Starting phenix.real_space_refine on Mon Feb 10 22:28:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7r_39825/02_2025/8z7r_39825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7r_39825/02_2025/8z7r_39825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7r_39825/02_2025/8z7r_39825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7r_39825/02_2025/8z7r_39825.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7r_39825/02_2025/8z7r_39825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7r_39825/02_2025/8z7r_39825.cif" } resolution = 3.15 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= 0.102 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 15 5.16 5 C 2091 2.51 5 N 463 2.21 5 O 529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3098 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3098 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 13, 'TRANS': 373} Chain breaks: 1 Time building chain proxies: 2.58, per 1000 atoms: 0.83 Number of scatterers: 3098 At special positions: 0 Unit cell: (64, 68, 67, 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 15 16.00 O 529 8.00 N 463 7.00 C 2091 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: 0.72 Conformation dependent library (CDL) restraints added in 397.9 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 734 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 28 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.535A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.756A pdb=" N TRP A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 79 through 99 removed outlier: 3.636A pdb=" N ILE A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 131 removed outlier: 3.923A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.572A pdb=" N PHE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 3.638A pdb=" N PHE A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 306 removed outlier: 4.126A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 337 Processing helix chain 'A' and resid 340 through 366 removed outlier: 5.482A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 Processing helix chain 'A' and resid 402 through 426 Processing helix chain 'A' and resid 434 through 460 removed outlier: 3.504A pdb=" N SER A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 753 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: 0.93 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 868 1.34 - 1.46: 715 1.46 - 1.58: 1582 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 3191 Sorted by residual: bond pdb=" N ILE A 314 " pdb=" CA ILE A 314 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.43e+00 bond pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 7.71e+00 bond pdb=" N SER A 312 " pdb=" CA SER A 312 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.27e-02 6.20e+03 7.43e+00 bond pdb=" N GLU A 320 " pdb=" CA GLU A 320 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.37e+00 bond pdb=" N ASN A 316 " pdb=" CA ASN A 316 " ideal model delta sigma weight residual 1.463 1.489 -0.026 1.08e-02 8.57e+03 6.00e+00 ... (remaining 3186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 4073 1.41 - 2.81: 231 2.81 - 4.22: 39 4.22 - 5.62: 16 5.62 - 7.03: 3 Bond angle restraints: 4362 Sorted by residual: angle pdb=" CA TYR A 336 " pdb=" C TYR A 336 " pdb=" N VAL A 337 " ideal model delta sigma weight residual 118.14 123.56 -5.42 1.56e+00 4.11e-01 1.21e+01 angle pdb=" N ILE A 460 " pdb=" CA ILE A 460 " pdb=" C ILE A 460 " ideal model delta sigma weight residual 111.77 108.51 3.26 1.04e+00 9.25e-01 9.83e+00 angle pdb=" CA ASP A 311 " pdb=" C ASP A 311 " pdb=" O ASP A 311 " ideal model delta sigma weight residual 122.45 118.40 4.05 1.30e+00 5.92e-01 9.70e+00 angle pdb=" N GLN A 86 " pdb=" CA GLN A 86 " pdb=" C GLN A 86 " ideal model delta sigma weight residual 111.36 108.02 3.34 1.09e+00 8.42e-01 9.39e+00 angle pdb=" N VAL A 435 " pdb=" CA VAL A 435 " pdb=" C VAL A 435 " ideal model delta sigma weight residual 110.42 113.36 -2.94 9.60e-01 1.09e+00 9.35e+00 ... (remaining 4357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 1527 16.34 - 32.68: 213 32.68 - 49.02: 51 49.02 - 65.36: 13 65.36 - 81.70: 4 Dihedral angle restraints: 1808 sinusoidal: 659 harmonic: 1149 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PRO A 434 " pdb=" C PRO A 434 " pdb=" N VAL A 435 " pdb=" CA VAL A 435 " ideal model delta harmonic sigma weight residual -180.00 -162.80 -17.20 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -163.90 -16.10 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 1805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 342 0.039 - 0.079: 124 0.079 - 0.118: 33 0.118 - 0.158: 4 0.158 - 0.197: 2 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA GLN A 310 " pdb=" N GLN A 310 " pdb=" C GLN A 310 " pdb=" CB GLN A 310 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" CA ILE A 314 " pdb=" N ILE A 314 " pdb=" C ILE A 314 " pdb=" CB ILE A 314 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA VAL A 400 " pdb=" N VAL A 400 " pdb=" C VAL A 400 " pdb=" CB VAL A 400 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 502 not shown) Planarity restraints: 523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 319 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.82e+00 pdb=" C VAL A 319 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL A 319 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 320 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 144 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C ARG A 144 " -0.037 2.00e-02 2.50e+03 pdb=" O ARG A 144 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 145 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 154 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C GLY A 154 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 154 " 0.014 2.00e-02 2.50e+03 pdb=" N SER A 155 " 0.012 2.00e-02 2.50e+03 ... (remaining 520 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 474 2.75 - 3.29: 3331 3.29 - 3.83: 5497 3.83 - 4.36: 6441 4.36 - 4.90: 10967 Nonbonded interactions: 26710 Sorted by model distance: nonbonded pdb=" OH TYR A 128 " pdb=" OG SER A 140 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP A 75 " pdb=" OH TYR A 79 " model vdw 2.295 3.040 nonbonded pdb=" O SER A 89 " pdb=" OG1 THR A 93 " model vdw 2.355 3.040 nonbonded pdb=" O PHE A 287 " pdb=" OH TYR A 445 " model vdw 2.357 3.040 nonbonded pdb=" OE1 GLU A 320 " pdb=" OH TYR A 376 " model vdw 2.368 3.040 ... (remaining 26705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.390 Find NCS groups from input model: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.005 0.042 3191 Z= 0.314 Angle : 0.773 7.031 4362 Z= 0.494 Chirality : 0.044 0.197 505 Planarity : 0.006 0.038 523 Dihedral : 16.633 81.698 1074 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.60 % Allowed : 22.52 % Favored : 76.88 % 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: -0.35 (0.42), residues: 383 helix: -0.14 (0.28), residues: 319 sheet: None (None), residues: 0 loop : 0.16 (0.90), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 94 HIS 0.001 0.001 HIS A 135 PHE 0.024 0.002 PHE A 71 TYR 0.019 0.002 TYR A 383 ARG 0.001 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.309 Fit side-chains REVERT: A 270 LYS cc_start: 0.8005 (mtpt) cc_final: 0.6875 (mmmt) REVERT: A 315 TYR cc_start: 0.7492 (OUTLIER) cc_final: 0.6953 (t80) outliers start: 2 outliers final: 0 residues processed: 49 average time/residue: 0.1547 time to fit residues: 9.3732 Evaluate side-chains 48 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125073 restraints weight = 3548.019| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.78 r_work: 0.3277 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3191 Z= 0.226 Angle : 0.652 8.630 4362 Z= 0.348 Chirality : 0.044 0.196 505 Planarity : 0.004 0.032 523 Dihedral : 5.230 53.729 425 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.30 % Allowed : 20.12 % Favored : 76.58 % 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: 0.69 (0.41), residues: 383 helix: 0.73 (0.27), residues: 315 sheet: None (None), residues: 0 loop : -0.35 (0.81), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 94 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.016 0.002 TYR A 280 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8449 (t) cc_final: 0.8185 (p) REVERT: A 270 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7115 (tptt) REVERT: A 315 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7205 (t80) outliers start: 11 outliers final: 7 residues processed: 60 average time/residue: 0.1280 time to fit residues: 9.7505 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.4980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.0670 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121415 restraints weight = 3618.581| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.84 r_work: 0.3295 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3191 Z= 0.232 Angle : 0.617 7.235 4362 Z= 0.328 Chirality : 0.044 0.193 505 Planarity : 0.004 0.032 523 Dihedral : 5.183 54.876 425 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.60 % Allowed : 20.42 % Favored : 75.98 % 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: 1.11 (0.41), residues: 383 helix: 0.98 (0.27), residues: 319 sheet: None (None), residues: 0 loop : -0.08 (0.84), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.019 0.002 TYR A 280 ARG 0.002 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7748 (mt) cc_final: 0.7514 (mp) REVERT: A 181 SER cc_start: 0.8396 (t) cc_final: 0.8070 (p) REVERT: A 270 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7157 (tptp) REVERT: A 315 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7116 (t80) REVERT: A 455 MET cc_start: 0.6805 (tmm) cc_final: 0.6554 (tmm) outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.1024 time to fit residues: 8.3316 Evaluate side-chains 56 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.149715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123589 restraints weight = 3690.120| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.86 r_work: 0.3291 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3191 Z= 0.226 Angle : 0.605 6.769 4362 Z= 0.321 Chirality : 0.043 0.198 505 Planarity : 0.004 0.033 523 Dihedral : 5.163 55.881 425 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.71 % Allowed : 17.72 % Favored : 76.58 % 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: 1.33 (0.41), residues: 383 helix: 1.09 (0.27), residues: 324 sheet: None (None), residues: 0 loop : 0.20 (0.89), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.020 0.002 TYR A 280 ARG 0.001 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7782 (mt) cc_final: 0.7548 (mp) REVERT: A 181 SER cc_start: 0.8395 (t) cc_final: 0.8053 (p) REVERT: A 270 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7226 (tptp) REVERT: A 296 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8310 (mp) REVERT: A 315 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.7113 (t80) REVERT: A 322 ILE cc_start: 0.7623 (pt) cc_final: 0.7253 (mm) REVERT: A 427 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: A 455 MET cc_start: 0.6664 (tmm) cc_final: 0.6406 (tmm) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 0.1105 time to fit residues: 9.3711 Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.148445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122398 restraints weight = 3677.118| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.84 r_work: 0.3271 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3191 Z= 0.239 Angle : 0.604 6.213 4362 Z= 0.321 Chirality : 0.043 0.197 505 Planarity : 0.004 0.034 523 Dihedral : 5.171 56.605 425 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.80 % Allowed : 19.52 % Favored : 75.68 % 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: 1.40 (0.41), residues: 383 helix: 1.14 (0.27), residues: 324 sheet: None (None), residues: 0 loop : 0.21 (0.88), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.001 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.022 0.002 TYR A 280 ARG 0.001 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8421 (t) cc_final: 0.8071 (p) REVERT: A 270 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7249 (tptp) REVERT: A 296 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 315 TYR cc_start: 0.7630 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 322 ILE cc_start: 0.7662 (pt) cc_final: 0.7351 (mm) REVERT: A 427 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: A 455 MET cc_start: 0.6577 (tmm) cc_final: 0.6301 (tmm) outliers start: 16 outliers final: 12 residues processed: 63 average time/residue: 0.1077 time to fit residues: 8.8251 Evaluate side-chains 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125401 restraints weight = 3713.276| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.87 r_work: 0.3320 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3191 Z= 0.191 Angle : 0.585 6.368 4362 Z= 0.308 Chirality : 0.042 0.183 505 Planarity : 0.004 0.035 523 Dihedral : 5.093 56.495 425 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.11 % Allowed : 20.42 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.41), residues: 383 helix: 1.21 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.61 (0.93), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.020 0.001 PHE A 71 TYR 0.019 0.002 TYR A 280 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8397 (t) cc_final: 0.8059 (p) REVERT: A 270 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7208 (tptp) REVERT: A 296 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8375 (mp) REVERT: A 315 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6955 (t80) REVERT: A 322 ILE cc_start: 0.7691 (pt) cc_final: 0.7395 (mm) REVERT: A 427 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: A 455 MET cc_start: 0.6578 (tmm) cc_final: 0.6307 (tmm) outliers start: 17 outliers final: 10 residues processed: 61 average time/residue: 0.1186 time to fit residues: 9.4563 Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.151496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124484 restraints weight = 3545.679| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.85 r_work: 0.3259 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3191 Z= 0.210 Angle : 0.596 6.822 4362 Z= 0.313 Chirality : 0.042 0.185 505 Planarity : 0.004 0.034 523 Dihedral : 5.080 56.766 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.11 % Allowed : 20.12 % Favored : 74.77 % 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: 1.62 (0.42), residues: 383 helix: 1.24 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.61 (0.93), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.021 0.002 TYR A 280 ARG 0.000 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8358 (t) cc_final: 0.8023 (p) REVERT: A 270 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7188 (tptt) REVERT: A 296 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 315 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6875 (t80) REVERT: A 322 ILE cc_start: 0.7740 (pt) cc_final: 0.7438 (mm) REVERT: A 455 MET cc_start: 0.6469 (tmm) cc_final: 0.6220 (tmm) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 0.1254 time to fit residues: 9.7063 Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.2980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.151484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.125600 restraints weight = 3627.329| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.84 r_work: 0.3313 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3191 Z= 0.203 Angle : 0.616 8.355 4362 Z= 0.318 Chirality : 0.042 0.183 505 Planarity : 0.004 0.035 523 Dihedral : 5.116 57.275 425 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.80 % Allowed : 20.42 % Favored : 74.77 % 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: 1.68 (0.42), residues: 383 helix: 1.28 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.65 (0.94), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.001 0.001 HIS A 364 PHE 0.020 0.001 PHE A 71 TYR 0.028 0.002 TYR A 373 ARG 0.001 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8387 (t) cc_final: 0.8043 (p) REVERT: A 270 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7174 (tptt) REVERT: A 296 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8511 (mp) REVERT: A 315 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6827 (t80) REVERT: A 322 ILE cc_start: 0.7680 (pt) cc_final: 0.7393 (mm) REVERT: A 455 MET cc_start: 0.6501 (tmm) cc_final: 0.6275 (tmm) outliers start: 16 outliers final: 10 residues processed: 62 average time/residue: 0.1074 time to fit residues: 8.7895 Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.151171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125210 restraints weight = 3643.719| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.86 r_work: 0.3302 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3191 Z= 0.216 Angle : 0.623 8.157 4362 Z= 0.320 Chirality : 0.043 0.185 505 Planarity : 0.004 0.034 523 Dihedral : 5.121 57.347 425 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.20 % Allowed : 21.32 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.42), residues: 383 helix: 1.27 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.75 (0.97), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.023 0.002 TYR A 280 ARG 0.000 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8393 (t) cc_final: 0.8046 (p) REVERT: A 270 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7177 (tptt) REVERT: A 315 TYR cc_start: 0.7343 (OUTLIER) cc_final: 0.6821 (t80) REVERT: A 322 ILE cc_start: 0.7673 (pt) cc_final: 0.7385 (mm) REVERT: A 455 MET cc_start: 0.6483 (tmm) cc_final: 0.6261 (tmm) outliers start: 14 outliers final: 12 residues processed: 58 average time/residue: 0.1098 time to fit residues: 8.4103 Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.150872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124990 restraints weight = 3566.338| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.83 r_work: 0.3280 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3191 Z= 0.221 Angle : 0.629 8.272 4362 Z= 0.325 Chirality : 0.043 0.187 505 Planarity : 0.004 0.035 523 Dihedral : 5.160 57.415 425 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.20 % Allowed : 21.62 % Favored : 74.17 % 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: 1.70 (0.42), residues: 383 helix: 1.27 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.74 (0.97), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.024 0.002 TYR A 373 ARG 0.001 0.000 ARG A 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8419 (t) cc_final: 0.8095 (p) REVERT: A 270 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7129 (tptt) REVERT: A 296 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8480 (mp) REVERT: A 315 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6816 (t80) REVERT: A 322 ILE cc_start: 0.7717 (pt) cc_final: 0.7424 (mm) REVERT: A 455 MET cc_start: 0.6496 (tmm) cc_final: 0.6271 (tmm) outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.1039 time to fit residues: 8.0305 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 315 TYR Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 441 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.151019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125064 restraints weight = 3625.289| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.85 r_work: 0.3314 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3191 Z= 0.220 Angle : 0.633 8.308 4362 Z= 0.326 Chirality : 0.043 0.189 505 Planarity : 0.004 0.035 523 Dihedral : 5.160 57.099 425 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.20 % Allowed : 21.92 % Favored : 73.87 % 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: 1.63 (0.42), residues: 383 helix: 1.24 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.63 (0.96), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.021 0.001 PHE A 71 TYR 0.023 0.002 TYR A 280 ARG 0.001 0.000 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.23 seconds wall clock time: 34 minutes 50.58 seconds (2090.58 seconds total)