Starting phenix.real_space_refine on Sat May 10 04:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wqd_37740/05_2025/8wqd_37740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wqd_37740/05_2025/8wqd_37740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wqd_37740/05_2025/8wqd_37740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wqd_37740/05_2025/8wqd_37740.map" model { file = "/net/cci-nas-00/data/ceres_data/8wqd_37740/05_2025/8wqd_37740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wqd_37740/05_2025/8wqd_37740.cif" } resolution = 3.55 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= 0.019 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 29 5.16 5 C 3166 2.51 5 N 905 2.21 5 O 946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5046 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4929 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 117 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain breaks: 1 Time building chain proxies: 5.66, per 1000 atoms: 1.12 Number of scatterers: 5046 At special positions: 0 Unit cell: (104.14, 98.4, 85.28, 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 29 16.00 O 946 8.00 N 905 7.00 C 3166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.16 Conformation dependent library (CDL) restraints added in 586.3 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 1 sheets defined 66.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'D' and resid 1 through 14 removed outlier: 3.707A pdb=" N ALA D 5 " --> pdb=" O MET D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 28 through 38 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 58 through 68 removed outlier: 3.857A pdb=" N HIS D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 100 through 109 removed outlier: 3.860A pdb=" N LEU D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 removed outlier: 3.598A pdb=" N ALA D 127 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 143 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 189 through 198 removed outlier: 4.098A pdb=" N PHE D 193 " --> pdb=" O THR D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 221 through 229 Processing helix chain 'D' and resid 231 through 239 removed outlier: 3.520A pdb=" N VAL D 235 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 237 " --> pdb=" O ASP D 233 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 246 through 262 Processing helix chain 'D' and resid 269 through 285 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.502A pdb=" N LEU D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 337 removed outlier: 3.616A pdb=" N LEU D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 359 through 378 Processing helix chain 'D' and resid 382 through 398 removed outlier: 3.765A pdb=" N LEU D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 428 Processing helix chain 'D' and resid 432 through 456 Processing helix chain 'D' and resid 460 through 478 Processing helix chain 'D' and resid 488 through 493 Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 511 through 520 Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.760A pdb=" N ILE D 538 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE D 539 " --> pdb=" O ALA D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 removed outlier: 3.963A pdb=" N ILE D 555 " --> pdb=" O THR D 551 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D 558 " --> pdb=" O SER D 554 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 559 " --> pdb=" O ILE D 555 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 560 " --> pdb=" O ILE D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 591 Processing helix chain 'D' and resid 596 through 608 removed outlier: 3.833A pdb=" N ASN D 608 " --> pdb=" O ALA D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 627 removed outlier: 4.179A pdb=" N GLU D 622 " --> pdb=" O ARG D 618 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 623 " --> pdb=" O THR D 619 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS D 627 " --> pdb=" O PHE D 623 " (cutoff:3.500A) Processing helix chain 'G' and resid -21 through -17 removed outlier: 3.622A pdb=" N ASP G -18 " --> pdb=" O HIS G -21 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G -17 " --> pdb=" O SER G -20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid -21 through -17' Processing sheet with id=AA1, first strand: chain 'D' and resid 40 through 41 260 hydrogen bonds defined for protein. 762 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: 1.28 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1721 1.34 - 1.46: 768 1.46 - 1.57: 2603 1.57 - 1.69: 0 1.69 - 1.81: 41 Bond restraints: 5133 Sorted by residual: bond pdb=" C ALA D 404 " pdb=" N PRO D 405 " ideal model delta sigma weight residual 1.335 1.364 -0.030 1.28e-02 6.10e+03 5.37e+00 bond pdb=" CB ILE D 555 " pdb=" CG2 ILE D 555 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.29e+00 bond pdb=" CA GLU D 307 " pdb=" CB GLU D 307 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.86e-02 2.89e+03 1.08e+00 bond pdb=" CB PHE D 388 " pdb=" CG PHE D 388 " ideal model delta sigma weight residual 1.502 1.478 0.024 2.30e-02 1.89e+03 1.07e+00 bond pdb=" CA ILE D 616 " pdb=" CB ILE D 616 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.01e+00 ... (remaining 5128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 6729 1.49 - 2.97: 187 2.97 - 4.46: 23 4.46 - 5.94: 12 5.94 - 7.43: 4 Bond angle restraints: 6955 Sorted by residual: angle pdb=" C ASN D 289 " pdb=" CA ASN D 289 " pdb=" CB ASN D 289 " ideal model delta sigma weight residual 116.54 111.16 5.38 1.15e+00 7.56e-01 2.19e+01 angle pdb=" N ASP G -18 " pdb=" CA ASP G -18 " pdb=" C ASP G -18 " ideal model delta sigma weight residual 114.75 109.27 5.48 1.26e+00 6.30e-01 1.89e+01 angle pdb=" N THR D 306 " pdb=" CA THR D 306 " pdb=" C THR D 306 " ideal model delta sigma weight residual 111.55 107.45 4.10 1.37e+00 5.33e-01 8.96e+00 angle pdb=" CA ASN D 289 " pdb=" C ASN D 289 " pdb=" N ILE D 290 " ideal model delta sigma weight residual 119.52 117.24 2.28 7.90e-01 1.60e+00 8.31e+00 angle pdb=" CA ASP G -18 " pdb=" C ASP G -18 " pdb=" N LEU G -17 " ideal model delta sigma weight residual 119.80 116.12 3.68 1.34e+00 5.57e-01 7.53e+00 ... (remaining 6950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 2744 16.80 - 33.60: 292 33.60 - 50.40: 57 50.40 - 67.19: 13 67.19 - 83.99: 4 Dihedral angle restraints: 3110 sinusoidal: 1231 harmonic: 1879 Sorted by residual: dihedral pdb=" CA ASP D 478 " pdb=" CB ASP D 478 " pdb=" CG ASP D 478 " pdb=" OD1 ASP D 478 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CB GLU D 586 " pdb=" CG GLU D 586 " pdb=" CD GLU D 586 " pdb=" OE1 GLU D 586 " ideal model delta sinusoidal sigma weight residual 0.00 83.99 -83.99 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CG ARG D 80 " pdb=" CD ARG D 80 " pdb=" NE ARG D 80 " pdb=" CZ ARG D 80 " ideal model delta sinusoidal sigma weight residual 180.00 138.50 41.50 2 1.50e+01 4.44e-03 9.37e+00 ... (remaining 3107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 426 0.029 - 0.057: 264 0.057 - 0.086: 81 0.086 - 0.115: 28 0.115 - 0.143: 5 Chirality restraints: 804 Sorted by residual: chirality pdb=" CG LEU D 238 " pdb=" CB LEU D 238 " pdb=" CD1 LEU D 238 " pdb=" CD2 LEU D 238 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE D 616 " pdb=" N ILE D 616 " pdb=" C ILE D 616 " pdb=" CB ILE D 616 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO D 576 " pdb=" N PRO D 576 " pdb=" C PRO D 576 " pdb=" CB PRO D 576 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 801 not shown) Planarity restraints: 902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 221 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 222 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 222 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 222 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 404 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO D 405 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 405 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 405 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 123 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO D 124 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 124 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 124 " 0.028 5.00e-02 4.00e+02 ... (remaining 899 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1233 2.79 - 3.32: 4988 3.32 - 3.85: 8291 3.85 - 4.37: 9423 4.37 - 4.90: 16449 Nonbonded interactions: 40384 Sorted by model distance: nonbonded pdb=" O ASP D 87 " pdb=" OG1 THR D 118 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR D 449 " pdb=" O PRO D 497 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU D 2 " pdb=" OH TYR D 38 " model vdw 2.318 3.040 nonbonded pdb=" NH2 ARG D 126 " pdb=" O SER G -2 " model vdw 2.323 3.120 nonbonded pdb=" OG SER D 28 " pdb=" OD2 ASP D 31 " model vdw 2.327 3.040 ... (remaining 40379 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 group one per residue 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: 14.560 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.870 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5133 Z= 0.179 Angle : 0.624 7.431 6955 Z= 0.344 Chirality : 0.041 0.143 804 Planarity : 0.005 0.056 902 Dihedral : 14.561 83.992 1892 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.78 (0.33), residues: 635 helix: 0.05 (0.26), residues: 394 sheet: None (None), residues: 0 loop : -1.36 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 93 HIS 0.005 0.001 HIS D 476 PHE 0.010 0.002 PHE D 388 TYR 0.013 0.001 TYR D 440 ARG 0.003 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.16862 ( 260) hydrogen bonds : angle 5.23883 ( 762) covalent geometry : bond 0.00416 ( 5133) covalent geometry : angle 0.62409 ( 6955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.535 Fit side-chains REVERT: D 135 ASP cc_start: 0.8123 (m-30) cc_final: 0.7669 (m-30) REVERT: D 172 TYR cc_start: 0.8386 (t80) cc_final: 0.7901 (t80) REVERT: D 300 HIS cc_start: 0.7876 (t70) cc_final: 0.7500 (t70) REVERT: D 307 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7453 (tm-30) REVERT: D 419 GLU cc_start: 0.7940 (tp30) cc_final: 0.7688 (tp30) REVERT: D 472 TYR cc_start: 0.7457 (t80) cc_final: 0.7171 (t80) REVERT: D 517 LEU cc_start: 0.8861 (tp) cc_final: 0.8642 (tp) REVERT: D 622 GLU cc_start: 0.6999 (mp0) cc_final: 0.6734 (mp0) REVERT: G -18 ASP cc_start: 0.8083 (t0) cc_final: 0.7827 (t0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1594 time to fit residues: 20.3129 Evaluate side-chains 60 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 262 ASN D 476 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116964 restraints weight = 6842.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119160 restraints weight = 11135.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121131 restraints weight = 7254.738| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5133 Z= 0.155 Angle : 0.529 6.586 6955 Z= 0.281 Chirality : 0.039 0.136 804 Planarity : 0.005 0.047 902 Dihedral : 4.176 27.482 698 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.28 % Allowed : 9.84 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.14 (0.34), residues: 635 helix: 0.58 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 93 HIS 0.003 0.001 HIS D 100 PHE 0.009 0.001 PHE D 388 TYR 0.019 0.001 TYR D 472 ARG 0.004 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 260) hydrogen bonds : angle 4.03241 ( 762) covalent geometry : bond 0.00366 ( 5133) covalent geometry : angle 0.52917 ( 6955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8433 (t80) cc_final: 0.8030 (t80) REVERT: D 280 MET cc_start: 0.7592 (tmm) cc_final: 0.6812 (tmm) REVERT: D 472 TYR cc_start: 0.7321 (t80) cc_final: 0.7088 (t80) REVERT: D 517 LEU cc_start: 0.8998 (tp) cc_final: 0.8782 (tp) REVERT: G -18 ASP cc_start: 0.8530 (t0) cc_final: 0.8186 (t0) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.1788 time to fit residues: 17.2355 Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 40 optimal weight: 0.0370 chunk 31 optimal weight: 0.0870 overall best weight: 0.2436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.128084 restraints weight = 6683.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128338 restraints weight = 8638.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129404 restraints weight = 7265.137| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5133 Z= 0.095 Angle : 0.453 5.364 6955 Z= 0.243 Chirality : 0.036 0.127 804 Planarity : 0.004 0.050 902 Dihedral : 3.841 26.027 698 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.09 % Allowed : 12.75 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.23 (0.35), residues: 635 helix: 0.97 (0.27), residues: 413 sheet: None (None), residues: 0 loop : -1.37 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.002 0.001 HIS D 537 PHE 0.008 0.001 PHE D 101 TYR 0.019 0.001 TYR D 472 ARG 0.002 0.000 ARG D 126 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 260) hydrogen bonds : angle 3.67932 ( 762) covalent geometry : bond 0.00212 ( 5133) covalent geometry : angle 0.45320 ( 6955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8284 (t80) cc_final: 0.7734 (t80) REVERT: D 280 MET cc_start: 0.7710 (tmm) cc_final: 0.7028 (tmm) REVERT: D 472 TYR cc_start: 0.7182 (t80) cc_final: 0.6744 (t80) REVERT: G -18 ASP cc_start: 0.8552 (t0) cc_final: 0.8182 (t0) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.1503 time to fit residues: 15.3008 Evaluate side-chains 62 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116710 restraints weight = 6964.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.118090 restraints weight = 10726.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120376 restraints weight = 7192.757| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5133 Z= 0.145 Angle : 0.495 6.801 6955 Z= 0.263 Chirality : 0.038 0.132 804 Planarity : 0.004 0.047 902 Dihedral : 3.890 25.491 698 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.28 % Allowed : 14.57 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.34 (0.35), residues: 635 helix: 1.05 (0.27), residues: 413 sheet: None (None), residues: 0 loop : -1.33 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.002 0.001 HIS D 369 PHE 0.009 0.001 PHE D 388 TYR 0.016 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 260) hydrogen bonds : angle 3.75823 ( 762) covalent geometry : bond 0.00345 ( 5133) covalent geometry : angle 0.49549 ( 6955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8383 (t80) cc_final: 0.7793 (t80) REVERT: D 280 MET cc_start: 0.7626 (tmm) cc_final: 0.6985 (tmm) REVERT: D 472 TYR cc_start: 0.7323 (t80) cc_final: 0.6860 (t80) REVERT: G -18 ASP cc_start: 0.8600 (t0) cc_final: 0.8202 (t0) outliers start: 7 outliers final: 6 residues processed: 65 average time/residue: 0.1540 time to fit residues: 13.8456 Evaluate side-chains 62 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 59 optimal weight: 0.0020 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116783 restraints weight = 6826.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117266 restraints weight = 9710.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118439 restraints weight = 8402.852| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5133 Z= 0.125 Angle : 0.483 6.535 6955 Z= 0.255 Chirality : 0.038 0.130 804 Planarity : 0.004 0.048 902 Dihedral : 3.829 23.313 698 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.19 % Allowed : 15.66 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.42 (0.35), residues: 635 helix: 1.11 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.002 0.001 HIS D 382 PHE 0.009 0.001 PHE D 447 TYR 0.015 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 260) hydrogen bonds : angle 3.70951 ( 762) covalent geometry : bond 0.00298 ( 5133) covalent geometry : angle 0.48308 ( 6955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8378 (t80) cc_final: 0.7821 (t80) REVERT: D 280 MET cc_start: 0.7784 (tmm) cc_final: 0.7000 (tmm) REVERT: D 472 TYR cc_start: 0.7306 (t80) cc_final: 0.6784 (t80) REVERT: G -18 ASP cc_start: 0.8621 (t0) cc_final: 0.8226 (t0) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 0.1364 time to fit residues: 12.8508 Evaluate side-chains 59 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 7 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116684 restraints weight = 6885.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.117408 restraints weight = 10375.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119521 restraints weight = 8002.198| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5133 Z= 0.136 Angle : 0.489 7.080 6955 Z= 0.259 Chirality : 0.038 0.129 804 Planarity : 0.004 0.047 902 Dihedral : 3.841 21.546 698 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.00 % Allowed : 16.76 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.43 (0.35), residues: 635 helix: 1.11 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.26 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 93 HIS 0.002 0.001 HIS D 382 PHE 0.010 0.001 PHE D 447 TYR 0.014 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 260) hydrogen bonds : angle 3.72018 ( 762) covalent geometry : bond 0.00324 ( 5133) covalent geometry : angle 0.48861 ( 6955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8411 (t80) cc_final: 0.7955 (t80) REVERT: D 280 MET cc_start: 0.7764 (tmm) cc_final: 0.7010 (tmt) REVERT: D 368 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (mp) REVERT: D 472 TYR cc_start: 0.7358 (t80) cc_final: 0.6798 (t80) REVERT: G -18 ASP cc_start: 0.8626 (t0) cc_final: 0.8221 (t0) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1531 time to fit residues: 13.9483 Evaluate side-chains 61 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 504 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116316 restraints weight = 6783.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.116619 restraints weight = 9863.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117614 restraints weight = 9063.975| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5133 Z= 0.136 Angle : 0.489 7.342 6955 Z= 0.260 Chirality : 0.038 0.140 804 Planarity : 0.004 0.047 902 Dihedral : 3.845 20.205 698 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.19 % Allowed : 17.30 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.41 (0.35), residues: 635 helix: 1.09 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.002 0.001 HIS D 382 PHE 0.009 0.001 PHE D 101 TYR 0.014 0.001 TYR D 472 ARG 0.002 0.000 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.03125 ( 260) hydrogen bonds : angle 3.69348 ( 762) covalent geometry : bond 0.00325 ( 5133) covalent geometry : angle 0.48869 ( 6955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8413 (t80) cc_final: 0.7996 (t80) REVERT: D 280 MET cc_start: 0.7879 (tmm) cc_final: 0.7114 (tmt) REVERT: D 368 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8285 (mp) REVERT: G -18 ASP cc_start: 0.8656 (t0) cc_final: 0.8244 (t0) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.1512 time to fit residues: 14.1727 Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 0.0570 chunk 29 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN D 262 ASN D 504 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118460 restraints weight = 6865.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.119151 restraints weight = 9615.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119968 restraints weight = 8875.308| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5133 Z= 0.099 Angle : 0.474 6.586 6955 Z= 0.252 Chirality : 0.037 0.145 804 Planarity : 0.004 0.048 902 Dihedral : 3.716 19.510 698 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.00 % Allowed : 18.03 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.47 (0.35), residues: 635 helix: 1.14 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.27 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.003 0.000 HIS D 476 PHE 0.009 0.001 PHE D 101 TYR 0.017 0.001 TYR D 472 ARG 0.003 0.000 ARG D 544 Details of bonding type rmsd hydrogen bonds : bond 0.02934 ( 260) hydrogen bonds : angle 3.60661 ( 762) covalent geometry : bond 0.00225 ( 5133) covalent geometry : angle 0.47407 ( 6955) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.601 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8357 (t80) cc_final: 0.7911 (t80) REVERT: D 280 MET cc_start: 0.7856 (tmm) cc_final: 0.7081 (tmt) REVERT: D 368 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8251 (mp) REVERT: D 472 TYR cc_start: 0.7156 (t80) cc_final: 0.6753 (t80) REVERT: G -18 ASP cc_start: 0.8647 (t0) cc_final: 0.8222 (t0) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.1470 time to fit residues: 13.7181 Evaluate side-chains 64 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 0.0770 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119195 restraints weight = 6750.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120290 restraints weight = 9859.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121385 restraints weight = 7385.212| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5133 Z= 0.111 Angle : 0.485 6.819 6955 Z= 0.256 Chirality : 0.037 0.160 804 Planarity : 0.004 0.048 902 Dihedral : 3.708 20.109 698 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.82 % Allowed : 18.94 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.51 (0.35), residues: 635 helix: 1.18 (0.27), residues: 414 sheet: None (None), residues: 0 loop : -1.26 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 93 HIS 0.003 0.000 HIS D 476 PHE 0.009 0.001 PHE D 101 TYR 0.024 0.001 TYR D 163 ARG 0.002 0.000 ARG D 544 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 260) hydrogen bonds : angle 3.59811 ( 762) covalent geometry : bond 0.00260 ( 5133) covalent geometry : angle 0.48496 ( 6955) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8354 (t80) cc_final: 0.7869 (t80) REVERT: D 368 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (mp) REVERT: D 472 TYR cc_start: 0.7129 (t80) cc_final: 0.6692 (t80) REVERT: G -18 ASP cc_start: 0.8634 (t0) cc_final: 0.8210 (t0) outliers start: 10 outliers final: 9 residues processed: 62 average time/residue: 0.1420 time to fit residues: 12.2529 Evaluate side-chains 64 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.142226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117779 restraints weight = 6839.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119451 restraints weight = 11274.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120906 restraints weight = 7494.164| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5133 Z= 0.143 Angle : 0.509 7.658 6955 Z= 0.267 Chirality : 0.039 0.169 804 Planarity : 0.004 0.046 902 Dihedral : 3.786 20.222 698 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.19 % Allowed : 18.76 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 (0.35), residues: 635 helix: 1.13 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.010 0.001 PHE D 101 TYR 0.022 0.001 TYR D 163 ARG 0.002 0.000 ARG D 544 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 260) hydrogen bonds : angle 3.67680 ( 762) covalent geometry : bond 0.00343 ( 5133) covalent geometry : angle 0.50899 ( 6955) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: D 172 TYR cc_start: 0.8394 (t80) cc_final: 0.7822 (t80) REVERT: D 280 MET cc_start: 0.7564 (tmm) cc_final: 0.6891 (tmt) REVERT: D 368 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8249 (mp) REVERT: D 472 TYR cc_start: 0.7211 (t80) cc_final: 0.6771 (t80) REVERT: G -18 ASP cc_start: 0.8654 (t0) cc_final: 0.8230 (t0) outliers start: 12 outliers final: 10 residues processed: 63 average time/residue: 0.1582 time to fit residues: 13.4875 Evaluate side-chains 63 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 455 THR Chi-restraints excluded: chain D residue 475 ILE Chi-restraints excluded: chain D residue 551 THR Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain G residue -3 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117154 restraints weight = 6940.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117723 restraints weight = 10658.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119851 restraints weight = 8069.705| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.004 0.032 5133 Z= 0.147 Angle : 0.513 7.566 6955 Z= 0.270 Chirality : 0.039 0.166 804 Planarity : 0.004 0.046 902 Dihedral : 3.828 19.580 698 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.00 % Allowed : 18.76 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.41 (0.35), residues: 635 helix: 1.09 (0.27), residues: 412 sheet: None (None), residues: 0 loop : -1.25 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 93 HIS 0.003 0.001 HIS D 476 PHE 0.011 0.001 PHE D 101 TYR 0.022 0.001 TYR D 163 ARG 0.005 0.000 ARG D 544 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 260) hydrogen bonds : angle 3.69597 ( 762) covalent geometry : bond 0.00354 ( 5133) covalent geometry : angle 0.51327 ( 6955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.18 seconds wall clock time: 42 minutes 14.18 seconds (2534.18 seconds total)