Starting phenix.real_space_refine on Wed Mar 5 21:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc4_40337/03_2025/8sc4_40337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc4_40337/03_2025/8sc4_40337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sc4_40337/03_2025/8sc4_40337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc4_40337/03_2025/8sc4_40337.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc4_40337/03_2025/8sc4_40337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc4_40337/03_2025/8sc4_40337.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 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 31 5.16 5 C 2335 2.51 5 N 579 2.21 5 O 599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3544 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3535 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 24, 'TRANS': 431} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'MF8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.69, per 1000 atoms: 0.76 Number of scatterers: 3544 At special positions: 0 Unit cell: (88.803, 81.972, 67.4561, 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 31 16.00 O 599 8.00 N 579 7.00 C 2335 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " 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: 0.88 Conformation dependent library (CDL) restraints added in 406.2 milliseconds 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 2 sheets defined 82.0% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 4.356A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 63 Processing helix chain 'A' and resid 65 through 73 removed outlier: 4.048A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.570A pdb=" N GLY A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.946A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.942A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 4.152A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 258 removed outlier: 4.439A pdb=" N ARG A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 245 " --> pdb=" O GLN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 280 Proline residue: A 271 - end of helix removed outlier: 3.680A pdb=" N LEU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 340 through 372 Processing helix chain 'A' and resid 374 through 401 removed outlier: 3.666A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 402 through 423 removed outlier: 3.580A pdb=" N ILE A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 456 removed outlier: 3.580A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 485 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.824A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 253 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1089 1.35 - 1.46: 929 1.46 - 1.58: 1575 1.58 - 1.70: 0 1.70 - 1.82: 46 Bond restraints: 3639 Sorted by residual: bond pdb=" N GLN A 241 " pdb=" CA GLN A 241 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.19e-02 7.06e+03 5.32e+00 bond pdb=" C07 MF8 A 601 " pdb=" N09 MF8 A 601 " ideal model delta sigma weight residual 1.358 1.317 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C07 MF8 A 601 " pdb=" N06 MF8 A 601 " ideal model delta sigma weight residual 1.393 1.354 0.039 2.00e-02 2.50e+03 3.87e+00 bond pdb=" C07 MF8 A 601 " pdb=" N08 MF8 A 601 " ideal model delta sigma weight residual 1.281 1.314 -0.033 2.00e-02 2.50e+03 2.78e+00 bond pdb=" C04 MF8 A 601 " pdb=" N05 MF8 A 601 " ideal model delta sigma weight residual 1.284 1.316 -0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 3634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4628 1.21 - 2.43: 270 2.43 - 3.64: 45 3.64 - 4.86: 16 4.86 - 6.07: 4 Bond angle restraints: 4963 Sorted by residual: angle pdb=" C LEU A 180 " pdb=" N GLY A 181 " pdb=" CA GLY A 181 " ideal model delta sigma weight residual 119.94 122.86 -2.92 1.11e+00 8.12e-01 6.93e+00 angle pdb=" CA CYS A 50 " pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " ideal model delta sigma weight residual 114.40 120.31 -5.91 2.30e+00 1.89e-01 6.60e+00 angle pdb=" N GLN A 241 " pdb=" CA GLN A 241 " pdb=" C GLN A 241 " ideal model delta sigma weight residual 111.07 108.38 2.69 1.07e+00 8.73e-01 6.34e+00 angle pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta sigma weight residual 120.54 123.86 -3.32 1.35e+00 5.49e-01 6.06e+00 angle pdb=" CA GLN A 241 " pdb=" C GLN A 241 " pdb=" O GLN A 241 " ideal model delta sigma weight residual 120.82 118.35 2.47 1.05e+00 9.07e-01 5.52e+00 ... (remaining 4958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.28: 1938 14.28 - 28.56: 130 28.56 - 42.84: 35 42.84 - 57.12: 5 57.12 - 71.40: 2 Dihedral angle restraints: 2110 sinusoidal: 804 harmonic: 1306 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -47.29 -38.71 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" CA SER A 424 " pdb=" C SER A 424 " pdb=" N PRO A 425 " pdb=" CA PRO A 425 " ideal model delta harmonic sigma weight residual 180.00 -165.86 -14.14 0 5.00e+00 4.00e-02 8.00e+00 dihedral pdb=" CA ASN A 374 " pdb=" C ASN A 374 " pdb=" N LEU A 375 " pdb=" CA LEU A 375 " ideal model delta harmonic sigma weight residual -180.00 -165.96 -14.04 0 5.00e+00 4.00e-02 7.88e+00 ... (remaining 2107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 361 0.033 - 0.066: 159 0.066 - 0.099: 41 0.099 - 0.132: 12 0.132 - 0.165: 1 Chirality restraints: 574 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PRO A 286 " pdb=" N PRO A 286 " pdb=" C PRO A 286 " pdb=" CB PRO A 286 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL A 126 " pdb=" N VAL A 126 " pdb=" C VAL A 126 " pdb=" CB VAL A 126 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.73e-01 ... (remaining 571 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 MF8 A 601 " -1.308 2.00e-02 2.50e+03 6.51e-01 9.54e+03 pdb=" C03 MF8 A 601 " 1.075 2.00e-02 2.50e+03 pdb=" C04 MF8 A 601 " -0.093 2.00e-02 2.50e+03 pdb=" C07 MF8 A 601 " 0.035 2.00e-02 2.50e+03 pdb=" N02 MF8 A 601 " -0.105 2.00e-02 2.50e+03 pdb=" N05 MF8 A 601 " 0.321 2.00e-02 2.50e+03 pdb=" N06 MF8 A 601 " -0.546 2.00e-02 2.50e+03 pdb=" N08 MF8 A 601 " 0.721 2.00e-02 2.50e+03 pdb=" N09 MF8 A 601 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 406 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET A 406 " 0.041 2.00e-02 2.50e+03 pdb=" O MET A 406 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA A 407 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 182 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C THR A 182 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 182 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A 183 " 0.013 2.00e-02 2.50e+03 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 964 2.82 - 3.34: 3680 3.34 - 3.86: 5933 3.86 - 4.38: 6701 4.38 - 4.90: 11468 Nonbonded interactions: 28746 Sorted by model distance: nonbonded pdb=" OG SER A 196 " pdb=" OG SER A 201 " model vdw 2.296 3.040 nonbonded pdb=" NH1 ARG A 175 " pdb=" O LEU A 290 " model vdw 2.334 3.120 nonbonded pdb=" O VAL A 74 " pdb=" NH2 ARG A 113 " model vdw 2.385 3.120 nonbonded pdb=" OG1 THR A 245 " pdb=" OE1 GLU A 386 " model vdw 2.437 3.040 nonbonded pdb=" O ALA A 506 " pdb=" OG1 THR A 510 " model vdw 2.472 3.040 ... (remaining 28741 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.910 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.030 Find NCS groups from input model: 0.030 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3639 Z= 0.241 Angle : 0.683 6.073 4963 Z= 0.390 Chirality : 0.039 0.165 574 Planarity : 0.027 0.651 613 Dihedral : 10.980 71.396 1265 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.96 (0.38), residues: 452 helix: -0.84 (0.26), residues: 329 sheet: None (None), residues: 0 loop : 0.59 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 288 HIS 0.003 0.001 HIS A 48 PHE 0.032 0.002 PHE A 173 TYR 0.012 0.002 TYR A 168 ARG 0.006 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 132 SER cc_start: 0.8553 (p) cc_final: 0.8200 (m) REVERT: A 218 MET cc_start: 0.7252 (mmm) cc_final: 0.6998 (mmt) REVERT: A 346 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7634 (mtt90) REVERT: A 378 ASP cc_start: 0.7707 (m-30) cc_final: 0.7330 (m-30) REVERT: A 418 LEU cc_start: 0.8570 (tp) cc_final: 0.8242 (tp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1687 time to fit residues: 24.8328 Evaluate side-chains 86 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 115 HIS A 428 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.207970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.161786 restraints weight = 4531.370| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.74 r_work: 0.3807 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3639 Z= 0.186 Angle : 0.688 15.080 4963 Z= 0.330 Chirality : 0.040 0.214 574 Planarity : 0.005 0.074 613 Dihedral : 4.279 17.434 491 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Rotamer: Outliers : 2.63 % Allowed : 10.53 % Favored : 86.84 % 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: 1.81 (0.42), residues: 452 helix: 1.22 (0.29), residues: 329 sheet: None (None), residues: 0 loop : 1.51 (0.66), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 288 HIS 0.002 0.001 HIS A 49 PHE 0.021 0.002 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.007 0.001 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.343 Fit side-chains REVERT: A 22 PHE cc_start: 0.6459 (t80) cc_final: 0.6088 (t80) REVERT: A 121 CYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5235 (m) REVERT: A 227 PHE cc_start: 0.7945 (t80) cc_final: 0.7556 (t80) REVERT: A 346 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7621 (mtt90) REVERT: A 418 LEU cc_start: 0.8600 (tp) cc_final: 0.8295 (tp) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.1321 time to fit residues: 15.8257 Evaluate side-chains 84 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.205293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158881 restraints weight = 4560.649| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.75 r_work: 0.3782 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3639 Z= 0.204 Angle : 0.672 14.473 4963 Z= 0.316 Chirality : 0.040 0.167 574 Planarity : 0.005 0.060 613 Dihedral : 4.126 17.661 491 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.42 % Allowed : 10.79 % Favored : 85.79 % 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: 2.21 (0.43), residues: 452 helix: 1.52 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.67 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.033 0.002 PHE A 22 TYR 0.012 0.001 TYR A 240 ARG 0.006 0.001 ARG A 402 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5844 (OUTLIER) cc_final: 0.5483 (m) REVERT: A 227 PHE cc_start: 0.8028 (t80) cc_final: 0.7715 (t80) REVERT: A 346 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7575 (mtt90) REVERT: A 418 LEU cc_start: 0.8574 (tp) cc_final: 0.8216 (tp) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 0.1276 time to fit residues: 14.8237 Evaluate side-chains 90 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 410 ASN A 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.201746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.155879 restraints weight = 4610.261| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.77 r_work: 0.3745 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3639 Z= 0.230 Angle : 0.662 14.493 4963 Z= 0.310 Chirality : 0.040 0.191 574 Planarity : 0.004 0.053 613 Dihedral : 4.073 16.665 491 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 5.53 % Allowed : 10.53 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.43), residues: 452 helix: 1.67 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.69 (0.69), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.023 0.002 PHE A 22 TYR 0.009 0.001 TYR A 352 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5612 (m) REVERT: A 227 PHE cc_start: 0.8075 (t80) cc_final: 0.7767 (t80) REVERT: A 346 ARG cc_start: 0.7992 (mtt180) cc_final: 0.7541 (mtt90) outliers start: 21 outliers final: 16 residues processed: 91 average time/residue: 0.1381 time to fit residues: 15.7970 Evaluate side-chains 100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 473 CYS Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 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 60 GLN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.200956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154920 restraints weight = 4653.350| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.74 r_work: 0.3692 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3639 Z= 0.198 Angle : 0.646 14.525 4963 Z= 0.299 Chirality : 0.039 0.159 574 Planarity : 0.004 0.046 613 Dihedral : 4.060 17.809 491 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.21 % Allowed : 13.16 % Favored : 82.63 % 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: 2.57 (0.43), residues: 452 helix: 1.86 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.55 (0.69), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.022 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.004 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.377 Fit side-chains REVERT: A 121 CYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5550 (m) REVERT: A 218 MET cc_start: 0.7697 (mmt) cc_final: 0.7357 (mmt) REVERT: A 227 PHE cc_start: 0.8076 (t80) cc_final: 0.7751 (t80) REVERT: A 346 ARG cc_start: 0.7996 (mtt180) cc_final: 0.7517 (mtt90) outliers start: 16 outliers final: 14 residues processed: 92 average time/residue: 0.1288 time to fit residues: 15.2530 Evaluate side-chains 96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0000 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.0030 chunk 37 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.202696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156601 restraints weight = 4718.698| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.90 r_work: 0.3702 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3639 Z= 0.177 Angle : 0.635 14.568 4963 Z= 0.295 Chirality : 0.039 0.162 574 Planarity : 0.004 0.043 613 Dihedral : 3.957 17.805 491 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.95 % Allowed : 14.21 % Favored : 81.84 % 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: 2.67 (0.43), residues: 452 helix: 1.96 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.51 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.022 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.006 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.381 Fit side-chains REVERT: A 121 CYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5400 (m) REVERT: A 227 PHE cc_start: 0.8015 (t80) cc_final: 0.7668 (t80) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.1215 time to fit residues: 13.5393 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.0970 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 27 optimal weight: 0.0970 overall best weight: 0.1814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 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 = 0.4362 r_free = 0.4362 target = 0.205475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159643 restraints weight = 4673.099| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.88 r_work: 0.3742 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3639 Z= 0.150 Angle : 0.650 14.632 4963 Z= 0.295 Chirality : 0.038 0.189 574 Planarity : 0.004 0.036 613 Dihedral : 3.892 17.560 491 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.68 % Allowed : 16.84 % Favored : 79.47 % 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: 2.79 (0.43), residues: 452 helix: 2.06 (0.30), residues: 328 sheet: None (None), residues: 0 loop : 1.52 (0.68), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.021 0.001 PHE A 22 TYR 0.006 0.001 TYR A 352 ARG 0.003 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5698 (OUTLIER) cc_final: 0.5387 (m) REVERT: A 227 PHE cc_start: 0.7961 (t80) cc_final: 0.7585 (t80) REVERT: A 242 MET cc_start: 0.7260 (mtm) cc_final: 0.6992 (mtt) REVERT: A 378 ASP cc_start: 0.8020 (t0) cc_final: 0.7519 (m-30) REVERT: A 418 LEU cc_start: 0.8480 (tp) cc_final: 0.8133 (tp) outliers start: 14 outliers final: 11 residues processed: 93 average time/residue: 0.1165 time to fit residues: 14.4451 Evaluate side-chains 92 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 0.1980 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 = 0.4342 r_free = 0.4342 target = 0.201825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156819 restraints weight = 4758.263| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.78 r_work: 0.3727 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3639 Z= 0.177 Angle : 0.668 14.580 4963 Z= 0.308 Chirality : 0.039 0.208 574 Planarity : 0.004 0.034 613 Dihedral : 3.916 16.510 491 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.16 % Allowed : 17.89 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.74 (0.42), residues: 452 helix: 2.02 (0.29), residues: 327 sheet: None (None), residues: 0 loop : 1.51 (0.68), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.020 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5841 (OUTLIER) cc_final: 0.5528 (m) REVERT: A 227 PHE cc_start: 0.7920 (t80) cc_final: 0.7540 (t80) REVERT: A 242 MET cc_start: 0.7379 (mtm) cc_final: 0.7128 (mtt) REVERT: A 378 ASP cc_start: 0.8010 (t0) cc_final: 0.7657 (m-30) outliers start: 12 outliers final: 11 residues processed: 89 average time/residue: 0.1105 time to fit residues: 13.0842 Evaluate side-chains 91 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.4331 r_free = 0.4331 target = 0.200408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154847 restraints weight = 4627.502| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.77 r_work: 0.3705 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3639 Z= 0.191 Angle : 0.669 14.560 4963 Z= 0.309 Chirality : 0.040 0.229 574 Planarity : 0.004 0.034 613 Dihedral : 3.917 16.634 491 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.89 % Allowed : 18.95 % Favored : 78.16 % 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: 2.70 (0.42), residues: 452 helix: 1.99 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 1.49 (0.67), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.020 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5520 (m) REVERT: A 218 MET cc_start: 0.7726 (mmt) cc_final: 0.7473 (mmt) REVERT: A 227 PHE cc_start: 0.7946 (t80) cc_final: 0.7561 (t80) REVERT: A 378 ASP cc_start: 0.7892 (t0) cc_final: 0.7622 (m-30) REVERT: A 447 GLN cc_start: 0.8460 (tp40) cc_final: 0.8069 (tm-30) outliers start: 11 outliers final: 10 residues processed: 89 average time/residue: 0.1090 time to fit residues: 12.9715 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 3 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.0670 chunk 11 optimal weight: 0.7980 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.4328 r_free = 0.4328 target = 0.200268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.154725 restraints weight = 4737.521| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.80 r_work: 0.3711 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3639 Z= 0.199 Angle : 0.696 14.564 4963 Z= 0.322 Chirality : 0.041 0.230 574 Planarity : 0.004 0.034 613 Dihedral : 3.940 16.869 491 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.89 % Allowed : 19.47 % Favored : 77.63 % 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: 2.59 (0.42), residues: 452 helix: 1.90 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 1.49 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.021 0.001 PHE A 348 TYR 0.008 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 904 Ramachandran restraints generated. 452 Oldfield, 0 Emsley, 452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7967 (t80) cc_final: 0.7572 (t80) REVERT: A 378 ASP cc_start: 0.7904 (t0) cc_final: 0.7635 (m-30) REVERT: A 447 GLN cc_start: 0.8494 (tp40) cc_final: 0.8218 (tm-30) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.1142 time to fit residues: 12.7711 Evaluate side-chains 87 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 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 = 0.4333 r_free = 0.4333 target = 0.200315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155012 restraints weight = 4779.414| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.81 r_work: 0.3697 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3639 Z= 0.209 Angle : 0.699 14.547 4963 Z= 0.325 Chirality : 0.041 0.230 574 Planarity : 0.004 0.034 613 Dihedral : 4.005 16.839 491 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.89 % Allowed : 19.21 % Favored : 77.89 % 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: 2.58 (0.42), residues: 452 helix: 1.89 (0.29), residues: 328 sheet: None (None), residues: 0 loop : 1.48 (0.66), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.020 0.001 PHE A 348 TYR 0.012 0.001 TYR A 352 ARG 0.002 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.66 seconds wall clock time: 37 minutes 20.63 seconds (2240.63 seconds total)