Starting phenix.real_space_refine on Wed Mar 5 17:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7r_39825/03_2025/8z7r_39825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7r_39825/03_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_39825/03_2025/8z7r_39825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7r_39825/03_2025/8z7r_39825.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7r_39825/03_2025/8z7r_39825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7r_39825/03_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-5624/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: 2.63, per 1000 atoms: 0.85 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: 0.83 Conformation dependent library (CDL) restraints added in 384.3 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: 0.26 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: 0.86 Time building geometry restraints manager: 0.98 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: 0.880 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- 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 : 0.305 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: 0.1623 time to fit residues: 9.7612 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 : 0.339 ------------------------------------------------------------------------------- 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: 0.4980 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.125225 restraints weight = 3541.944| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.83 r_work: 0.3282 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1190 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= 0.222 Angle : 0.646 8.591 4362 Z= 0.345 Chirality : 0.043 0.191 505 Planarity : 0.004 0.032 523 Dihedral : 5.207 53.535 425 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.70 % Allowed : 21.02 % Favored : 76.28 % 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: 0.65 (0.41), residues: 383 helix: 0.70 (0.27), residues: 316 sheet: None (None), residues: 0 loop : -0.39 (0.82), residues: 67 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 0.001 PHE A 71 TYR 0.017 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 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8480 (t) cc_final: 0.8196 (p) REVERT: A 270 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7134 (tptt) REVERT: A 315 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.7200 (t80) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 0.1210 time to fit residues: 8.9385 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122399 restraints weight = 3608.084| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.82 r_work: 0.3061 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1585 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= 0.260 Angle : 0.633 7.526 4362 Z= 0.336 Chirality : 0.044 0.194 505 Planarity : 0.004 0.032 523 Dihedral : 5.224 55.213 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.20 % Allowed : 20.42 % Favored : 75.38 % 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: 1.03 (0.42), residues: 383 helix: 0.93 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -0.10 (0.84), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.023 0.002 PHE A 71 TYR 0.020 0.002 TYR A 280 ARG 0.001 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 66 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8142 (t) cc_final: 0.7787 (p) REVERT: A 270 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.6897 (tptp) REVERT: A 315 TYR cc_start: 0.7458 (OUTLIER) cc_final: 0.6880 (t80) REVERT: A 382 SER cc_start: 0.8448 (t) cc_final: 0.8231 (m) REVERT: A 455 MET cc_start: 0.6580 (tmm) cc_final: 0.6329 (tmm) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.1004 time to fit residues: 8.3802 Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.149656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123621 restraints weight = 3689.100| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.85 r_work: 0.3295 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3191 Z= 0.224 Angle : 0.603 6.741 4362 Z= 0.321 Chirality : 0.043 0.199 505 Planarity : 0.004 0.033 523 Dihedral : 5.178 55.880 425 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 : 5.11 % Allowed : 18.92 % 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: 1.29 (0.41), residues: 383 helix: 1.11 (0.27), residues: 319 sheet: None (None), residues: 0 loop : -0.01 (0.84), residues: 64 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 0.021 0.002 PHE A 71 TYR 0.019 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 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.7785 (mt) cc_final: 0.7563 (mp) REVERT: A 181 SER cc_start: 0.8441 (t) cc_final: 0.8113 (p) REVERT: A 270 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7267 (tptp) REVERT: A 296 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8380 (mp) REVERT: A 315 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7151 (t80) REVERT: A 322 ILE cc_start: 0.7677 (pt) cc_final: 0.7236 (mm) REVERT: A 427 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 455 MET cc_start: 0.6720 (tmm) cc_final: 0.6464 (tmm) outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 0.1043 time to fit residues: 8.8900 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 : 0.291 ------------------------------------------------------------------------------- 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 130 VAL 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 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: 3.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3703 r_free = 0.3703 target = 0.148392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122294 restraints weight = 3675.520| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.85 r_work: 0.3277 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3191 Z= 0.242 Angle : 0.607 6.360 4362 Z= 0.323 Chirality : 0.043 0.200 505 Planarity : 0.004 0.034 523 Dihedral : 5.193 56.829 425 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.71 % Allowed : 18.02 % Favored : 76.28 % 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: 1.37 (0.41), residues: 383 helix: 1.10 (0.27), residues: 324 sheet: None (None), residues: 0 loop : 0.29 (0.89), residues: 59 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 0.022 0.002 PHE A 71 TYR 0.022 0.002 TYR A 280 ARG 0.001 0.000 ARG A 144 *********************** 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 68 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8443 (t) cc_final: 0.8111 (p) REVERT: A 270 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7244 (tptp) REVERT: A 296 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 315 TYR cc_start: 0.7690 (OUTLIER) cc_final: 0.7159 (t80) REVERT: A 322 ILE cc_start: 0.7639 (pt) cc_final: 0.7286 (mm) REVERT: A 427 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: A 455 MET cc_start: 0.6690 (tmm) cc_final: 0.6418 (tmm) outliers start: 19 outliers final: 13 residues processed: 64 average time/residue: 0.1127 time to fit residues: 9.4128 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 : 0.320 ------------------------------------------------------------------------------- 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 343 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.150362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.124220 restraints weight = 3719.970| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.88 r_work: 0.3298 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2149 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= 0.209 Angle : 0.593 6.417 4362 Z= 0.313 Chirality : 0.043 0.190 505 Planarity : 0.004 0.035 523 Dihedral : 5.142 57.061 425 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.80 % Allowed : 20.12 % Favored : 75.08 % 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: 1.53 (0.42), residues: 383 helix: 1.16 (0.27), residues: 326 sheet: None (None), residues: 0 loop : 0.67 (0.94), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 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 0.000 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 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8439 (t) cc_final: 0.8107 (p) REVERT: A 270 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7244 (tptp) REVERT: A 296 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 315 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6959 (t80) REVERT: A 322 ILE cc_start: 0.7735 (pt) cc_final: 0.7375 (mm) REVERT: A 455 MET cc_start: 0.6593 (tmm) cc_final: 0.6328 (tmm) outliers start: 16 outliers final: 13 residues processed: 61 average time/residue: 0.1245 time to fit residues: 9.9530 Evaluate side-chains 59 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 385 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.149440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123291 restraints weight = 3627.143| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.85 r_work: 0.3288 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3191 Z= 0.227 Angle : 0.603 6.838 4362 Z= 0.318 Chirality : 0.043 0.193 505 Planarity : 0.004 0.035 523 Dihedral : 5.163 57.739 425 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.41 % Allowed : 19.22 % Favored : 75.38 % 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: 1.50 (0.42), residues: 383 helix: 1.14 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.70 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.021 0.002 PHE A 71 TYR 0.026 0.002 TYR A 373 ARG 0.000 0.000 ARG A 138 *********************** 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: 18 poor density : 46 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8453 (t) cc_final: 0.8117 (p) REVERT: A 270 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7272 (tptp) REVERT: A 296 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 315 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.6977 (t80) REVERT: A 322 ILE cc_start: 0.7728 (pt) cc_final: 0.7408 (mm) REVERT: A 455 MET cc_start: 0.6584 (tmm) cc_final: 0.6341 (tmm) outliers start: 18 outliers final: 13 residues processed: 60 average time/residue: 0.1118 time to fit residues: 8.7373 Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 343 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.150671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.124494 restraints weight = 3632.530| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.86 r_work: 0.3272 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2251 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 : 0.600 7.233 4362 Z= 0.316 Chirality : 0.043 0.188 505 Planarity : 0.004 0.035 523 Dihedral : 5.161 57.629 425 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.11 % Allowed : 21.62 % Favored : 73.27 % 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: 1.53 (0.42), residues: 383 helix: 1.17 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.59 (0.94), 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 0.020 0.001 PHE A 71 TYR 0.022 0.002 TYR A 280 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 62 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8403 (t) cc_final: 0.8067 (p) REVERT: A 270 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7175 (tptt) REVERT: A 296 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 315 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6838 (t80) REVERT: A 322 ILE cc_start: 0.7659 (pt) cc_final: 0.7360 (mm) REVERT: A 455 MET cc_start: 0.6479 (tmm) cc_final: 0.6233 (tmm) outliers start: 17 outliers final: 11 residues processed: 58 average time/residue: 0.1195 time to fit residues: 8.9873 Evaluate side-chains 58 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 385 LEU 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: 0.1980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125394 restraints weight = 3643.673| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.85 r_work: 0.3287 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3191 Z= 0.199 Angle : 0.614 8.187 4362 Z= 0.318 Chirality : 0.043 0.188 505 Planarity : 0.004 0.036 523 Dihedral : 5.115 57.202 425 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 1.62 (0.42), residues: 383 helix: 1.22 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.68 (0.95), 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 0.020 0.001 PHE A 71 TYR 0.022 0.002 TYR A 280 ARG 0.001 0.000 ARG A 29 *********************** 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 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 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: A 181 SER cc_start: 0.8399 (t) cc_final: 0.8075 (p) REVERT: A 270 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7170 (tptt) REVERT: A 296 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8462 (mp) REVERT: A 315 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6855 (t80) REVERT: A 322 ILE cc_start: 0.7672 (pt) cc_final: 0.7365 (mm) REVERT: A 455 MET cc_start: 0.6463 (tmm) cc_final: 0.6243 (tmm) outliers start: 14 outliers final: 11 residues processed: 57 average time/residue: 0.1089 time to fit residues: 8.2700 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 : 0.311 ------------------------------------------------------------------------------- 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 120 GLU 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 385 LEU 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: 3.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.149037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122523 restraints weight = 3499.636| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.81 r_work: 0.3235 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3191 Z= 0.251 Angle : 0.635 8.217 4362 Z= 0.330 Chirality : 0.044 0.200 505 Planarity : 0.004 0.034 523 Dihedral : 5.213 58.060 425 Min Nonbonded Distance : 2.588 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: 1.55 (0.42), residues: 383 helix: 1.18 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.62 (0.95), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 284 HIS 0.002 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.026 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 67 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 181 SER cc_start: 0.8424 (t) cc_final: 0.8093 (p) REVERT: A 270 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7135 (tptt) REVERT: A 296 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8456 (mp) REVERT: A 315 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6832 (t80) REVERT: A 322 ILE cc_start: 0.7758 (pt) cc_final: 0.7408 (mm) REVERT: A 455 MET cc_start: 0.6414 (tmm) cc_final: 0.6191 (tmm) outliers start: 17 outliers final: 12 residues processed: 64 average time/residue: 0.1100 time to fit residues: 9.4075 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 : 0.338 ------------------------------------------------------------------------------- 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 385 LEU Chi-restraints excluded: chain A residue 401 GLU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 416 VAL 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: 1.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3711 r_free = 0.3711 target = 0.150220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122844 restraints weight = 3565.285| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.89 r_work: 0.3241 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3191 Z= 0.238 Angle : 0.627 8.331 4362 Z= 0.326 Chirality : 0.044 0.194 505 Planarity : 0.004 0.035 523 Dihedral : 5.212 58.152 425 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.50 % Allowed : 21.62 % 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: 1.51 (0.41), residues: 383 helix: 1.16 (0.27), residues: 327 sheet: None (None), residues: 0 loop : 0.58 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 284 HIS 0.003 0.001 HIS A 364 PHE 0.022 0.002 PHE A 71 TYR 0.024 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: 1926.16 seconds wall clock time: 33 minutes 50.80 seconds (2030.80 seconds total)