Starting phenix.real_space_refine on Mon Feb 10 21:41:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kqa_62498/02_2025/9kqa_62498.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kqa_62498/02_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_62498/02_2025/9kqa_62498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kqa_62498/02_2025/9kqa_62498.map" model { file = "/net/cci-nas-00/data/ceres_data/9kqa_62498/02_2025/9kqa_62498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kqa_62498/02_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-5592/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: 0.83 Conformation dependent library (CDL) restraints added in 370.4 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: 0.31 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: 0.80 Time building geometry restraints manager: 0.92 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.560 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- 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 : 0.288 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: 0.1214 time to fit residues: 13.3003 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 : 0.319 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.131649 restraints weight = 3701.427| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.74 r_work: 0.3563 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.279 Fit side-chains REVERT: A 268 PHE cc_start: 0.7642 (t80) cc_final: 0.7087 (t80) REVERT: A 280 GLN cc_start: 0.8455 (mt0) cc_final: 0.8033 (mt0) REVERT: A 328 TRP cc_start: 0.5529 (m100) cc_final: 0.3102 (p90) REVERT: A 329 GLN cc_start: 0.7589 (mt0) cc_final: 0.6981 (mm110) REVERT: A 335 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6552 (tt) REVERT: A 354 LYS cc_start: 0.8637 (tttt) cc_final: 0.8226 (mtpp) REVERT: A 463 PHE cc_start: 0.7294 (t80) cc_final: 0.6866 (t80) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.0913 time to fit residues: 9.4793 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 : 0.277 ------------------------------------------------------------------------------- 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: 0.6980 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.144178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128607 restraints weight = 3883.806| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.92 r_work: 0.3541 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2278 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= 0.243 Angle : 0.636 6.885 3894 Z= 0.310 Chirality : 0.043 0.126 471 Planarity : 0.005 0.053 477 Dihedral : 11.204 142.764 428 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.55 % Allowed : 33.92 % Favored : 61.54 % 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: 0.38 (0.46), residues: 371 helix: 1.13 (0.31), residues: 295 sheet: None (None), residues: 0 loop : -3.33 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.001 0.001 HIS A 353 PHE 0.025 0.002 PHE A 348 TYR 0.012 0.001 TYR A 422 ARG 0.004 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: 13 poor density : 64 time to evaluate : 0.373 Fit side-chains REVERT: A 28 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7652 (tp) REVERT: A 155 ARG cc_start: 0.7740 (mtt180) cc_final: 0.7415 (ttm110) REVERT: A 268 PHE cc_start: 0.7661 (t80) cc_final: 0.7218 (t80) REVERT: A 280 GLN cc_start: 0.8544 (mt0) cc_final: 0.8124 (mt0) REVERT: A 329 GLN cc_start: 0.7534 (mt0) cc_final: 0.6949 (mm110) REVERT: A 354 LYS cc_start: 0.8651 (tttt) cc_final: 0.8230 (mtpp) REVERT: A 365 MET cc_start: 0.7859 (mmm) cc_final: 0.7553 (mmm) REVERT: A 463 PHE cc_start: 0.7365 (t80) cc_final: 0.7071 (t80) outliers start: 13 outliers final: 6 residues processed: 73 average time/residue: 0.1042 time to fit residues: 9.8500 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 447 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 0.0470 chunk 5 optimal weight: 0.0000 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.2680 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.147243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131560 restraints weight = 3670.366| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.93 r_work: 0.3493 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2682 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= 0.172 Angle : 0.616 7.860 3894 Z= 0.295 Chirality : 0.041 0.118 471 Planarity : 0.005 0.050 477 Dihedral : 11.212 148.283 428 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.50 % Allowed : 33.57 % Favored : 62.94 % 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: 1.01 (0.47), residues: 371 helix: 1.46 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -3.03 (0.70), 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 414 PHE 0.022 0.002 PHE A 468 TYR 0.012 0.001 TYR A 422 ARG 0.003 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 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.305 Fit side-chains REVERT: A 155 ARG cc_start: 0.7376 (mtt180) cc_final: 0.7082 (ttm110) REVERT: A 268 PHE cc_start: 0.7535 (t80) cc_final: 0.7054 (t80) REVERT: A 280 GLN cc_start: 0.8553 (mt0) cc_final: 0.8092 (mt0) REVERT: A 329 GLN cc_start: 0.7433 (mt0) cc_final: 0.6719 (mm110) REVERT: A 354 LYS cc_start: 0.8613 (tttt) cc_final: 0.8121 (mtpp) REVERT: A 415 VAL cc_start: 0.8376 (t) cc_final: 0.7931 (p) REVERT: A 463 PHE cc_start: 0.7028 (t80) cc_final: 0.6734 (t80) outliers start: 10 outliers final: 4 residues processed: 77 average time/residue: 0.1077 time to fit residues: 10.6354 Evaluate side-chains 68 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 405 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 6 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 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128655 restraints weight = 3700.645| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.87 r_work: 0.3470 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2852 Z= 0.213 Angle : 0.623 7.828 3894 Z= 0.299 Chirality : 0.042 0.142 471 Planarity : 0.005 0.050 477 Dihedral : 11.191 153.570 428 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 35.31 % Favored : 61.54 % 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: 1.16 (0.47), residues: 371 helix: 1.59 (0.32), residues: 302 sheet: None (None), residues: 0 loop : -3.04 (0.68), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.000 0.000 HIS A 353 PHE 0.018 0.002 PHE A 348 TYR 0.011 0.001 TYR A 422 ARG 0.003 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 71 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.288 Fit side-chains REVERT: A 268 PHE cc_start: 0.7528 (t80) cc_final: 0.7029 (t80) REVERT: A 280 GLN cc_start: 0.8484 (mt0) cc_final: 0.8052 (mt0) REVERT: A 329 GLN cc_start: 0.7451 (mt0) cc_final: 0.6747 (mm110) REVERT: A 354 LYS cc_start: 0.8653 (tttt) cc_final: 0.8167 (mtpp) REVERT: A 415 VAL cc_start: 0.8280 (t) cc_final: 0.7837 (p) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.1039 time to fit residues: 9.0507 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 : 0.289 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.0050 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.147236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131337 restraints weight = 3718.000| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.96 r_work: 0.3480 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3072 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= 0.183 Angle : 0.614 8.413 3894 Z= 0.290 Chirality : 0.041 0.140 471 Planarity : 0.005 0.047 477 Dihedral : 11.084 153.660 428 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.80 % Allowed : 36.01 % 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: 1.42 (0.47), residues: 371 helix: 1.74 (0.32), residues: 303 sheet: None (None), residues: 0 loop : -2.85 (0.67), 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 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 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 72 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.284 Fit side-chains REVERT: A 268 PHE cc_start: 0.7479 (t80) cc_final: 0.6982 (t80) REVERT: A 280 GLN cc_start: 0.8475 (mt0) cc_final: 0.8029 (mt0) REVERT: A 329 GLN cc_start: 0.7440 (mt0) cc_final: 0.6697 (mm110) REVERT: A 354 LYS cc_start: 0.8689 (tttt) cc_final: 0.8216 (mtpp) REVERT: A 415 VAL cc_start: 0.8276 (t) cc_final: 0.7839 (p) REVERT: A 451 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.7563 (m-90) REVERT: A 471 ARG cc_start: 0.7982 (ttt90) cc_final: 0.6672 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.0989 time to fit residues: 8.8310 Evaluate side-chains 69 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 15 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.0670 chunk 8 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.144748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.128822 restraints weight = 3861.464| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.08 r_work: 0.3458 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2852 Z= 0.189 Angle : 0.627 9.812 3894 Z= 0.295 Chirality : 0.041 0.118 471 Planarity : 0.005 0.047 477 Dihedral : 11.051 153.331 428 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.90 % Allowed : 34.27 % Favored : 60.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.47), residues: 371 helix: 1.71 (0.32), residues: 304 sheet: None (None), residues: 0 loop : -2.68 (0.68), residues: 67 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 0.017 0.002 PHE A 27 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: 14 poor density : 65 time to evaluate : 0.308 Fit side-chains REVERT: A 169 MET cc_start: 0.6526 (ttt) cc_final: 0.6315 (ttt) REVERT: A 268 PHE cc_start: 0.7480 (t80) cc_final: 0.6989 (t80) REVERT: A 280 GLN cc_start: 0.8406 (mt0) cc_final: 0.7947 (mt0) REVERT: A 329 GLN cc_start: 0.7441 (mt0) cc_final: 0.6645 (mm110) REVERT: A 351 LEU cc_start: 0.7932 (mt) cc_final: 0.7310 (tt) REVERT: A 354 LYS cc_start: 0.8705 (tttt) cc_final: 0.8213 (mtpp) REVERT: A 415 VAL cc_start: 0.8270 (t) cc_final: 0.7827 (p) REVERT: A 451 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.7554 (m-90) REVERT: A 471 ARG cc_start: 0.7986 (ttt90) cc_final: 0.6692 (ttp-170) outliers start: 14 outliers final: 7 residues processed: 72 average time/residue: 0.1127 time to fit residues: 10.4808 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 405 ILE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 455 ILE 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: 0.9980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.0170 chunk 8 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.145898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130154 restraints weight = 3782.039| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.01 r_work: 0.3487 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2852 Z= 0.208 Angle : 0.660 9.530 3894 Z= 0.303 Chirality : 0.041 0.118 471 Planarity : 0.005 0.046 477 Dihedral : 11.001 152.253 428 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.85 % Allowed : 36.71 % 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: 1.49 (0.46), residues: 371 helix: 1.73 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -2.55 (0.71), residues: 67 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 27 TYR 0.011 0.001 TYR A 341 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 73 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.310 Fit side-chains REVERT: A 169 MET cc_start: 0.6529 (ttt) cc_final: 0.6251 (ttt) REVERT: A 268 PHE cc_start: 0.7486 (t80) cc_final: 0.6993 (t80) REVERT: A 280 GLN cc_start: 0.8403 (mt0) cc_final: 0.7956 (mt0) REVERT: A 329 GLN cc_start: 0.7443 (mt0) cc_final: 0.6629 (mm110) REVERT: A 351 LEU cc_start: 0.7906 (mt) cc_final: 0.7284 (tt) REVERT: A 354 LYS cc_start: 0.8704 (tttt) cc_final: 0.8224 (mtpp) REVERT: A 402 MET cc_start: 0.8388 (mmt) cc_final: 0.7865 (mmt) REVERT: A 415 VAL cc_start: 0.8283 (t) cc_final: 0.7851 (p) REVERT: A 451 TRP cc_start: 0.7812 (OUTLIER) cc_final: 0.7565 (m-90) REVERT: A 471 ARG cc_start: 0.7998 (ttt90) cc_final: 0.6715 (ttp-170) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.1015 time to fit residues: 9.0988 Evaluate side-chains 70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 405 ILE 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: 0.6980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.144371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128640 restraints weight = 3735.903| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.94 r_work: 0.3456 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3467 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= 0.251 Angle : 0.680 9.599 3894 Z= 0.316 Chirality : 0.042 0.121 471 Planarity : 0.005 0.047 477 Dihedral : 11.140 151.286 428 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.20 % Allowed : 36.71 % 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: 1.45 (0.46), residues: 371 helix: 1.69 (0.31), residues: 304 sheet: None (None), residues: 0 loop : -2.52 (0.70), residues: 67 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 0.020 0.002 PHE A 27 TYR 0.011 0.001 TYR A 422 ARG 0.003 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 76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.315 Fit side-chains REVERT: A 169 MET cc_start: 0.6549 (ttt) cc_final: 0.6318 (ttt) REVERT: A 268 PHE cc_start: 0.7507 (t80) cc_final: 0.7031 (t80) REVERT: A 280 GLN cc_start: 0.8323 (mt0) cc_final: 0.7856 (mt0) REVERT: A 329 GLN cc_start: 0.7509 (mt0) cc_final: 0.6598 (mm-40) REVERT: A 354 LYS cc_start: 0.8766 (tttt) cc_final: 0.8283 (mtpp) REVERT: A 415 VAL cc_start: 0.8271 (t) cc_final: 0.7791 (p) REVERT: A 451 TRP cc_start: 0.7820 (OUTLIER) cc_final: 0.7434 (m-90) REVERT: A 471 ARG cc_start: 0.7959 (ttt90) cc_final: 0.6783 (ttp-170) outliers start: 12 outliers final: 7 residues processed: 72 average time/residue: 0.1012 time to fit residues: 9.5119 Evaluate side-chains 68 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126601 restraints weight = 3822.562| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.98 r_work: 0.3464 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.3587 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= 0.231 Angle : 0.694 9.081 3894 Z= 0.320 Chirality : 0.044 0.228 471 Planarity : 0.005 0.047 477 Dihedral : 10.732 151.399 426 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.15 % Allowed : 38.11 % Favored : 58.74 % 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: 1.72 (0.31), residues: 303 sheet: None (None), residues: 0 loop : -2.52 (0.70), 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 0.020 0.002 PHE A 27 TYR 0.010 0.001 TYR A 422 ARG 0.001 0.000 ARG A 357 ********************** 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: 9 poor density : 62 time to evaluate : 0.279 Fit side-chains REVERT: A 36 LEU cc_start: 0.7982 (tt) cc_final: 0.7713 (tt) REVERT: A 169 MET cc_start: 0.6484 (ttt) cc_final: 0.6249 (ttt) REVERT: A 268 PHE cc_start: 0.7580 (t80) cc_final: 0.7084 (t80) REVERT: A 280 GLN cc_start: 0.8344 (mt0) cc_final: 0.7863 (mt0) REVERT: A 329 GLN cc_start: 0.7499 (mt0) cc_final: 0.6572 (mm-40) REVERT: A 354 LYS cc_start: 0.8748 (tttt) cc_final: 0.8279 (mtpp) REVERT: A 415 VAL cc_start: 0.8301 (t) cc_final: 0.7824 (p) REVERT: A 451 TRP cc_start: 0.7822 (OUTLIER) cc_final: 0.7459 (m-90) REVERT: A 471 ARG cc_start: 0.7966 (ttt90) cc_final: 0.6785 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 66 average time/residue: 0.1111 time to fit residues: 9.4933 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 : 0.293 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 0.5980 chunk 18 optimal weight: 0.0070 chunk 23 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.145251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.129526 restraints weight = 3692.028| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.96 r_work: 0.3507 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2852 Z= 0.201 Angle : 0.682 9.768 3894 Z= 0.314 Chirality : 0.043 0.217 471 Planarity : 0.005 0.046 477 Dihedral : 10.686 150.186 426 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 38.11 % Favored : 58.74 % 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 (0.46), residues: 371 helix: 1.80 (0.31), residues: 300 sheet: None (None), residues: 0 loop : -2.42 (0.68), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 0.002 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.03 seconds wall clock time: 26 minutes 57.92 seconds (1617.92 seconds total)