Starting phenix.real_space_refine on Sat Apr 26 17:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xtx_38652/04_2025/8xtx_38652.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xtx_38652/04_2025/8xtx_38652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xtx_38652/04_2025/8xtx_38652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xtx_38652/04_2025/8xtx_38652.map" model { file = "/net/cci-nas-00/data/ceres_data/8xtx_38652/04_2025/8xtx_38652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xtx_38652/04_2025/8xtx_38652.cif" } resolution = 3.4 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= 0.002 sd= 0.161 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 17 5.16 5 C 1912 2.51 5 N 458 2.21 5 O 489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2876 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2876 Classifications: {'peptide': 382} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 3.05, per 1000 atoms: 1.06 Number of scatterers: 2876 At special positions: 0 Unit cell: (68.85, 72.25, 64.6, 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 17 16.00 O 489 8.00 N 458 7.00 C 1912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 449.9 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 82.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 4.121A pdb=" N VAL A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.568A pdb=" N GLY A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 Processing helix chain 'A' and resid 138 through 147 Proline residue: A 144 - end of helix removed outlier: 3.955A pdb=" N ASP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'A' and resid 174 through 204 removed outlier: 4.576A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 226 removed outlier: 3.678A pdb=" N ARG A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 removed outlier: 4.330A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 288 through 302 removed outlier: 4.193A pdb=" N VAL A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.747A pdb=" N GLU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 324 through 329 removed outlier: 4.128A pdb=" N GLY A 328 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 removed outlier: 3.549A pdb=" N ALA A 334 " --> pdb=" O TRP A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.705A pdb=" N ALA A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 Processing helix chain 'A' and resid 379 through 412 removed outlier: 3.688A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 4.007A pdb=" N ALA A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 Processing helix chain 'A' and resid 430 through 447 Proline residue: A 436 - end of helix removed outlier: 5.594A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 464 through 468 removed outlier: 3.501A pdb=" N LEU A 468 " --> pdb=" O VAL A 465 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 540 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: 0.76 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 439 1.31 - 1.43: 765 1.43 - 1.56: 1714 1.56 - 1.69: 1 1.69 - 1.81: 28 Bond restraints: 2947 Sorted by residual: bond pdb=" C VAL A 52 " pdb=" O VAL A 52 " ideal model delta sigma weight residual 1.240 1.181 0.059 1.49e-02 4.50e+03 1.57e+01 bond pdb=" C LEU A 49 " pdb=" N TYR A 50 " ideal model delta sigma weight residual 1.333 1.285 0.048 1.47e-02 4.63e+03 1.07e+01 bond pdb=" C TYR A 50 " pdb=" O TYR A 50 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.34e-02 5.57e+03 7.26e+00 bond pdb=" C MET A 51 " pdb=" O MET A 51 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.48e-02 4.57e+03 6.99e+00 bond pdb=" N CYS A 301 " pdb=" CA CYS A 301 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.60e+00 ... (remaining 2942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 3948 2.35 - 4.70: 68 4.70 - 7.05: 7 7.05 - 9.39: 4 9.39 - 11.74: 3 Bond angle restraints: 4030 Sorted by residual: angle pdb=" N TYR A 50 " pdb=" CA TYR A 50 " pdb=" C TYR A 50 " ideal model delta sigma weight residual 113.38 102.44 10.94 1.23e+00 6.61e-01 7.91e+01 angle pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" CD PRO A 58 " ideal model delta sigma weight residual 112.00 100.26 11.74 1.40e+00 5.10e-01 7.04e+01 angle pdb=" N VAL A 52 " pdb=" CA VAL A 52 " pdb=" C VAL A 52 " ideal model delta sigma weight residual 112.90 106.53 6.37 9.60e-01 1.09e+00 4.41e+01 angle pdb=" C LEU A 49 " pdb=" N TYR A 50 " pdb=" CA TYR A 50 " ideal model delta sigma weight residual 122.26 113.42 8.84 1.73e+00 3.34e-01 2.61e+01 angle pdb=" CA TYR A 50 " pdb=" CB TYR A 50 " pdb=" CG TYR A 50 " ideal model delta sigma weight residual 113.90 122.36 -8.46 1.80e+00 3.09e-01 2.21e+01 ... (remaining 4025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 1423 15.61 - 31.21: 215 31.21 - 46.82: 71 46.82 - 62.43: 15 62.43 - 78.03: 5 Dihedral angle restraints: 1729 sinusoidal: 627 harmonic: 1102 Sorted by residual: dihedral pdb=" CA MET A 320 " pdb=" C MET A 320 " pdb=" N ALA A 321 " pdb=" CA ALA A 321 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA MET A 149 " pdb=" C MET A 149 " pdb=" N SER A 150 " pdb=" CA SER A 150 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA THR A 399 " pdb=" C THR A 399 " pdb=" N ALA A 400 " pdb=" CA ALA A 400 " ideal model delta harmonic sigma weight residual 180.00 162.01 17.99 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 372 0.047 - 0.095: 108 0.095 - 0.142: 10 0.142 - 0.189: 2 0.189 - 0.236: 2 Chirality restraints: 494 Sorted by residual: chirality pdb=" CA GLN A 31 " pdb=" N GLN A 31 " pdb=" C GLN A 31 " pdb=" CB GLN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL A 52 " pdb=" CA VAL A 52 " pdb=" CG1 VAL A 52 " pdb=" CG2 VAL A 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PRO A 58 " pdb=" N PRO A 58 " pdb=" C PRO A 58 " pdb=" CB PRO A 58 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.37e-01 ... (remaining 491 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 57 " 0.076 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 58 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 58 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 58 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 49 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C LEU A 49 " -0.068 2.00e-02 2.50e+03 pdb=" O LEU A 49 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR A 50 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 332 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO A 333 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.046 5.00e-02 4.00e+02 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 437 2.75 - 3.29: 2667 3.29 - 3.83: 4667 3.83 - 4.36: 4858 4.36 - 4.90: 8772 Nonbonded interactions: 21401 Sorted by model distance: nonbonded pdb=" O LEU A 305 " pdb=" OE1 GLU A 309 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 410 " pdb=" OH TYR A 417 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLN A 135 " pdb=" OG SER A 429 " model vdw 2.290 3.040 nonbonded pdb=" N ASP A 147 " pdb=" OD1 ASP A 147 " model vdw 2.334 3.120 nonbonded pdb=" O GLY A 418 " pdb=" OG SER A 419 " model vdw 2.360 3.040 ... (remaining 21396 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: 1.170 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: 0.020 Set scattering table: 0.030 Process input model: 15.130 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: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 0.112 2947 Z= 0.213 Angle : 0.774 11.743 4030 Z= 0.448 Chirality : 0.042 0.236 494 Planarity : 0.009 0.107 495 Dihedral : 17.361 78.032 1021 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.66 % Allowed : 33.99 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.04 (0.49), residues: 376 helix: 1.29 (0.35), residues: 290 sheet: None (None), residues: 0 loop : -4.62 (0.52), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.008 0.001 HIS A 441 PHE 0.010 0.001 PHE A 169 TYR 0.020 0.002 TYR A 50 ARG 0.004 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.15544 ( 183) hydrogen bonds : angle 4.66725 ( 540) covalent geometry : bond 0.00437 ( 2947) covalent geometry : angle 0.77434 ( 4030) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.311 Fit side-chains REVERT: A 449 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7140 (mm-30) outliers start: 2 outliers final: 1 residues processed: 44 average time/residue: 0.1327 time to fit residues: 7.3985 Evaluate side-chains 42 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 0.0470 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.151919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125623 restraints weight = 3924.149| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.88 r_work: 0.3216 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2947 Z= 0.119 Angle : 0.597 5.724 4030 Z= 0.302 Chirality : 0.038 0.114 494 Planarity : 0.007 0.062 495 Dihedral : 4.658 29.669 411 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.30 % Allowed : 32.67 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.19 (0.49), residues: 376 helix: 1.44 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.36 (0.51), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.002 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 183) hydrogen bonds : angle 3.73371 ( 540) covalent geometry : bond 0.00288 ( 2947) covalent geometry : angle 0.59691 ( 4030) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.286 Fit side-chains REVERT: A 173 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 461 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7137 (tt) outliers start: 10 outliers final: 4 residues processed: 51 average time/residue: 0.1244 time to fit residues: 8.0879 Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.0270 chunk 7 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126350 restraints weight = 3824.378| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.81 r_work: 0.3277 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2947 Z= 0.110 Angle : 0.577 6.275 4030 Z= 0.287 Chirality : 0.037 0.110 494 Planarity : 0.006 0.061 495 Dihedral : 4.244 21.879 408 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.28 % Allowed : 31.02 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.26 (0.49), residues: 376 helix: 1.53 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.44 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.003 0.001 TYR A 50 ARG 0.002 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 183) hydrogen bonds : angle 3.59045 ( 540) covalent geometry : bond 0.00261 ( 2947) covalent geometry : angle 0.57719 ( 4030) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.324 Fit side-chains REVERT: A 173 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7298 (tm-30) REVERT: A 444 HIS cc_start: 0.7384 (t-90) cc_final: 0.7164 (t70) REVERT: A 453 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7353 (mm) REVERT: A 461 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7139 (tt) outliers start: 16 outliers final: 7 residues processed: 56 average time/residue: 0.1265 time to fit residues: 9.0620 Evaluate side-chains 52 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 441 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121288 restraints weight = 3861.541| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.88 r_work: 0.3180 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2947 Z= 0.123 Angle : 0.591 6.093 4030 Z= 0.292 Chirality : 0.037 0.114 494 Planarity : 0.006 0.060 495 Dihedral : 4.235 19.999 408 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.29 % Allowed : 31.68 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.30 (0.49), residues: 376 helix: 1.56 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.44 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.002 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 183) hydrogen bonds : angle 3.55185 ( 540) covalent geometry : bond 0.00304 ( 2947) covalent geometry : angle 0.59144 ( 4030) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.306 Fit side-chains REVERT: A 149 MET cc_start: 0.8137 (mtt) cc_final: 0.7868 (mtt) REVERT: A 173 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7102 (tm-30) REVERT: A 444 HIS cc_start: 0.7302 (t-90) cc_final: 0.7100 (t70) REVERT: A 453 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7238 (mm) REVERT: A 461 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7035 (tt) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 0.1120 time to fit residues: 7.7337 Evaluate side-chains 53 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.0470 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.147025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121745 restraints weight = 3875.612| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.88 r_work: 0.3187 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2947 Z= 0.115 Angle : 0.585 6.286 4030 Z= 0.288 Chirality : 0.037 0.111 494 Planarity : 0.005 0.061 495 Dihedral : 4.184 20.819 408 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 6.60 % Allowed : 29.37 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.49), residues: 376 helix: 1.65 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.39 (0.49), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.005 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.002 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 183) hydrogen bonds : angle 3.51743 ( 540) covalent geometry : bond 0.00280 ( 2947) covalent geometry : angle 0.58486 ( 4030) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.398 Fit side-chains REVERT: A 149 MET cc_start: 0.8198 (mtt) cc_final: 0.7803 (mtm) REVERT: A 173 GLU cc_start: 0.7494 (tm-30) cc_final: 0.7100 (tm-30) REVERT: A 354 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.6807 (p-80) REVERT: A 453 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7134 (mm) REVERT: A 461 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6984 (tt) outliers start: 20 outliers final: 12 residues processed: 58 average time/residue: 0.1113 time to fit residues: 8.4740 Evaluate side-chains 58 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.0000 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117367 restraints weight = 3949.869| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.78 r_work: 0.3192 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2947 Z= 0.108 Angle : 0.576 6.595 4030 Z= 0.283 Chirality : 0.037 0.110 494 Planarity : 0.005 0.061 495 Dihedral : 4.094 20.509 408 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.95 % Allowed : 32.01 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.59 (0.49), residues: 376 helix: 1.77 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.34 (0.50), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 315 HIS 0.007 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02801 ( 183) hydrogen bonds : angle 3.39990 ( 540) covalent geometry : bond 0.00260 ( 2947) covalent geometry : angle 0.57631 ( 4030) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.311 Fit side-chains REVERT: A 149 MET cc_start: 0.8165 (mtt) cc_final: 0.7747 (mtt) REVERT: A 173 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 354 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.6883 (p90) REVERT: A 453 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7189 (mm) REVERT: A 461 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6990 (tt) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.1159 time to fit residues: 8.0148 Evaluate side-chains 55 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.0030 chunk 3 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125473 restraints weight = 3899.966| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.88 r_work: 0.3192 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2947 Z= 0.109 Angle : 0.577 5.833 4030 Z= 0.284 Chirality : 0.037 0.112 494 Planarity : 0.005 0.061 495 Dihedral : 4.091 20.649 408 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.61 % Allowed : 32.01 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.69 (0.49), residues: 376 helix: 1.84 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.29 (0.50), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 315 HIS 0.006 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 183) hydrogen bonds : angle 3.38111 ( 540) covalent geometry : bond 0.00265 ( 2947) covalent geometry : angle 0.57716 ( 4030) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.294 Fit side-chains REVERT: A 149 MET cc_start: 0.8188 (mtt) cc_final: 0.7731 (mtt) REVERT: A 173 GLU cc_start: 0.7408 (tm-30) cc_final: 0.6846 (tm-30) REVERT: A 354 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.6888 (p90) REVERT: A 453 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7179 (mm) REVERT: A 461 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6998 (tt) outliers start: 17 outliers final: 12 residues processed: 55 average time/residue: 0.1060 time to fit residues: 7.7063 Evaluate side-chains 56 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117595 restraints weight = 3837.678| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.70 r_work: 0.3196 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2947 Z= 0.111 Angle : 0.591 9.558 4030 Z= 0.287 Chirality : 0.037 0.121 494 Planarity : 0.005 0.062 495 Dihedral : 4.050 21.146 408 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 6.27 % Allowed : 32.01 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.49), residues: 376 helix: 1.86 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.19 (0.51), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 315 HIS 0.004 0.001 HIS A 441 PHE 0.008 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 183) hydrogen bonds : angle 3.35724 ( 540) covalent geometry : bond 0.00268 ( 2947) covalent geometry : angle 0.59119 ( 4030) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.318 Fit side-chains REVERT: A 149 MET cc_start: 0.8162 (mtt) cc_final: 0.7734 (mtt) REVERT: A 173 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6742 (tm-30) REVERT: A 354 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.6862 (p90) REVERT: A 453 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7158 (mm) REVERT: A 461 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6981 (tt) outliers start: 19 outliers final: 14 residues processed: 56 average time/residue: 0.1121 time to fit residues: 8.1314 Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 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 = 0.3702 r_free = 0.3702 target = 0.149384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124146 restraints weight = 3839.641| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.82 r_work: 0.3244 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2947 Z= 0.113 Angle : 0.601 8.649 4030 Z= 0.292 Chirality : 0.037 0.122 494 Planarity : 0.005 0.062 495 Dihedral : 4.078 20.735 408 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.61 % Allowed : 32.01 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.83 (0.50), residues: 376 helix: 1.90 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.11 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 315 HIS 0.004 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02837 ( 183) hydrogen bonds : angle 3.35791 ( 540) covalent geometry : bond 0.00275 ( 2947) covalent geometry : angle 0.60083 ( 4030) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.316 Fit side-chains REVERT: A 149 MET cc_start: 0.8200 (mtt) cc_final: 0.7786 (mtt) REVERT: A 173 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6753 (tm-30) REVERT: A 354 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.6871 (p90) REVERT: A 453 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7183 (mm) REVERT: A 461 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.7018 (tt) outliers start: 17 outliers final: 14 residues processed: 55 average time/residue: 0.1190 time to fit residues: 8.5511 Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.143535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118097 restraints weight = 3887.145| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.73 r_work: 0.3253 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2947 Z= 0.113 Angle : 0.596 8.453 4030 Z= 0.290 Chirality : 0.037 0.119 494 Planarity : 0.005 0.062 495 Dihedral : 4.055 20.788 408 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.94 % Allowed : 31.68 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.85 (0.50), residues: 376 helix: 1.91 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.07 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 315 HIS 0.004 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 183) hydrogen bonds : angle 3.33722 ( 540) covalent geometry : bond 0.00272 ( 2947) covalent geometry : angle 0.59639 ( 4030) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.291 Fit side-chains REVERT: A 149 MET cc_start: 0.8192 (mtt) cc_final: 0.7804 (mtt) REVERT: A 173 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6777 (tm-30) REVERT: A 354 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.6892 (p90) REVERT: A 453 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7201 (mm) REVERT: A 461 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7037 (tt) outliers start: 18 outliers final: 13 residues processed: 55 average time/residue: 0.1163 time to fit residues: 8.3210 Evaluate side-chains 57 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 427 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 0.0170 chunk 19 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3723 r_free = 0.3723 target = 0.151142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125994 restraints weight = 3762.992| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.79 r_work: 0.3210 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2947 Z= 0.111 Angle : 0.596 8.198 4030 Z= 0.290 Chirality : 0.037 0.120 494 Planarity : 0.005 0.062 495 Dihedral : 4.083 20.895 408 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 5.61 % Allowed : 31.68 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.50), residues: 376 helix: 1.93 (0.35), residues: 284 sheet: None (None), residues: 0 loop : -4.07 (0.53), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 357 HIS 0.004 0.001 HIS A 441 PHE 0.009 0.001 PHE A 335 TYR 0.005 0.001 TYR A 417 ARG 0.003 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.02770 ( 183) hydrogen bonds : angle 3.32494 ( 540) covalent geometry : bond 0.00268 ( 2947) covalent geometry : angle 0.59649 ( 4030) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.65 seconds wall clock time: 29 minutes 29.82 seconds (1769.82 seconds total)