Starting phenix.real_space_refine on Wed Mar 5 16:37:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqa_62498/03_2025/9kqa_62498.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqa_62498/03_2025/9kqa_62498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kqa_62498/03_2025/9kqa_62498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqa_62498/03_2025/9kqa_62498.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqa_62498/03_2025/9kqa_62498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqa_62498/03_2025/9kqa_62498.cif" } resolution = 3.28 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= 0.075 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 23 5.16 5 C 1861 2.51 5 N 428 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 2783 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2760 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 23, 'TRANS': 353} Chain breaks: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.79, per 1000 atoms: 1.00 Number of scatterers: 2783 At special positions: 0 Unit cell: (69.9, 52.192, 63.376, 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 23 16.00 O 471 8.00 N 428 7.00 C 1861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 416.5 milliseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 678 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.328A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.795A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 4.161A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 171 " --> pdb=" O CYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.747A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.505A pdb=" N ARG A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.599A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.754A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.795A pdb=" N SER A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.541A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.689A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 4.144A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 431 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 436 through 448 Processing helix chain 'A' and resid 448 through 464 removed outlier: 4.814A pdb=" N THR A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.577A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 669 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: 0.81 Time building geometry restraints manager: 0.96 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: 831 1.34 - 1.46: 595 1.46 - 1.58: 1387 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 2852 Sorted by residual: bond pdb=" C12 EBZ A 601 " pdb=" N04 EBZ A 601 " ideal model delta sigma weight residual 1.452 1.545 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C05 EBZ A 601 " pdb=" N04 EBZ A 601 " ideal model delta sigma weight residual 1.460 1.544 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C11 EBZ A 601 " pdb=" N04 EBZ A 601 " ideal model delta sigma weight residual 1.465 1.548 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CA ILE A 265 " pdb=" C ILE A 265 " ideal model delta sigma weight residual 1.524 1.501 0.022 1.22e-02 6.72e+03 3.37e+00 bond pdb=" CA ILE A 456 " pdb=" C ILE A 456 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.22e-02 6.72e+03 2.91e+00 ... (remaining 2847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 3756 1.88 - 3.75: 110 3.75 - 5.63: 22 5.63 - 7.50: 4 7.50 - 9.38: 2 Bond angle restraints: 3894 Sorted by residual: angle pdb=" C ILE A 375 " pdb=" CA ILE A 375 " pdb=" CB ILE A 375 " ideal model delta sigma weight residual 113.70 107.75 5.95 9.50e-01 1.11e+00 3.92e+01 angle pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" C VAL A 332 " ideal model delta sigma weight residual 111.91 106.86 5.05 8.90e-01 1.26e+00 3.21e+01 angle pdb=" CA ILE A 375 " pdb=" C ILE A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 120.83 117.61 3.22 5.90e-01 2.87e+00 2.97e+01 angle pdb=" N LEU A 191 " pdb=" CA LEU A 191 " pdb=" C LEU A 191 " ideal model delta sigma weight residual 110.97 106.10 4.87 1.09e+00 8.42e-01 1.99e+01 angle pdb=" C ILE A 381 " pdb=" CA ILE A 381 " pdb=" CB ILE A 381 " ideal model delta sigma weight residual 112.02 107.22 4.80 1.31e+00 5.83e-01 1.34e+01 ... (remaining 3889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 1618 33.17 - 66.35: 47 66.35 - 99.52: 8 99.52 - 132.69: 0 132.69 - 165.87: 1 Dihedral angle restraints: 1674 sinusoidal: 610 harmonic: 1064 Sorted by residual: dihedral pdb=" C13 EBZ A 601 " pdb=" C18 EBZ A 601 " pdb=" C19 EBZ A 601 " pdb=" C23 EBZ A 601 " ideal model delta sinusoidal sigma weight residual 59.15 -134.98 -165.87 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C10 EBZ A 601 " pdb=" C11 EBZ A 601 " pdb=" C13 EBZ A 601 " pdb=" N04 EBZ A 601 " ideal model delta sinusoidal sigma weight residual 53.85 -39.25 93.10 1 3.00e+01 1.11e-03 1.12e+01 dihedral pdb=" C18 EBZ A 601 " pdb=" C11 EBZ A 601 " pdb=" C13 EBZ A 601 " pdb=" N04 EBZ A 601 " ideal model delta sinusoidal sigma weight residual -69.60 -162.56 92.96 1 3.00e+01 1.11e-03 1.12e+01 ... (remaining 1671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 287 0.032 - 0.065: 114 0.065 - 0.097: 51 0.097 - 0.129: 15 0.129 - 0.162: 4 Chirality restraints: 471 Sorted by residual: chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA VAL A 368 " pdb=" N VAL A 368 " pdb=" C VAL A 368 " pdb=" CB VAL A 368 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA VAL A 332 " pdb=" N VAL A 332 " pdb=" C VAL A 332 " pdb=" CB VAL A 332 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 468 not shown) Planarity restraints: 477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C05 EBZ A 601 " -0.364 2.00e-02 2.50e+03 2.39e-01 1.42e+03 pdb=" C06 EBZ A 601 " -0.102 2.00e-02 2.50e+03 pdb=" C07 EBZ A 601 " -0.100 2.00e-02 2.50e+03 pdb=" C09 EBZ A 601 " 0.381 2.00e-02 2.50e+03 pdb=" C14 EBZ A 601 " 0.200 2.00e-02 2.50e+03 pdb=" C15 EBZ A 601 " 0.287 2.00e-02 2.50e+03 pdb=" C16 EBZ A 601 " 0.066 2.00e-02 2.50e+03 pdb=" C17 EBZ A 601 " 0.100 2.00e-02 2.50e+03 pdb=" O01 EBZ A 601 " -0.122 2.00e-02 2.50e+03 pdb=" O02 EBZ A 601 " -0.346 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO A 161 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 449 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO A 450 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.021 5.00e-02 4.00e+02 ... (remaining 474 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 432 2.75 - 3.29: 2938 3.29 - 3.82: 4838 3.82 - 4.36: 5218 4.36 - 4.90: 9138 Nonbonded interactions: 22564 Sorted by model distance: nonbonded pdb=" O PHE A 176 " pdb=" OG SER A 179 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.266 3.040 nonbonded pdb=" ND2 ASN A 146 " pdb=" OD2 ASP A 426 " model vdw 2.406 3.120 nonbonded pdb=" OH TYR A 47 " pdb=" NZ LYS A 248 " model vdw 2.412 3.120 nonbonded pdb=" O ASP A 214 " pdb=" N ARG A 217 " model vdw 2.442 3.120 ... (remaining 22559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 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 0.093 2852 Z= 0.368 Angle : 0.791 9.378 3894 Z= 0.476 Chirality : 0.044 0.162 471 Planarity : 0.012 0.239 477 Dihedral : 17.319 165.867 996 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.35 % Allowed : 23.78 % Favored : 75.87 % 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: -2.72 (0.39), residues: 371 helix: -1.17 (0.27), residues: 297 sheet: None (None), residues: 0 loop : -3.86 (0.65), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.013 0.002 PHE A 238 TYR 0.011 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.317 Fit side-chains REVERT: A 146 ASN cc_start: 0.9039 (m-40) cc_final: 0.8578 (m-40) REVERT: A 268 PHE cc_start: 0.7354 (t80) cc_final: 0.6786 (t80) REVERT: A 280 GLN cc_start: 0.8512 (mt0) cc_final: 0.7988 (mt0) REVERT: A 289 LEU cc_start: 0.8433 (mt) cc_final: 0.8181 (mt) REVERT: A 328 TRP cc_start: 0.5209 (m100) cc_final: 0.3139 (p90) REVERT: A 329 GLN cc_start: 0.6983 (mt0) cc_final: 0.6713 (mm-40) REVERT: A 354 LYS cc_start: 0.8501 (tttt) cc_final: 0.8088 (mtpp) REVERT: A 463 PHE cc_start: 0.6722 (t80) cc_final: 0.6321 (t80) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.1242 time to fit residues: 13.5204 Evaluate side-chains 70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 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 34 ASN ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.146464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131655 restraints weight = 3701.427| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.74 r_work: 0.3561 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2852 Z= 0.266 Angle : 0.684 8.160 3894 Z= 0.335 Chirality : 0.044 0.172 471 Planarity : 0.006 0.057 477 Dihedral : 11.229 137.314 428 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.59 % Allowed : 30.42 % Favored : 63.99 % 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: -0.50 (0.45), residues: 371 helix: 0.52 (0.31), residues: 294 sheet: None (None), residues: 0 loop : -3.62 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.029 0.002 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.275 Fit side-chains REVERT: A 268 PHE cc_start: 0.7638 (t80) cc_final: 0.7081 (t80) REVERT: A 280 GLN cc_start: 0.8455 (mt0) cc_final: 0.8033 (mt0) REVERT: A 328 TRP cc_start: 0.5525 (m100) cc_final: 0.3092 (p90) REVERT: A 329 GLN cc_start: 0.7583 (mt0) cc_final: 0.6973 (mm110) REVERT: A 335 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6555 (tt) REVERT: A 354 LYS cc_start: 0.8634 (tttt) cc_final: 0.8222 (mtpp) REVERT: A 463 PHE cc_start: 0.7284 (t80) cc_final: 0.6851 (t80) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.0840 time to fit residues: 8.7203 Evaluate side-chains 75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 454 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128109 restraints weight = 3880.694| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 3.00 r_work: 0.3533 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2852 Z= 0.246 Angle : 0.637 6.868 3894 Z= 0.311 Chirality : 0.043 0.129 471 Planarity : 0.005 0.053 477 Dihedral : 11.215 143.652 428 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.90 % Allowed : 32.87 % Favored : 62.24 % 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: 0.51 (0.46), residues: 371 helix: 1.20 (0.31), residues: 296 sheet: None (None), residues: 0 loop : -3.21 (0.66), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.001 HIS A 353 PHE 0.026 0.002 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.003 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.281 Fit side-chains REVERT: A 155 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7402 (ttm110) REVERT: A 268 PHE cc_start: 0.7613 (t80) cc_final: 0.7182 (t80) REVERT: A 280 GLN cc_start: 0.8528 (mt0) cc_final: 0.8099 (mt0) REVERT: A 329 GLN cc_start: 0.7581 (mt0) cc_final: 0.7000 (mm110) REVERT: A 354 LYS cc_start: 0.8672 (tttt) cc_final: 0.8248 (mtpp) REVERT: A 365 MET cc_start: 0.7858 (mmm) cc_final: 0.7562 (mmm) REVERT: A 384 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.7020 (mp) REVERT: A 463 PHE cc_start: 0.7335 (t80) cc_final: 0.7044 (t80) outliers start: 14 outliers final: 6 residues processed: 72 average time/residue: 0.1050 time to fit residues: 9.7221 Evaluate side-chains 72 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 417 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.0070 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 18 optimal weight: 0.0770 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.145516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129802 restraints weight = 3698.804| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.93 r_work: 0.3483 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2852 Z= 0.178 Angle : 0.623 7.884 3894 Z= 0.297 Chirality : 0.041 0.138 471 Planarity : 0.005 0.050 477 Dihedral : 11.228 148.381 428 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.50 % Allowed : 34.27 % Favored : 62.24 % 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: 1.00 (0.47), residues: 371 helix: 1.47 (0.32), residues: 302 sheet: None (None), residues: 0 loop : -3.07 (0.69), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.021 0.002 PHE A 468 TYR 0.012 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.280 Fit side-chains REVERT: A 268 PHE cc_start: 0.7529 (t80) cc_final: 0.7042 (t80) REVERT: A 280 GLN cc_start: 0.8542 (mt0) cc_final: 0.8085 (mt0) REVERT: A 329 GLN cc_start: 0.7376 (mt0) cc_final: 0.6672 (mm110) REVERT: A 354 LYS cc_start: 0.8623 (tttt) cc_final: 0.8123 (mtpp) REVERT: A 415 VAL cc_start: 0.8364 (t) cc_final: 0.7909 (p) REVERT: A 463 PHE cc_start: 0.7027 (t80) cc_final: 0.6722 (t80) outliers start: 10 outliers final: 3 residues processed: 76 average time/residue: 0.0927 time to fit residues: 9.3349 Evaluate side-chains 67 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 30 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129334 restraints weight = 3702.863| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.86 r_work: 0.3480 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2852 Z= 0.190 Angle : 0.612 7.940 3894 Z= 0.292 Chirality : 0.041 0.139 471 Planarity : 0.005 0.048 477 Dihedral : 11.169 153.974 428 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.80 % Allowed : 36.71 % Favored : 60.49 % 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: 1.24 (0.47), residues: 371 helix: 1.62 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -2.97 (0.69), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 414 PHE 0.018 0.002 PHE A 468 TYR 0.011 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.279 Fit side-chains REVERT: A 268 PHE cc_start: 0.7467 (t80) cc_final: 0.6964 (t80) REVERT: A 280 GLN cc_start: 0.8469 (mt0) cc_final: 0.8022 (mt0) REVERT: A 329 GLN cc_start: 0.7435 (mt0) cc_final: 0.6666 (mm110) REVERT: A 354 LYS cc_start: 0.8650 (tttt) cc_final: 0.8161 (mtpp) REVERT: A 415 VAL cc_start: 0.8296 (t) cc_final: 0.7862 (p) REVERT: A 451 TRP cc_start: 0.7830 (OUTLIER) cc_final: 0.7556 (m-90) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.1042 time to fit residues: 9.5502 Evaluate side-chains 67 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 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 154 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125602 restraints weight = 3864.241| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.00 r_work: 0.3448 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2852 Z= 0.227 Angle : 0.630 8.206 3894 Z= 0.300 Chirality : 0.041 0.121 471 Planarity : 0.005 0.048 477 Dihedral : 11.134 153.906 428 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.50 % Allowed : 35.31 % Favored : 61.19 % 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: 1.30 (0.47), residues: 371 helix: 1.66 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -2.89 (0.67), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.002 PHE A 27 TYR 0.011 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.305 Fit side-chains REVERT: A 169 MET cc_start: 0.6730 (ttt) cc_final: 0.6497 (ttt) REVERT: A 268 PHE cc_start: 0.7475 (t80) cc_final: 0.6980 (t80) REVERT: A 280 GLN cc_start: 0.8434 (mt0) cc_final: 0.7968 (mt0) REVERT: A 329 GLN cc_start: 0.7423 (mt0) cc_final: 0.6682 (mm110) REVERT: A 354 LYS cc_start: 0.8707 (tttt) cc_final: 0.8218 (mtpp) REVERT: A 415 VAL cc_start: 0.8272 (t) cc_final: 0.7820 (p) REVERT: A 451 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.7547 (m-90) REVERT: A 471 ARG cc_start: 0.8000 (ttt90) cc_final: 0.6689 (ttp-170) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.1038 time to fit residues: 9.1026 Evaluate side-chains 72 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 455 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 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 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.142397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126373 restraints weight = 3885.633| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.02 r_work: 0.3407 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2852 Z= 0.209 Angle : 0.631 9.845 3894 Z= 0.298 Chirality : 0.041 0.120 471 Planarity : 0.005 0.047 477 Dihedral : 11.073 153.877 428 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.20 % Allowed : 35.66 % Favored : 60.14 % 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: 1.38 (0.47), residues: 371 helix: 1.69 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -2.73 (0.69), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.019 0.002 PHE A 468 TYR 0.010 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.289 Fit side-chains REVERT: A 169 MET cc_start: 0.6646 (ttt) cc_final: 0.6353 (ttt) REVERT: A 268 PHE cc_start: 0.7512 (t80) cc_final: 0.7030 (t80) REVERT: A 280 GLN cc_start: 0.8390 (mt0) cc_final: 0.7940 (mt0) REVERT: A 329 GLN cc_start: 0.7467 (mt0) cc_final: 0.6678 (mm110) REVERT: A 351 LEU cc_start: 0.7938 (mt) cc_final: 0.7342 (tt) REVERT: A 354 LYS cc_start: 0.8712 (tttt) cc_final: 0.8240 (mtpp) REVERT: A 402 MET cc_start: 0.8528 (mmt) cc_final: 0.8101 (mmt) REVERT: A 405 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6726 (tt) REVERT: A 415 VAL cc_start: 0.8308 (t) cc_final: 0.7865 (p) REVERT: A 451 TRP cc_start: 0.7861 (OUTLIER) cc_final: 0.7558 (m-90) REVERT: A 471 ARG cc_start: 0.8015 (ttt90) cc_final: 0.6733 (ttp-170) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.1029 time to fit residues: 9.7662 Evaluate side-chains 70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 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 154 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129625 restraints weight = 3848.119| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.02 r_work: 0.3432 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2852 Z= 0.252 Angle : 0.671 9.766 3894 Z= 0.311 Chirality : 0.042 0.121 471 Planarity : 0.005 0.047 477 Dihedral : 11.089 153.741 428 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.55 % Allowed : 36.01 % Favored : 59.44 % 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: 1.48 (0.46), residues: 371 helix: 1.77 (0.32), residues: 301 sheet: None (None), residues: 0 loop : -2.63 (0.70), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.018 0.002 PHE A 27 TYR 0.011 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.300 Fit side-chains REVERT: A 169 MET cc_start: 0.6691 (ttt) cc_final: 0.6391 (ttt) REVERT: A 268 PHE cc_start: 0.7524 (t80) cc_final: 0.7047 (t80) REVERT: A 280 GLN cc_start: 0.8383 (mt0) cc_final: 0.7927 (mt0) REVERT: A 329 GLN cc_start: 0.7536 (mt0) cc_final: 0.6650 (mm-40) REVERT: A 351 LEU cc_start: 0.7943 (mt) cc_final: 0.7329 (tt) REVERT: A 354 LYS cc_start: 0.8748 (tttt) cc_final: 0.8260 (mtpp) REVERT: A 415 VAL cc_start: 0.8300 (t) cc_final: 0.7849 (p) REVERT: A 451 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.7513 (m-90) REVERT: A 471 ARG cc_start: 0.8006 (ttt90) cc_final: 0.6804 (ttp-170) outliers start: 13 outliers final: 8 residues processed: 71 average time/residue: 0.1016 time to fit residues: 9.3462 Evaluate side-chains 69 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 455 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.145037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130169 restraints weight = 3846.096| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.99 r_work: 0.3440 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2852 Z= 0.237 Angle : 0.667 9.757 3894 Z= 0.311 Chirality : 0.042 0.122 471 Planarity : 0.005 0.047 477 Dihedral : 10.707 152.995 426 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.85 % Allowed : 37.76 % Favored : 58.39 % 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: 1.38 (0.46), residues: 371 helix: 1.68 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -2.68 (0.71), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.001 0.000 HIS A 353 PHE 0.019 0.002 PHE A 27 TYR 0.010 0.001 TYR A 422 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.280 Fit side-chains REVERT: A 169 MET cc_start: 0.6617 (ttt) cc_final: 0.6343 (ttt) REVERT: A 268 PHE cc_start: 0.7569 (t80) cc_final: 0.7071 (t80) REVERT: A 280 GLN cc_start: 0.8329 (mt0) cc_final: 0.7877 (mt0) REVERT: A 329 GLN cc_start: 0.7464 (mt0) cc_final: 0.6540 (mm-40) REVERT: A 354 LYS cc_start: 0.8759 (tttt) cc_final: 0.8287 (mtpp) REVERT: A 415 VAL cc_start: 0.8291 (t) cc_final: 0.7806 (p) REVERT: A 451 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7397 (m-90) REVERT: A 471 ARG cc_start: 0.7977 (ttt90) cc_final: 0.6790 (ttp-170) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.0995 time to fit residues: 8.7566 Evaluate side-chains 69 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 455 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 0.0020 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 305 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.148648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132968 restraints weight = 3812.377| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.09 r_work: 0.3450 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2852 Z= 0.205 Angle : 0.652 8.678 3894 Z= 0.306 Chirality : 0.041 0.119 471 Planarity : 0.005 0.047 477 Dihedral : 10.669 153.333 426 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.50 % Allowed : 37.41 % Favored : 59.09 % 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 (0.47), residues: 371 helix: 1.76 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -2.50 (0.72), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 318 HIS 0.001 0.000 HIS A 414 PHE 0.018 0.002 PHE A 27 TYR 0.011 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.299 Fit side-chains REVERT: A 169 MET cc_start: 0.6562 (ttt) cc_final: 0.6304 (ttt) REVERT: A 268 PHE cc_start: 0.7559 (t80) cc_final: 0.7026 (t80) REVERT: A 280 GLN cc_start: 0.8345 (mt0) cc_final: 0.7841 (mt0) REVERT: A 329 GLN cc_start: 0.7459 (mt0) cc_final: 0.6533 (mm-40) REVERT: A 354 LYS cc_start: 0.8754 (tttt) cc_final: 0.8286 (mtpp) REVERT: A 415 VAL cc_start: 0.8294 (t) cc_final: 0.7831 (p) REVERT: A 451 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.7428 (m-90) REVERT: A 471 ARG cc_start: 0.7995 (ttt90) cc_final: 0.6819 (ttp-170) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.1047 time to fit residues: 8.8867 Evaluate side-chains 69 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.1486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134201 restraints weight = 3642.687| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.94 r_work: 0.3505 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2852 Z= 0.172 Angle : 0.648 8.490 3894 Z= 0.303 Chirality : 0.040 0.117 471 Planarity : 0.005 0.046 477 Dihedral : 10.762 152.382 426 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.80 % Allowed : 38.81 % Favored : 58.39 % 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: 1.61 (0.46), residues: 371 helix: 1.83 (0.31), residues: 301 sheet: None (None), residues: 0 loop : -2.46 (0.68), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.001 0.000 HIS A 414 PHE 0.019 0.002 PHE A 27 TYR 0.010 0.001 TYR A 422 ARG 0.001 0.000 ARG A 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1514.80 seconds wall clock time: 26 minutes 44.47 seconds (1604.47 seconds total)