), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 PHE 0.012 0.001 PHE A 283 TYR 0.017 0.001 TYR A 299 ARG 0.005 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04417 ( 269) hydrogen bonds : angle 4.15386 ( 798) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.44244 ( 4) covalent geometry : bond 0.00306 ( 4311) covalent geometry : angle 0.61386 ( 5873) *********************** 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: 12 poor density : 89 time to evaluate : 0.496 Fit side-chains REVERT: A 40 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7645 (tp) REVERT: A 332 LEU cc_start: 0.8131 (tp) cc_final: 0.7872 (tp) REVERT: A 366 MET cc_start: 0.8713 (tpp) cc_final: 0.8323 (tpp) REVERT: A 377 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: B 57 ASP cc_start: 0.8594 (t70) cc_final: 0.8240 (t0) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1461 time to fit residues: 18.3512 Evaluate side-chains 93 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 377 MET Chi-restraints excluded: chain A residue 427 HIS 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 36 optimal weight: 0.1980 chunk 22 optimal weight: 0.0370 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- 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 = 0.3520 r_free = 0.3520 target = 0.129851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121029 restraints weight = 5951.368| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.77 r_work: 0.3312 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2096 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= 0.132 Angle : 0.620 8.860 5877 Z= 0.297 Chirality : 0.040 0.155 672 Planarity : 0.004 0.044 733 Dihedral : 7.721 83.555 612 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.75 % Allowed : 21.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.37), residues: 545 helix: 1.64 (0.29), residues: 340 sheet: -2.67 (0.73), residues: 39 loop : -2.53 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 PHE 0.012 0.001 PHE A 283 TYR 0.016 0.001 TYR A 299 ARG 0.006 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 269) hydrogen bonds : angle 4.06453 ( 798) SS BOND : bond 0.00232 ( 2) SS BOND : angle 0.45253 ( 4) covalent geometry : bond 0.00293 ( 4311) covalent geometry : angle 0.62054 ( 5873) *********************** 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 101 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.543 Fit side-chains REVERT: A 332 LEU cc_start: 0.8143 (tp) cc_final: 0.7875 (tp) REVERT: A 366 MET cc_start: 0.8750 (tpp) cc_final: 0.8337 (tpp) REVERT: A 377 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7977 (mtm) outliers start: 12 outliers final: 9 residues processed: 96 average time/residue: 0.1525 time to fit residues: 19.7965 Evaluate side-chains 94 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 275 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain B residue 4 LEU 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 43 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.125550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116903 restraints weight = 5895.000| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.71 r_work: 0.3264 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4313 Z= 0.209 Angle : 0.679 8.851 5877 Z= 0.329 Chirality : 0.043 0.169 672 Planarity : 0.005 0.040 733 Dihedral : 7.949 84.994 612 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.43 % Allowed : 19.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.37), residues: 545 helix: 1.51 (0.29), residues: 337 sheet: -2.91 (0.72), residues: 40 loop : -2.59 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 HIS 0.003 0.001 HIS B 50 PHE 0.014 0.002 PHE A 220 TYR 0.017 0.002 TYR A 299 ARG 0.006 0.001 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 269) hydrogen bonds : angle 4.20837 ( 798) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.52257 ( 4) covalent geometry : bond 0.00472 ( 4311) covalent geometry : angle 0.67888 ( 5873) *********************** 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 102 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.462 Fit side-chains REVERT: A 332 LEU cc_start: 0.8201 (tp) cc_final: 0.7931 (tp) REVERT: A 366 MET cc_start: 0.8767 (tpp) cc_final: 0.8383 (tpp) REVERT: A 377 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8027 (mtm) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.1375 time to fit residues: 17.3970 Evaluate side-chains 96 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 377 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.128850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120141 restraints weight = 5824.399| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.73 r_work: 0.3306 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2123 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 : 0.644 9.115 5877 Z= 0.309 Chirality : 0.041 0.153 672 Planarity : 0.005 0.042 733 Dihedral : 7.779 83.110 612 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.37), residues: 545 helix: 1.69 (0.29), residues: 336 sheet: -2.19 (0.69), residues: 49 loop : -2.58 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 PHE 0.012 0.001 PHE A 283 TYR 0.020 0.001 TYR A 299 ARG 0.007 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 269) hydrogen bonds : angle 4.09251 ( 798) SS BOND : bond 0.00261 ( 2) SS BOND : angle 0.52112 ( 4) covalent geometry : bond 0.00322 ( 4311) covalent geometry : angle 0.64453 ( 5873) *********************** 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 104 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.426 Fit side-chains REVERT: A 332 LEU cc_start: 0.8148 (tp) cc_final: 0.7873 (tp) REVERT: A 366 MET cc_start: 0.8785 (tpp) cc_final: 0.8397 (tpp) REVERT: A 377 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7953 (mtm) outliers start: 17 outliers final: 12 residues processed: 98 average time/residue: 0.1365 time to fit residues: 17.4133 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 : 0.425 ------------------------------------------------------------------------------- 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 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 377 MET 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 4 optimal weight: 0.1980 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 13 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.132033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123380 restraints weight = 5792.937| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.73 r_work: 0.3350 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4313 Z= 0.118 Angle : 0.626 9.013 5877 Z= 0.296 Chirality : 0.040 0.154 672 Planarity : 0.004 0.044 733 Dihedral : 7.623 82.945 612 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.66 % Allowed : 21.05 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.37), residues: 545 helix: 1.84 (0.29), residues: 338 sheet: -2.49 (0.65), residues: 46 loop : -2.40 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.018 0.001 TYR A 299 ARG 0.005 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04027 ( 269) hydrogen bonds : angle 3.97972 ( 798) SS BOND : bond 0.00181 ( 2) SS BOND : angle 0.70953 ( 4) covalent geometry : bond 0.00255 ( 4311) covalent geometry : angle 0.62556 ( 5873) *********************** 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 111 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.438 Fit side-chains REVERT: A 40 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7576 (tp) REVERT: A 205 VAL cc_start: 0.7612 (t) cc_final: 0.7385 (t) REVERT: A 332 LEU cc_start: 0.8120 (tp) cc_final: 0.7847 (tp) REVERT: A 377 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7926 (mtm) REVERT: B 54 SER cc_start: 0.8912 (t) cc_final: 0.8530 (p) outliers start: 16 outliers final: 9 residues processed: 103 average time/residue: 0.1752 time to fit residues: 22.3346 Evaluate side-chains 99 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 370 TYR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 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 = 0.3509 r_free = 0.3509 target = 0.128835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120134 restraints weight = 5873.714| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.75 r_work: 0.3310 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2291 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= 0.162 Angle : 0.661 9.125 5877 Z= 0.316 Chirality : 0.042 0.161 672 Planarity : 0.005 0.042 733 Dihedral : 7.738 84.543 612 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 22.20 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.37), residues: 545 helix: 1.77 (0.29), residues: 338 sheet: -1.64 (0.72), residues: 49 loop : -2.54 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 307 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.002 PHE A 283 TYR 0.018 0.001 TYR A 299 ARG 0.006 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04361 ( 269) hydrogen bonds : angle 4.03167 ( 798) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.70658 ( 4) covalent geometry : bond 0.00368 ( 4311) covalent geometry : angle 0.66146 ( 5873) *********************** 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 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.425 Fit side-chains REVERT: A 40 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7677 (tp) REVERT: A 332 LEU cc_start: 0.8208 (tp) cc_final: 0.7929 (tp) REVERT: A 366 MET cc_start: 0.8774 (tpp) cc_final: 0.8398 (tpp) REVERT: A 377 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7953 (mtm) REVERT: B 54 SER cc_start: 0.8954 (t) cc_final: 0.8580 (p) outliers start: 13 outliers final: 11 residues processed: 99 average time/residue: 0.1478 time to fit residues: 18.7443 Evaluate side-chains 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 377 MET 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 8 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.0770 chunk 14 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121770 restraints weight = 5842.404| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.75 r_work: 0.3332 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2429 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= 0.132 Angle : 0.637 8.440 5877 Z= 0.303 Chirality : 0.041 0.155 672 Planarity : 0.005 0.043 733 Dihedral : 7.653 83.905 612 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.97 % Allowed : 22.43 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.37), residues: 545 helix: 1.82 (0.29), residues: 338 sheet: -1.91 (0.75), residues: 39 loop : -2.41 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 307 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.017 0.001 TYR A 299 ARG 0.005 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 269) hydrogen bonds : angle 3.97003 ( 798) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.52177 ( 4) covalent geometry : bond 0.00296 ( 4311) covalent geometry : angle 0.63676 ( 5873) ********************** 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 105 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.430 Fit side-chains REVERT: A 40 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7525 (tp) REVERT: A 332 LEU cc_start: 0.8173 (tp) cc_final: 0.7906 (tp) REVERT: A 366 MET cc_start: 0.8765 (tpp) cc_final: 0.8389 (tpp) REVERT: A 377 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7909 (mtm) REVERT: B 54 SER cc_start: 0.8884 (t) cc_final: 0.8527 (p) outliers start: 13 outliers final: 10 residues processed: 99 average time/residue: 0.1551 time to fit residues: 19.8550 Evaluate side-chains 102 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 370 TYR Chi-restraints excluded: chain A residue 377 MET 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 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.132111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.123539 restraints weight = 5743.343| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.70 r_work: 0.3357 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2604 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= 0.118 Angle : 0.612 8.170 5877 Z= 0.292 Chirality : 0.040 0.153 672 Planarity : 0.004 0.044 733 Dihedral : 7.439 84.145 612 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.75 % Allowed : 23.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.37), residues: 545 helix: 1.91 (0.29), residues: 338 sheet: -1.82 (0.71), residues: 46 loop : -2.26 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 307 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.016 0.001 TYR A 299 ARG 0.004 0.000 ARG A 430 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 269) hydrogen bonds : angle 3.92212 ( 798) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.59833 ( 4) covalent geometry : bond 0.00260 ( 4311) covalent geometry : angle 0.61184 ( 5873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.26 seconds wall clock time: 41 minutes 15.96 seconds (2475.96 seconds total)