Starting phenix.real_space_refine on Thu Nov 14 07:18:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omu_16977/11_2024/8omu_16977.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omu_16977/11_2024/8omu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omu_16977/11_2024/8omu_16977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omu_16977/11_2024/8omu_16977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omu_16977/11_2024/8omu_16977.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omu_16977/11_2024/8omu_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.65, per 1000 atoms: 0.77 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: 1.18 Conformation dependent library (CDL) restraints added in 616.6 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: 0.41 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: 1.30 Time building geometry restraints manager: 1.36 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: 1.090 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.460 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- 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 : 0.536 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: 0.1685 time to fit residues: 16.3593 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 : 0.511 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.515 Fit side-chains REVERT: A 72 GLN cc_start: 0.7796 (tp40) cc_final: 0.7580 (mm-40) REVERT: B 90 ASP cc_start: 0.7561 (m-30) cc_final: 0.6950 (m-30) outliers start: 23 outliers final: 13 residues processed: 99 average time/residue: 0.1528 time to fit residues: 19.9411 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 : 0.500 ------------------------------------------------------------------------------- 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 30 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4851 Z= 0.235 Angle : 0.595 8.561 6596 Z= 0.304 Chirality : 0.040 0.134 755 Planarity : 0.004 0.030 824 Dihedral : 3.973 17.511 667 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.48 % Allowed : 28.49 % Favored : 65.03 % 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: 1.30 (0.28), residues: 361 sheet: -1.04 (0.79), residues: 42 loop : -0.41 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 247 HIS 0.003 0.001 HIS A 130 PHE 0.014 0.001 PHE A 351 TYR 0.019 0.001 TYR A 354 ARG 0.005 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 113 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8206 (mmtt) REVERT: A 31 MET cc_start: 0.7711 (tpt) cc_final: 0.7477 (tpt) REVERT: A 72 GLN cc_start: 0.7829 (tp40) cc_final: 0.7531 (mm-40) REVERT: A 80 ARG cc_start: 0.8501 (ttp80) cc_final: 0.8155 (ttp80) REVERT: B 90 ASP cc_start: 0.7601 (m-30) cc_final: 0.7345 (m-30) outliers start: 33 outliers final: 18 residues processed: 106 average time/residue: 0.1792 time to fit residues: 24.6754 Evaluate side-chains 95 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 263 ILE Chi-restraints excluded: chain A residue 277 SER 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 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4851 Z= 0.275 Angle : 0.625 9.442 6596 Z= 0.320 Chirality : 0.042 0.134 755 Planarity : 0.004 0.032 824 Dihedral : 4.072 17.346 667 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.29 % Allowed : 28.88 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.36), residues: 604 helix: 1.26 (0.28), residues: 361 sheet: -0.93 (0.80), residues: 42 loop : -0.42 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 247 HIS 0.003 0.001 HIS A 130 PHE 0.015 0.001 PHE A 351 TYR 0.020 0.002 TYR A 354 ARG 0.006 0.000 ARG A 395 *********************** 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 115 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8592 (mt) REVERT: A 80 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8268 (ttp80) REVERT: B 90 ASP cc_start: 0.7636 (m-30) cc_final: 0.7381 (m-30) outliers start: 32 outliers final: 24 residues processed: 112 average time/residue: 0.1599 time to fit residues: 23.1677 Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 29 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 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 275 TYR Chi-restraints excluded: chain A residue 277 SER 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 102 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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** B 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1192 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= 0.182 Angle : 0.600 10.130 6596 Z= 0.301 Chirality : 0.040 0.131 755 Planarity : 0.004 0.033 824 Dihedral : 3.977 17.575 667 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.70 % Allowed : 29.27 % Favored : 65.03 % 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: 0.92 (0.36), residues: 604 helix: 1.37 (0.28), residues: 361 sheet: -0.87 (0.81), residues: 42 loop : -0.34 (0.48), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.011 0.001 PHE A 351 TYR 0.017 0.001 TYR A 354 ARG 0.007 0.000 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 115 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 80 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8198 (ttp80) REVERT: B 90 ASP cc_start: 0.7581 (m-30) cc_final: 0.7248 (m-30) outliers start: 29 outliers final: 23 residues processed: 111 average time/residue: 0.1531 time to fit residues: 22.2219 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 : 0.516 ------------------------------------------------------------------------------- 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 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 264 TYR Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 277 SER 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 B residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 chunk 42 optimal weight: 1.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4851 Z= 0.178 Angle : 0.602 10.730 6596 Z= 0.299 Chirality : 0.040 0.125 755 Planarity : 0.004 0.035 824 Dihedral : 3.909 17.602 667 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.68 % Allowed : 28.88 % 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: 0.98 (0.36), residues: 604 helix: 1.46 (0.28), residues: 361 sheet: -0.90 (0.82), residues: 42 loop : -0.39 (0.48), 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 0.013 0.001 PHE A 351 TYR 0.018 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: 34 poor density : 82 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.7822 (tp40) cc_final: 0.7593 (tp40) REVERT: A 80 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8190 (ttp80) REVERT: A 390 ASN cc_start: 0.8261 (m-40) cc_final: 0.8023 (m-40) REVERT: B 60 TYR cc_start: 0.8013 (m-80) cc_final: 0.7463 (m-80) outliers start: 34 outliers final: 25 residues processed: 112 average time/residue: 0.1601 time to fit residues: 23.6219 Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 29 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 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 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 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4851 Z= 0.194 Angle : 0.616 10.815 6596 Z= 0.306 Chirality : 0.040 0.175 755 Planarity : 0.004 0.036 824 Dihedral : 3.920 17.620 667 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.89 % Allowed : 29.86 % 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: 1.05 (0.36), residues: 604 helix: 1.45 (0.28), residues: 361 sheet: -0.31 (0.75), residues: 52 loop : -0.35 (0.50), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.001 0.000 HIS A 130 PHE 0.013 0.001 PHE A 351 TYR 0.018 0.001 TYR A 354 ARG 0.007 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 113 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 72 GLN cc_start: 0.7833 (tp40) cc_final: 0.7598 (tp40) REVERT: A 80 ARG cc_start: 0.8454 (ttp80) cc_final: 0.8181 (ttp80) REVERT: A 390 ASN cc_start: 0.8257 (m-40) cc_final: 0.8015 (m-40) REVERT: B 60 TYR cc_start: 0.7859 (m-80) cc_final: 0.7443 (m-80) outliers start: 30 outliers final: 25 residues processed: 110 average time/residue: 0.1481 time to fit residues: 21.4280 Evaluate side-chains 107 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 53 optimal weight: 0.0050 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1425 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= 0.199 Angle : 0.624 11.174 6596 Z= 0.308 Chirality : 0.040 0.147 755 Planarity : 0.004 0.037 824 Dihedral : 3.946 17.665 667 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.09 % Allowed : 30.06 % 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: 0.98 (0.36), residues: 604 helix: 1.42 (0.28), residues: 362 sheet: -0.52 (0.72), residues: 52 loop : -0.40 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 346 HIS 0.002 0.001 HIS A 130 PHE 0.013 0.001 PHE A 351 TYR 0.018 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 111 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8586 (mt) REVERT: A 72 GLN cc_start: 0.7866 (tp40) cc_final: 0.7638 (tp40) REVERT: A 80 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8184 (ttp80) REVERT: A 390 ASN cc_start: 0.8264 (m-40) cc_final: 0.8019 (m-40) REVERT: B 60 TYR cc_start: 0.7857 (m-80) cc_final: 0.7546 (m-80) REVERT: B 90 ASP cc_start: 0.7353 (m-30) cc_final: 0.6868 (m-30) outliers start: 31 outliers final: 27 residues processed: 107 average time/residue: 0.1567 time to fit residues: 21.8230 Evaluate side-chains 106 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 121 VAL 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 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 A residue 475 VAL 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 48 optimal weight: 0.8980 chunk 50 optimal weight: 0.0060 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.0270 overall best weight: 0.5654 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1485 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= 0.186 Angle : 0.626 11.479 6596 Z= 0.309 Chirality : 0.040 0.142 755 Planarity : 0.004 0.038 824 Dihedral : 3.925 17.564 667 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.89 % Allowed : 30.45 % 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: 1.02 (0.36), residues: 604 helix: 1.44 (0.28), residues: 363 sheet: -0.47 (0.72), residues: 52 loop : -0.37 (0.50), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.002 0.000 HIS A 130 PHE 0.013 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 110 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 80 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8586 (mt) REVERT: A 72 GLN cc_start: 0.7868 (tp40) cc_final: 0.7641 (tp40) REVERT: A 80 ARG cc_start: 0.8425 (ttp80) cc_final: 0.8175 (ttp80) REVERT: A 390 ASN cc_start: 0.8244 (m-40) cc_final: 0.8001 (m-40) REVERT: B 60 TYR cc_start: 0.7861 (m-80) cc_final: 0.7470 (m-80) REVERT: B 90 ASP cc_start: 0.7322 (m-30) cc_final: 0.6804 (m-30) outliers start: 30 outliers final: 25 residues processed: 107 average time/residue: 0.1516 time to fit residues: 21.3787 Evaluate side-chains 104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 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 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 69 THR 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: 0.1980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1535 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= 0.200 Angle : 0.638 11.468 6596 Z= 0.314 Chirality : 0.040 0.143 755 Planarity : 0.004 0.038 824 Dihedral : 3.949 17.569 667 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.50 % Allowed : 30.26 % 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: 0.93 (0.36), residues: 604 helix: 1.41 (0.28), residues: 363 sheet: -1.16 (0.76), residues: 42 loop : -0.34 (0.49), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 109 HIS 0.002 0.001 HIS A 130 PHE 0.013 0.001 PHE A 351 TYR 0.019 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 106 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 72 GLN cc_start: 0.7897 (tp40) cc_final: 0.7670 (tp40) REVERT: A 80 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8170 (ttp80) REVERT: A 390 ASN cc_start: 0.8253 (m-40) cc_final: 0.8004 (m-40) REVERT: B 60 TYR cc_start: 0.7817 (m-80) cc_final: 0.7527 (m-80) REVERT: B 90 ASP cc_start: 0.7301 (m-30) cc_final: 0.7053 (m-30) outliers start: 28 outliers final: 26 residues processed: 103 average time/residue: 0.1533 time to fit residues: 20.7119 Evaluate side-chains 105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 121 VAL 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 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 69 THR 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 48 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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** ** B 82 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 = 0.4382 r_free = 0.4382 target = 0.207688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.171614 restraints weight = 6150.133| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.27 r_work: 0.3921 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4851 Z= 0.177 Angle : 0.626 11.313 6596 Z= 0.308 Chirality : 0.040 0.137 755 Planarity : 0.004 0.038 824 Dihedral : 3.933 17.498 667 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.09 % Allowed : 29.86 % 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: 1.01 (0.36), residues: 604 helix: 1.45 (0.28), residues: 363 sheet: -1.19 (0.76), residues: 42 loop : -0.24 (0.49), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 346 HIS 0.001 0.000 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.018 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: 1459.17 seconds wall clock time: 27 minutes 12.84 seconds (1632.84 seconds total)