Starting phenix.real_space_refine on Fri May 9 20:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sc4_40337/05_2025/8sc4_40337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sc4_40337/05_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_40337/05_2025/8sc4_40337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sc4_40337/05_2025/8sc4_40337.map" model { file = "/net/cci-nas-00/data/ceres_data/8sc4_40337/05_2025/8sc4_40337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sc4_40337/05_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-5687/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: 2.78, per 1000 atoms: 0.78 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: 0.93 Conformation dependent library (CDL) restraints added in 430.9 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: 0.37 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: 0.97 Time building geometry restraints manager: 1.09 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: 1.080 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.200 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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 3642 Z= 0.176 Angle : 0.686 6.073 4969 Z= 0.391 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 Details of bonding type rmsd hydrogen bonds : bond 0.12882 ( 253) hydrogen bonds : angle 6.64435 ( 735) SS BOND : bond 0.00215 ( 3) SS BOND : angle 1.87409 ( 6) covalent geometry : bond 0.00356 ( 3639) covalent geometry : angle 0.68309 ( 4963) *********************** 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: 0.1614 time to fit residues: 23.7893 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 : 0.391 ------------------------------------------------------------------------------- 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: 0.3813 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 3642 Z= 0.136 Angle : 0.690 15.080 4969 Z= 0.331 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 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 253) hydrogen bonds : angle 4.82743 ( 735) SS BOND : bond 0.00294 ( 3) SS BOND : angle 1.70790 ( 6) covalent geometry : bond 0.00279 ( 3639) covalent geometry : angle 0.68819 ( 4963) *********************** 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 : 0.384 Fit side-chains REVERT: A 22 PHE cc_start: 0.6467 (t80) cc_final: 0.6093 (t80) REVERT: A 121 CYS cc_start: 0.5655 (OUTLIER) cc_final: 0.5247 (m) REVERT: A 227 PHE cc_start: 0.7942 (t80) cc_final: 0.7556 (t80) REVERT: A 346 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7619 (mtt90) REVERT: A 418 LEU cc_start: 0.8598 (tp) cc_final: 0.8294 (tp) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.1299 time to fit residues: 15.3996 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 : 0.329 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 1 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 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 = 0.4371 r_free = 0.4371 target = 0.204003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158204 restraints weight = 4587.625| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.80 r_work: 0.3777 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3642 Z= 0.138 Angle : 0.675 14.513 4969 Z= 0.317 Chirality : 0.040 0.167 574 Planarity : 0.005 0.060 613 Dihedral : 4.122 17.346 491 Min Nonbonded Distance : 2.638 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: 2.22 (0.43), residues: 452 helix: 1.52 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.68 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS A 49 PHE 0.029 0.002 PHE A 22 TYR 0.012 0.001 TYR A 240 ARG 0.005 0.001 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 253) hydrogen bonds : angle 4.60080 ( 735) SS BOND : bond 0.00396 ( 3) SS BOND : angle 1.36870 ( 6) covalent geometry : bond 0.00299 ( 3639) covalent geometry : angle 0.67352 ( 4963) *********************** 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 : 0.344 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5857 (OUTLIER) cc_final: 0.5500 (m) REVERT: A 227 PHE cc_start: 0.8031 (t80) cc_final: 0.7718 (t80) REVERT: A 346 ARG cc_start: 0.7925 (mtt180) cc_final: 0.7575 (mtt90) REVERT: A 418 LEU cc_start: 0.8575 (tp) cc_final: 0.8200 (tp) outliers start: 13 outliers final: 11 residues processed: 91 average time/residue: 0.1256 time to fit residues: 14.6128 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 : 0.336 ------------------------------------------------------------------------------- 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 394 LEU 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: 0.8980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 428 HIS A 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.203543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.157974 restraints weight = 4599.953| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 2.77 r_work: 0.3771 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3642 Z= 0.129 Angle : 0.649 14.540 4969 Z= 0.301 Chirality : 0.039 0.192 574 Planarity : 0.004 0.051 613 Dihedral : 4.020 16.931 491 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 5.26 % Allowed : 10.79 % 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: 2.48 (0.43), residues: 452 helix: 1.74 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.70 (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 0.023 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.004 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 253) hydrogen bonds : angle 4.47034 ( 735) SS BOND : bond 0.00187 ( 3) SS BOND : angle 1.33556 ( 6) covalent geometry : bond 0.00286 ( 3639) covalent geometry : angle 0.64763 ( 4963) *********************** 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 98 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.336 Fit side-chains REVERT: A 121 CYS cc_start: 0.5955 (OUTLIER) cc_final: 0.5606 (m) REVERT: A 132 SER cc_start: 0.8754 (p) cc_final: 0.8404 (m) REVERT: A 218 MET cc_start: 0.7612 (mmt) cc_final: 0.7270 (mmt) REVERT: A 227 PHE cc_start: 0.8052 (t80) cc_final: 0.7741 (t80) REVERT: A 346 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7561 (mtt90) REVERT: A 418 LEU cc_start: 0.8574 (tp) cc_final: 0.8197 (tp) outliers start: 20 outliers final: 15 residues processed: 87 average time/residue: 0.1238 time to fit residues: 13.7497 Evaluate side-chains 94 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 2 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.201899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.155598 restraints weight = 4644.996| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.84 r_work: 0.3689 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3642 Z= 0.132 Angle : 0.646 14.521 4969 Z= 0.304 Chirality : 0.039 0.153 574 Planarity : 0.004 0.046 613 Dihedral : 4.047 17.280 491 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.47 % Allowed : 12.37 % Favored : 83.16 % 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: 2.56 (0.43), residues: 452 helix: 1.84 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.60 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 0.004 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 253) hydrogen bonds : angle 4.42566 ( 735) SS BOND : bond 0.00148 ( 3) SS BOND : angle 1.23590 ( 6) covalent geometry : bond 0.00299 ( 3639) covalent geometry : angle 0.64469 ( 4963) *********************** 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 100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.357 Fit side-chains REVERT: A 121 CYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5481 (m) REVERT: A 218 MET cc_start: 0.7706 (mmt) cc_final: 0.7361 (mmt) REVERT: A 227 PHE cc_start: 0.8111 (t80) cc_final: 0.7777 (t80) REVERT: A 241 GLN cc_start: 0.6956 (tm-30) cc_final: 0.6549 (tm-30) REVERT: A 346 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7521 (mtt90) REVERT: A 378 ASP cc_start: 0.8134 (m-30) cc_final: 0.7563 (m-30) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.1236 time to fit residues: 14.4127 Evaluate side-chains 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 Chi-restraints excluded: chain A residue 505 LEU 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: 2.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4327 r_free = 0.4327 target = 0.201662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154804 restraints weight = 4731.723| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.91 r_work: 0.3695 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3642 Z= 0.132 Angle : 0.661 14.538 4969 Z= 0.306 Chirality : 0.040 0.168 574 Planarity : 0.004 0.041 613 Dihedral : 4.011 17.689 491 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.21 % Allowed : 13.95 % 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: 2.57 (0.43), residues: 452 helix: 1.90 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.44 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.005 0.001 HIS A 49 PHE 0.022 0.001 PHE A 22 TYR 0.008 0.001 TYR A 352 ARG 0.007 0.001 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 253) hydrogen bonds : angle 4.41323 ( 735) SS BOND : bond 0.00170 ( 3) SS BOND : angle 1.45502 ( 6) covalent geometry : bond 0.00298 ( 3639) covalent geometry : angle 0.65918 ( 4963) *********************** 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 99 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5745 (OUTLIER) cc_final: 0.5437 (m) REVERT: A 227 PHE cc_start: 0.8082 (t80) cc_final: 0.7734 (t80) REVERT: A 346 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7422 (mtt90) REVERT: A 378 ASP cc_start: 0.8165 (m-30) cc_final: 0.7657 (m-30) outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.1192 time to fit residues: 14.2565 Evaluate side-chains 96 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.199716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.153719 restraints weight = 4681.424| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.77 r_work: 0.3711 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3642 Z= 0.145 Angle : 0.680 14.514 4969 Z= 0.318 Chirality : 0.040 0.179 574 Planarity : 0.004 0.041 613 Dihedral : 4.034 16.930 491 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.47 % Allowed : 16.58 % 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: 2.62 (0.43), residues: 452 helix: 1.90 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.55 (0.68), 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 0.020 0.001 PHE A 22 TYR 0.010 0.001 TYR A 352 ARG 0.002 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 253) hydrogen bonds : angle 4.43343 ( 735) SS BOND : bond 0.00178 ( 3) SS BOND : angle 1.39723 ( 6) covalent geometry : bond 0.00332 ( 3639) covalent geometry : angle 0.67898 ( 4963) *********************** 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 101 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5611 (m) REVERT: A 227 PHE cc_start: 0.8053 (t80) cc_final: 0.7709 (t80) REVERT: A 378 ASP cc_start: 0.8064 (m-30) cc_final: 0.7608 (m-30) REVERT: A 486 ARG cc_start: 0.8037 (mmp80) cc_final: 0.7473 (mmm160) outliers start: 17 outliers final: 15 residues processed: 93 average time/residue: 0.1239 time to fit residues: 14.8342 Evaluate side-chains 100 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 132 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 0.0370 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 0.0570 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.200271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.154865 restraints weight = 4709.843| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.79 r_work: 0.3689 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3642 Z= 0.122 Angle : 0.677 14.576 4969 Z= 0.311 Chirality : 0.039 0.207 574 Planarity : 0.004 0.038 613 Dihedral : 3.943 17.217 491 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.68 % Allowed : 16.32 % Favored : 80.00 % 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: 2.68 (0.43), residues: 452 helix: 1.95 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.54 (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 0.020 0.001 PHE A 348 TYR 0.009 0.001 TYR A 352 ARG 0.004 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 253) hydrogen bonds : angle 4.35882 ( 735) SS BOND : bond 0.00154 ( 3) SS BOND : angle 1.14414 ( 6) covalent geometry : bond 0.00269 ( 3639) covalent geometry : angle 0.67594 ( 4963) *********************** 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 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5545 (m) REVERT: A 227 PHE cc_start: 0.7978 (t80) cc_final: 0.7622 (t80) REVERT: A 378 ASP cc_start: 0.8034 (m-30) cc_final: 0.7598 (m-30) REVERT: A 486 ARG cc_start: 0.7887 (mmp80) cc_final: 0.7484 (mmm160) outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.1053 time to fit residues: 12.6611 Evaluate side-chains 90 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.198485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152973 restraints weight = 4644.769| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.74 r_work: 0.3673 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3642 Z= 0.140 Angle : 0.693 14.530 4969 Z= 0.320 Chirality : 0.040 0.215 574 Planarity : 0.004 0.039 613 Dihedral : 3.998 16.521 491 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.21 % Allowed : 16.58 % Favored : 79.21 % 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: 2.63 (0.43), residues: 452 helix: 1.92 (0.30), residues: 329 sheet: None (None), residues: 0 loop : 1.49 (0.68), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.021 0.001 PHE A 348 TYR 0.012 0.001 TYR A 352 ARG 0.003 0.000 ARG A 488 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 253) hydrogen bonds : angle 4.43066 ( 735) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.27720 ( 6) covalent geometry : bond 0.00321 ( 3639) covalent geometry : angle 0.69188 ( 4963) *********************** 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 95 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5585 (m) REVERT: A 227 PHE cc_start: 0.8007 (t80) cc_final: 0.7643 (t80) REVERT: A 378 ASP cc_start: 0.8071 (m-30) cc_final: 0.7579 (m-30) outliers start: 16 outliers final: 14 residues processed: 88 average time/residue: 0.1109 time to fit residues: 12.8410 Evaluate side-chains 89 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 132 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.197554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151967 restraints weight = 4688.012| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.76 r_work: 0.3669 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3642 Z= 0.144 Angle : 0.698 14.526 4969 Z= 0.326 Chirality : 0.041 0.224 574 Planarity : 0.004 0.040 613 Dihedral : 4.043 16.789 491 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.95 % Allowed : 17.11 % 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: 2.52 (0.42), residues: 452 helix: 1.85 (0.30), residues: 328 sheet: None (None), residues: 0 loop : 1.45 (0.68), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.021 0.001 PHE A 348 TYR 0.017 0.001 TYR A 256 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 253) hydrogen bonds : angle 4.49582 ( 735) SS BOND : bond 0.00189 ( 3) SS BOND : angle 1.21010 ( 6) covalent geometry : bond 0.00329 ( 3639) covalent geometry : angle 0.69741 ( 4963) ********************** 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 93 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 121 CYS cc_start: 0.5874 (OUTLIER) cc_final: 0.5555 (m) REVERT: A 227 PHE cc_start: 0.8009 (t80) cc_final: 0.7643 (t80) REVERT: A 378 ASP cc_start: 0.8097 (m-30) cc_final: 0.7606 (m-30) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1161 time to fit residues: 13.5201 Evaluate side-chains 91 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 132 SER 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 473 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.4293 r_free = 0.4293 target = 0.197008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151563 restraints weight = 4622.605| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.73 r_work: 0.3680 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3642 Z= 0.142 Angle : 0.715 14.536 4969 Z= 0.333 Chirality : 0.041 0.221 574 Planarity : 0.004 0.040 613 Dihedral : 4.036 16.692 491 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.68 % Allowed : 18.95 % Favored : 77.37 % 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: 2.49 (0.42), residues: 452 helix: 1.84 (0.30), residues: 328 sheet: None (None), residues: 0 loop : 1.42 (0.67), residues: 124 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 0.020 0.001 PHE A 348 TYR 0.010 0.001 TYR A 352 ARG 0.005 0.000 ARG A 233 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 253) hydrogen bonds : angle 4.49360 ( 735) SS BOND : bond 0.00190 ( 3) SS BOND : angle 1.25030 ( 6) covalent geometry : bond 0.00324 ( 3639) covalent geometry : angle 0.71424 ( 4963) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.70 seconds wall clock time: 35 minutes 58.76 seconds (2158.76 seconds total)