Starting phenix.real_space_refine on Tue Feb 11 07:56:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8omu_16977/02_2025/8omu_16977.cif Found real_map, /net/cci-nas-00/data/ceres_data/8omu_16977/02_2025/8omu_16977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8omu_16977/02_2025/8omu_16977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8omu_16977/02_2025/8omu_16977.map" model { file = "/net/cci-nas-00/data/ceres_data/8omu_16977/02_2025/8omu_16977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8omu_16977/02_2025/8omu_16977.cif" } resolution = 3.43 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= -0.001 sd= 0.060 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 35 5.16 5 C 3064 2.51 5 N 804 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4737 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3842 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 25, 'TRANS': 471} Chain breaks: 2 Chain: "B" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Time building chain proxies: 3.61, per 1000 atoms: 0.76 Number of scatterers: 4737 At special positions: 0 Unit cell: (117.312, 68.224, 81.536, 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 35 16.00 O 834 8.00 N 804 7.00 C 3064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.02 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 556.3 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1124 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 64.7% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.856A pdb=" N LEU A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.533A pdb=" N LEU A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 160 removed outlier: 3.955A pdb=" N PHE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR A 154 " --> pdb=" O MET A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 181 Processing helix chain 'A' and resid 184 through 214 removed outlier: 4.144A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.592A pdb=" N ALA A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.847A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.624A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.576A pdb=" N GLY A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 332 through 358 Processing helix chain 'A' and resid 366 through 392 removed outlier: 4.259A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 415 removed outlier: 3.543A pdb=" N LEU A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 501 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.574A pdb=" N ARG A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.298A pdb=" N SER B 56 " --> pdb=" O SER B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.238A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 removed outlier: 3.575A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 69 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.386A pdb=" N GLY B 10 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 109 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 92 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 849 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: 1.35 Time building geometry restraints manager: 1.33 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: 1491 1.34 - 1.46: 1127 1.46 - 1.58: 2178 1.58 - 1.70: 0 1.70 - 1.82: 55 Bond restraints: 4851 Sorted by residual: bond pdb=" CA GLN A 510 " pdb=" CB GLN A 510 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.44e+00 bond pdb=" C SER B 114 " pdb=" O SER B 114 " ideal model delta sigma weight residual 1.242 1.231 0.010 1.00e-02 1.00e+04 1.02e+00 bond pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.48e-01 bond pdb=" CA THR A 36 " pdb=" C THR A 36 " ideal model delta sigma weight residual 1.522 1.535 -0.013 1.37e-02 5.33e+03 8.51e-01 bond pdb=" C MET A 485 " pdb=" N PRO A 486 " ideal model delta sigma weight residual 1.335 1.347 -0.012 1.36e-02 5.41e+03 7.79e-01 ... (remaining 4846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 6489 2.11 - 4.23: 87 4.23 - 6.34: 12 6.34 - 8.45: 6 8.45 - 10.56: 2 Bond angle restraints: 6596 Sorted by residual: angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 121.20 113.31 7.89 1.61e+00 3.86e-01 2.40e+01 angle pdb=" CA LYS A 297 " pdb=" CB LYS A 297 " pdb=" CG LYS A 297 " ideal model delta sigma weight residual 114.10 121.59 -7.49 2.00e+00 2.50e-01 1.40e+01 angle pdb=" CA GLN B 39 " pdb=" CB GLN B 39 " pdb=" CG GLN B 39 " ideal model delta sigma weight residual 114.10 121.02 -6.92 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CB MET A 464 " pdb=" CG MET A 464 " pdb=" SD MET A 464 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 angle pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " pdb=" CG LEU A 18 " ideal model delta sigma weight residual 116.30 126.86 -10.56 3.50e+00 8.16e-02 9.11e+00 ... (remaining 6591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 2367 17.39 - 34.78: 352 34.78 - 52.17: 115 52.17 - 69.56: 14 69.56 - 86.95: 7 Dihedral angle restraints: 2855 sinusoidal: 1097 harmonic: 1758 Sorted by residual: dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -140.51 54.51 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -47.78 -38.22 1 1.00e+01 1.00e-02 2.06e+01 dihedral pdb=" CA CYS A 49 " pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " ideal model delta sinusoidal sigma weight residual -73.00 -6.88 -66.12 1 2.00e+01 2.50e-03 1.43e+01 ... (remaining 2852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 435 0.026 - 0.053: 191 0.053 - 0.079: 75 0.079 - 0.106: 42 0.106 - 0.132: 12 Chirality restraints: 755 Sorted by residual: chirality pdb=" CA ASN A 125 " pdb=" N ASN A 125 " pdb=" C ASN A 125 " pdb=" CB ASN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CG LEU A 434 " pdb=" CB LEU A 434 " pdb=" CD1 LEU A 434 " pdb=" CD2 LEU A 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.47 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 752 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.043 2.00e-02 2.50e+03 8.02e-02 6.43e+01 pdb=" C SER B 114 " -0.139 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.050 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 220 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C ALA A 220 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 220 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR A 221 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 36 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C THR A 36 " 0.033 2.00e-02 2.50e+03 pdb=" O THR A 36 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 37 " -0.011 2.00e-02 2.50e+03 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 886 2.76 - 3.30: 4667 3.30 - 3.83: 8318 3.83 - 4.37: 8848 4.37 - 4.90: 15563 Nonbonded interactions: 38282 Sorted by model distance: nonbonded pdb=" O MET A 23 " pdb=" OH TYR A 264 " model vdw 2.230 3.040 nonbonded pdb=" O PHE A 133 " pdb=" OH TYR A 185 " model vdw 2.251 3.040 nonbonded pdb=" OG1 THR A 451 " pdb=" OD1 ASP A 514 " model vdw 2.298 3.040 nonbonded pdb=" OE1 GLU B 35 " pdb=" OH TYR B 37 " model vdw 2.326 3.040 nonbonded pdb=" O LYS A 520 " pdb=" OG SER A 523 " model vdw 2.358 3.040 ... (remaining 38277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.410 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.003 0.032 4851 Z= 0.200 Angle : 0.650 10.565 6596 Z= 0.329 Chirality : 0.040 0.132 755 Planarity : 0.005 0.080 824 Dihedral : 18.005 86.945 1722 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.79 % Allowed : 35.56 % Favored : 63.65 % 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: 0.64 (0.36), residues: 604 helix: 1.35 (0.29), residues: 355 sheet: -1.36 (0.75), residues: 42 loop : -0.73 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.000 HIS A 130 PHE 0.012 0.001 PHE A 351 TYR 0.022 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.502 Fit side-chains REVERT: B 29 VAL cc_start: 0.5845 (OUTLIER) cc_final: 0.5645 (m) REVERT: B 90 ASP cc_start: 0.7781 (m-30) cc_final: 0.7430 (m-30) outliers start: 4 outliers final: 0 residues processed: 75 average time/residue: 0.1699 time to fit residues: 16.3956 Evaluate side-chains 74 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.0000 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.209532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.172795 restraints weight = 6150.301| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.24 r_work: 0.3908 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4851 Z= 0.191 Angle : 0.600 8.407 6596 Z= 0.308 Chirality : 0.040 0.137 755 Planarity : 0.004 0.030 824 Dihedral : 4.048 18.560 668 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.52 % Allowed : 31.04 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.36), residues: 604 helix: 1.36 (0.28), residues: 360 sheet: -1.21 (0.76), residues: 42 loop : -0.49 (0.47), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.012 0.001 PHE A 351 TYR 0.021 0.001 TYR A 354 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.519 Fit side-chains REVERT: B 90 ASP cc_start: 0.7669 (m-30) cc_final: 0.7040 (m-30) outliers start: 23 outliers final: 13 residues processed: 99 average time/residue: 0.1607 time to fit residues: 20.7194 Evaluate side-chains 87 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 0.0000 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.208786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.173142 restraints weight = 6129.162| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.20 r_work: 0.3960 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4851 Z= 0.173 Angle : 0.573 8.743 6596 Z= 0.291 Chirality : 0.039 0.134 755 Planarity : 0.004 0.029 824 Dihedral : 3.882 17.646 667 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.70 % Allowed : 30.06 % Favored : 64.24 % 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: 0.90 (0.36), residues: 604 helix: 1.40 (0.28), residues: 361 sheet: -1.07 (0.78), residues: 42 loop : -0.40 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.000 HIS A 130 PHE 0.011 0.001 PHE A 351 TYR 0.018 0.001 TYR A 354 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8205 (ttp80) REVERT: B 82 GLN cc_start: 0.6259 (pp30) cc_final: 0.5682 (tm-30) REVERT: B 90 ASP cc_start: 0.7801 (m-30) cc_final: 0.7438 (m-30) outliers start: 29 outliers final: 17 residues processed: 106 average time/residue: 0.1662 time to fit residues: 22.5907 Evaluate side-chains 93 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.0670 chunk 10 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** 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 = 0.4385 r_free = 0.4385 target = 0.207709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.171906 restraints weight = 6176.371| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.19 r_work: 0.3939 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4851 Z= 0.186 Angle : 0.587 9.498 6596 Z= 0.296 Chirality : 0.040 0.143 755 Planarity : 0.004 0.029 824 Dihedral : 3.876 17.647 667 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.50 % Allowed : 30.65 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.36), residues: 604 helix: 1.46 (0.28), residues: 361 sheet: -1.00 (0.79), residues: 42 loop : -0.36 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.002 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.017 0.001 TYR A 354 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8312 (ttp80) REVERT: A 390 ASN cc_start: 0.8213 (m-40) cc_final: 0.7976 (m-40) REVERT: B 90 ASP cc_start: 0.7765 (m-30) cc_final: 0.7386 (m-30) outliers start: 28 outliers final: 20 residues processed: 107 average time/residue: 0.1556 time to fit residues: 21.6515 Evaluate side-chains 100 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** 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 = 0.4344 r_free = 0.4344 target = 0.203762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166864 restraints weight = 6232.796| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.26 r_work: 0.3825 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4851 Z= 0.319 Angle : 0.660 9.926 6596 Z= 0.336 Chirality : 0.043 0.147 755 Planarity : 0.004 0.033 824 Dihedral : 4.131 17.528 667 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 6.88 % Allowed : 29.08 % Favored : 64.05 % 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 (0.36), residues: 604 helix: 1.24 (0.28), residues: 361 sheet: -0.97 (0.81), residues: 42 loop : -0.40 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.003 0.001 HIS A 130 PHE 0.016 0.002 PHE A 351 TYR 0.023 0.002 TYR A 354 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8455 (ttp80) cc_final: 0.8080 (ttp80) REVERT: A 390 ASN cc_start: 0.8333 (m-40) cc_final: 0.8045 (m-40) REVERT: B 90 ASP cc_start: 0.7694 (m-30) cc_final: 0.7362 (m-30) outliers start: 35 outliers final: 26 residues processed: 116 average time/residue: 0.1574 time to fit residues: 23.7110 Evaluate side-chains 108 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 30.0000 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.206874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.170301 restraints weight = 6184.428| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.27 r_work: 0.3870 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4851 Z= 0.222 Angle : 0.625 10.457 6596 Z= 0.313 Chirality : 0.041 0.128 755 Planarity : 0.004 0.029 824 Dihedral : 4.056 17.607 667 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.48 % Allowed : 29.27 % Favored : 64.24 % 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: 0.86 (0.36), residues: 604 helix: 1.34 (0.28), residues: 361 sheet: -1.02 (0.79), residues: 42 loop : -0.36 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 346 HIS 0.003 0.001 HIS A 130 PHE 0.012 0.001 PHE A 351 TYR 0.021 0.001 TYR A 354 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8108 (ttp80) REVERT: B 90 ASP cc_start: 0.7643 (m-30) cc_final: 0.7245 (m-30) outliers start: 33 outliers final: 25 residues processed: 111 average time/residue: 0.1702 time to fit residues: 24.2200 Evaluate side-chains 102 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.203618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167832 restraints weight = 6160.762| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.19 r_work: 0.3889 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4851 Z= 0.223 Angle : 0.638 11.069 6596 Z= 0.317 Chirality : 0.041 0.126 755 Planarity : 0.004 0.031 824 Dihedral : 4.048 17.526 667 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 6.29 % Allowed : 29.67 % Favored : 64.05 % 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: 0.81 (0.36), residues: 604 helix: 1.32 (0.28), residues: 362 sheet: -1.17 (0.78), residues: 42 loop : -0.40 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.013 0.001 PHE A 351 TYR 0.020 0.001 TYR A 354 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.518 Fit side-chains REVERT: A 8 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8373 (mmtt) REVERT: A 80 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8302 (ttp80) REVERT: A 390 ASN cc_start: 0.8362 (m-40) cc_final: 0.8083 (m-40) REVERT: B 83 MET cc_start: 0.6539 (tpt) cc_final: 0.6242 (tpt) REVERT: B 90 ASP cc_start: 0.7754 (m-30) cc_final: 0.7093 (m-30) outliers start: 32 outliers final: 29 residues processed: 107 average time/residue: 0.1700 time to fit residues: 23.7043 Evaluate side-chains 106 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.0070 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.205013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.168991 restraints weight = 6178.936| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.26 r_work: 0.3886 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4851 Z= 0.190 Angle : 0.632 11.243 6596 Z= 0.312 Chirality : 0.040 0.128 755 Planarity : 0.004 0.033 824 Dihedral : 4.010 17.514 667 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.70 % Allowed : 30.45 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.36), residues: 604 helix: 1.39 (0.28), residues: 362 sheet: -1.18 (0.78), residues: 42 loop : -0.39 (0.49), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.012 0.001 PHE A 351 TYR 0.020 0.001 TYR A 354 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.473 Fit side-chains REVERT: A 80 ARG cc_start: 0.8517 (ttp80) cc_final: 0.8295 (ttp80) REVERT: A 390 ASN cc_start: 0.8311 (m-40) cc_final: 0.8037 (m-40) REVERT: B 90 ASP cc_start: 0.7703 (m-30) cc_final: 0.7047 (m-30) outliers start: 29 outliers final: 23 residues processed: 104 average time/residue: 0.1594 time to fit residues: 21.6477 Evaluate side-chains 100 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 5 optimal weight: 0.0050 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.206466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.171187 restraints weight = 6174.075| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.19 r_work: 0.3934 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4851 Z= 0.185 Angle : 0.632 11.462 6596 Z= 0.311 Chirality : 0.040 0.125 755 Planarity : 0.004 0.036 824 Dihedral : 3.979 17.508 667 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.30 % Allowed : 31.04 % Favored : 63.65 % 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: 0.94 (0.36), residues: 604 helix: 1.39 (0.28), residues: 364 sheet: -1.18 (0.78), residues: 42 loop : -0.29 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 33 HIS 0.002 0.000 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.019 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.554 Fit side-chains REVERT: A 80 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8319 (ttp80) REVERT: A 390 ASN cc_start: 0.8286 (m-40) cc_final: 0.8013 (m-40) REVERT: B 90 ASP cc_start: 0.7690 (m-30) cc_final: 0.7248 (m-30) outliers start: 27 outliers final: 24 residues processed: 102 average time/residue: 0.1660 time to fit residues: 22.3499 Evaluate side-chains 100 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.0020 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 overall best weight: 0.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.209822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.174723 restraints weight = 6102.081| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.20 r_work: 0.3969 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4851 Z= 0.159 Angle : 0.645 11.969 6596 Z= 0.316 Chirality : 0.040 0.146 755 Planarity : 0.004 0.032 824 Dihedral : 3.907 17.596 667 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.52 % Allowed : 31.63 % Favored : 63.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.36), residues: 604 helix: 1.45 (0.29), residues: 363 sheet: -1.32 (0.76), residues: 42 loop : -0.34 (0.48), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 33 HIS 0.001 0.000 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.017 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.525 Fit side-chains REVERT: A 72 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7923 (tp40) REVERT: A 80 ARG cc_start: 0.8476 (ttp80) cc_final: 0.8252 (ttp80) REVERT: A 390 ASN cc_start: 0.8226 (m-40) cc_final: 0.7987 (m-40) REVERT: A 485 MET cc_start: 0.7319 (ppp) cc_final: 0.7013 (ppp) REVERT: B 90 ASP cc_start: 0.7598 (m-30) cc_final: 0.7163 (m-30) outliers start: 23 outliers final: 20 residues processed: 97 average time/residue: 0.1569 time to fit residues: 20.2139 Evaluate side-chains 97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 GLN ** 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 = 0.4386 r_free = 0.4386 target = 0.208068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.172279 restraints weight = 6210.063| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.23 r_work: 0.3948 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4851 Z= 0.179 Angle : 0.634 11.739 6596 Z= 0.312 Chirality : 0.040 0.125 755 Planarity : 0.004 0.033 824 Dihedral : 3.875 17.697 667 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.32 % Allowed : 31.63 % Favored : 64.05 % 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: 0.90 (0.36), residues: 604 helix: 1.40 (0.28), residues: 364 sheet: -1.47 (0.73), residues: 42 loop : -0.30 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 109 HIS 0.002 0.000 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.019 0.001 TYR A 354 ARG 0.008 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2741.10 seconds wall clock time: 49 minutes 24.78 seconds (2964.78 seconds total)