Starting phenix.real_space_refine on Tue Feb 11 02:48:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sdy_40354/02_2025/8sdy_40354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sdy_40354/02_2025/8sdy_40354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sdy_40354/02_2025/8sdy_40354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sdy_40354/02_2025/8sdy_40354.map" model { file = "/net/cci-nas-00/data/ceres_data/8sdy_40354/02_2025/8sdy_40354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sdy_40354/02_2025/8sdy_40354.cif" } resolution = 2.79 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= 0.002 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 30 5.16 5 C 2528 2.51 5 N 653 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3894 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 494, 3831 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 25, 'TRANS': 468} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 494, 3831 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 25, 'TRANS': 468} Chain breaks: 3 bond proxies already assigned to first conformer: 3912 Chain: "A" Number of atoms: 54 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Conformer: "B" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Conformer: "C" Number of residues, atoms: 13, 26 Unusual residues: {'ZWD': 1} Classifications: {'undetermined': 1, 'water': 12} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 382 " occ=0.52 ... (16 atoms not shown) pdb=" NZ BLYS A 382 " occ=0.48 residue: pdb=" C01AZWD A 601 " occ=0.85 ... (40 atoms not shown) pdb=" O13CZWD A 601 " occ=0.14 Time building chain proxies: 4.50, per 1000 atoms: 1.16 Number of scatterers: 3894 At special positions: 0 Unit cell: (85.49, 68.89, 94.62, 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 30 16.00 O 683 8.00 N 653 7.00 C 2528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.02 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: 1.10 Conformation dependent library (CDL) restraints added in 912.7 milliseconds 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 2 sheets defined 82.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.786A pdb=" N GLY A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 36 removed outlier: 4.003A pdb=" N ALA A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 131 through 160 removed outlier: 4.204A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 181 Processing helix chain 'A' and resid 184 through 213 removed outlier: 3.844A pdb=" N MET A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 removed outlier: 3.563A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.966A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 296 Processing helix chain 'A' and resid 297 through 304 removed outlier: 3.786A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.623A pdb=" N ARG A 331 " --> pdb=" O MET A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.861A pdb=" N LEU A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 4.128A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 377 through 392 Processing helix chain 'A' and resid 393 through 415 removed outlier: 3.500A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 449 removed outlier: 3.684A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 477 Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix removed outlier: 3.813A pdb=" N ALA A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 274 hydrogen bonds defined for protein. 811 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: 1.19 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 586 1.31 - 1.44: 1105 1.44 - 1.56: 2236 1.56 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 3974 Sorted by residual: bond pdb=" C07AZWD A 601 " pdb=" N09AZWD A 601 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C07BZWD A 601 " pdb=" N09BZWD A 601 " ideal model delta sigma weight residual 1.350 1.451 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C07CZWD A 601 " pdb=" N09CZWD A 601 " ideal model delta sigma weight residual 1.350 1.450 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C03AZWD A 601 " pdb=" N14AZWD A 601 " ideal model delta sigma weight residual 1.379 1.451 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C03BZWD A 601 " pdb=" N14BZWD A 601 " ideal model delta sigma weight residual 1.379 1.450 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 3969 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 5217 1.46 - 2.91: 121 2.91 - 4.37: 50 4.37 - 5.82: 10 5.82 - 7.28: 4 Bond angle restraints: 5402 Sorted by residual: angle pdb=" CA GLN A 289 " pdb=" CB GLN A 289 " pdb=" CG GLN A 289 " ideal model delta sigma weight residual 114.10 120.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA TYR A 264 " pdb=" CB TYR A 264 " pdb=" CG TYR A 264 " ideal model delta sigma weight residual 113.90 119.00 -5.10 1.80e+00 3.09e-01 8.02e+00 angle pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " pdb=" NE ARG A 290 " ideal model delta sigma weight residual 112.00 117.66 -5.66 2.20e+00 2.07e-01 6.62e+00 angle pdb=" O12AZWD A 601 " pdb=" C11AZWD A 601 " pdb=" O13AZWD A 601 " ideal model delta sigma weight residual 127.09 119.81 7.28 3.00e+00 1.11e-01 5.89e+00 angle pdb=" O12BZWD A 601 " pdb=" C11BZWD A 601 " pdb=" O13BZWD A 601 " ideal model delta sigma weight residual 127.09 120.13 6.96 3.00e+00 1.11e-01 5.39e+00 ... (remaining 5397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 2001 17.59 - 35.18: 255 35.18 - 52.77: 80 52.77 - 70.36: 9 70.36 - 87.95: 4 Dihedral angle restraints: 2349 sinusoidal: 920 harmonic: 1429 Sorted by residual: dihedral pdb=" CG ARG A 290 " pdb=" CD ARG A 290 " pdb=" NE ARG A 290 " pdb=" CZ ARG A 290 " ideal model delta sinusoidal sigma weight residual 90.00 41.14 48.86 2 1.50e+01 4.44e-03 1.21e+01 dihedral pdb=" CG ARG A 280 " pdb=" CD ARG A 280 " pdb=" NE ARG A 280 " pdb=" CZ ARG A 280 " ideal model delta sinusoidal sigma weight residual 180.00 136.55 43.45 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG A 80 " pdb=" CD ARG A 80 " pdb=" NE ARG A 80 " pdb=" CZ ARG A 80 " ideal model delta sinusoidal sigma weight residual 90.00 133.22 -43.22 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 2346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 390 0.027 - 0.055: 149 0.055 - 0.082: 58 0.082 - 0.110: 20 0.110 - 0.137: 8 Chirality restraints: 625 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 269 " pdb=" N ILE A 269 " pdb=" C ILE A 269 " pdb=" CB ILE A 269 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA ILE A 415 " pdb=" N ILE A 415 " pdb=" C ILE A 415 " pdb=" CB ILE A 415 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 622 not shown) Planarity restraints: 673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 290 " -0.202 9.50e-02 1.11e+02 9.10e-02 5.88e+00 pdb=" NE ARG A 290 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 290 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 290 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 290 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 395 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO A 396 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 332 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A 333 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " -0.015 5.00e-02 4.00e+02 ... (remaining 670 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 40 2.59 - 3.17: 3437 3.17 - 3.75: 6386 3.75 - 4.32: 8807 4.32 - 4.90: 14720 Nonbonded interactions: 33390 Sorted by model distance: nonbonded pdb=" OH TYR A 444 " pdb=" O PRO A 505 " model vdw 2.018 3.040 nonbonded pdb=" OG SER A 33 " pdb=" O HOH A 701 " model vdw 2.066 3.040 nonbonded pdb=" OD1 ASN A 168 " pdb=" OG SER A 201 " model vdw 2.201 3.040 nonbonded pdb=" NH2 ARG A 80 " pdb=" OE2 GLU A 103 " model vdw 2.222 3.120 nonbonded pdb=" OG1 THR A 172 " pdb=" OG SER A 198 " model vdw 2.226 3.040 ... (remaining 33385 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=0.01 max=1.00 mean=0.99 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: 0.160 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 0.103 3974 Z= 0.343 Angle : 0.660 7.279 5402 Z= 0.319 Chirality : 0.037 0.137 625 Planarity : 0.005 0.091 673 Dihedral : 16.845 87.947 1425 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.72 % Allowed : 23.50 % Favored : 75.78 % 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: 2.03 (0.38), residues: 489 helix: 1.62 (0.27), residues: 374 sheet: -2.13 (1.49), residues: 10 loop : 1.03 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.003 0.001 HIS A 217 PHE 0.013 0.001 PHE A 442 TYR 0.016 0.001 TYR A 264 ARG 0.016 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.429 Fit side-chains REVERT: A 290 ARG cc_start: 0.6347 (mtp85) cc_final: 0.6129 (mmm-85) REVERT: A 389 ILE cc_start: 0.7839 (mt) cc_final: 0.7617 (mp) REVERT: A 437 SER cc_start: 0.8553 (t) cc_final: 0.8204 (p) REVERT: A 460 MET cc_start: 0.7089 (mmm) cc_final: 0.6785 (mmm) outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 1.1071 time to fit residues: 59.9959 Evaluate side-chains 52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 462 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 17 GLN A 289 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.181144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138343 restraints weight = 12521.243| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.89 r_work: 0.3488 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3974 Z= 0.204 Angle : 0.570 6.190 5402 Z= 0.289 Chirality : 0.039 0.137 625 Planarity : 0.004 0.033 673 Dihedral : 6.595 54.834 563 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.68 % Allowed : 22.06 % Favored : 76.26 % 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: 2.21 (0.39), residues: 489 helix: 1.78 (0.27), residues: 375 sheet: -1.65 (1.45), residues: 10 loop : 0.88 (0.68), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 346 HIS 0.003 0.001 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.009 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.406 Fit side-chains REVERT: A 313 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6683 (mm) REVERT: A 437 SER cc_start: 0.8571 (t) cc_final: 0.8147 (p) REVERT: A 460 MET cc_start: 0.6840 (mmm) cc_final: 0.6569 (mmm) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.1497 time to fit residues: 64.4543 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 6 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.0870 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.185071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.141259 restraints weight = 10843.137| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.76 r_work: 0.3552 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3974 Z= 0.157 Angle : 0.522 7.029 5402 Z= 0.264 Chirality : 0.037 0.130 625 Planarity : 0.004 0.030 673 Dihedral : 5.853 53.276 561 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.64 % Allowed : 21.34 % Favored : 76.02 % 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: 2.49 (0.39), residues: 489 helix: 2.00 (0.27), residues: 373 sheet: -1.37 (1.46), residues: 10 loop : 0.88 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 274 HIS 0.003 0.001 HIS A 217 PHE 0.015 0.001 PHE A 351 TYR 0.015 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.395 Fit side-chains REVERT: A 103 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: A 437 SER cc_start: 0.8592 (t) cc_final: 0.8197 (p) REVERT: A 460 MET cc_start: 0.6734 (mmt) cc_final: 0.6466 (mmm) outliers start: 11 outliers final: 3 residues processed: 55 average time/residue: 1.1071 time to fit residues: 63.3040 Evaluate side-chains 51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.0060 chunk 34 optimal weight: 0.0670 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.142845 restraints weight = 18070.633| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.48 r_work: 0.3541 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3974 Z= 0.147 Angle : 0.508 7.192 5402 Z= 0.256 Chirality : 0.037 0.150 625 Planarity : 0.004 0.036 673 Dihedral : 5.468 51.741 561 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.12 % Allowed : 20.62 % Favored : 76.26 % 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: 2.52 (0.39), residues: 489 helix: 2.02 (0.27), residues: 373 sheet: -1.32 (1.45), residues: 10 loop : 0.91 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 274 HIS 0.001 0.000 HIS A 48 PHE 0.014 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.411 Fit side-chains REVERT: A 103 GLU cc_start: 0.7013 (pt0) cc_final: 0.5993 (pm20) REVERT: A 313 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6607 (mm) REVERT: A 358 MET cc_start: 0.8420 (mmm) cc_final: 0.8199 (mmm) REVERT: A 359 ASP cc_start: 0.7460 (t70) cc_final: 0.7241 (m-30) REVERT: A 392 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4936 (mtm) REVERT: A 437 SER cc_start: 0.8588 (t) cc_final: 0.8205 (p) REVERT: A 460 MET cc_start: 0.6814 (mmt) cc_final: 0.6567 (mmm) outliers start: 13 outliers final: 3 residues processed: 60 average time/residue: 0.9928 time to fit residues: 62.2951 Evaluate side-chains 52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 392 MET Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141388 restraints weight = 11563.317| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.87 r_work: 0.3558 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3974 Z= 0.156 Angle : 0.518 7.016 5402 Z= 0.260 Chirality : 0.038 0.157 625 Planarity : 0.004 0.033 673 Dihedral : 5.190 50.453 561 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.40 % Allowed : 22.06 % Favored : 75.54 % 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: 2.47 (0.39), residues: 489 helix: 1.98 (0.27), residues: 373 sheet: -1.31 (1.45), residues: 10 loop : 0.89 (0.68), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 274 HIS 0.001 0.000 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.009 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.434 Fit side-chains REVERT: A 103 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.5987 (pm20) REVERT: A 313 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6492 (mm) REVERT: A 437 SER cc_start: 0.8620 (t) cc_final: 0.8240 (p) REVERT: A 460 MET cc_start: 0.6793 (mmt) cc_final: 0.6537 (mmm) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 1.0798 time to fit residues: 60.6952 Evaluate side-chains 54 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.184193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140205 restraints weight = 10751.462| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.75 r_work: 0.3550 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3533 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3533 r_free = 0.3533 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3533 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3974 Z= 0.174 Angle : 0.536 7.243 5402 Z= 0.269 Chirality : 0.038 0.185 625 Planarity : 0.004 0.032 673 Dihedral : 5.035 49.712 561 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.64 % Allowed : 21.34 % Favored : 76.02 % 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: 2.42 (0.39), residues: 489 helix: 1.93 (0.26), residues: 374 sheet: -1.26 (1.43), residues: 10 loop : 0.96 (0.70), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.018 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.398 Fit side-chains REVERT: A 7 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6771 (mt) REVERT: A 103 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.5968 (pm20) REVERT: A 289 GLN cc_start: 0.7947 (tp40) cc_final: 0.7712 (tp-100) REVERT: A 313 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6589 (mm) REVERT: A 389 ILE cc_start: 0.7363 (mt) cc_final: 0.7154 (mp) REVERT: A 437 SER cc_start: 0.8588 (t) cc_final: 0.8181 (p) REVERT: A 460 MET cc_start: 0.6733 (mmt) cc_final: 0.6461 (mmm) outliers start: 11 outliers final: 4 residues processed: 55 average time/residue: 1.1672 time to fit residues: 66.6972 Evaluate side-chains 58 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.184304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140642 restraints weight = 15488.180| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.20 r_work: 0.3531 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3974 Z= 0.170 Angle : 0.541 6.843 5402 Z= 0.269 Chirality : 0.038 0.178 625 Planarity : 0.004 0.031 673 Dihedral : 4.866 48.852 561 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.16 % Allowed : 21.82 % Favored : 76.02 % 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: 2.43 (0.39), residues: 489 helix: 1.93 (0.26), residues: 374 sheet: -1.18 (1.44), residues: 10 loop : 0.92 (0.69), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.013 0.001 PHE A 351 TYR 0.017 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.443 Fit side-chains REVERT: A 7 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6793 (mt) REVERT: A 103 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6056 (pm20) REVERT: A 289 GLN cc_start: 0.8018 (tp40) cc_final: 0.7805 (tp-100) REVERT: A 313 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6509 (mm) REVERT: A 437 SER cc_start: 0.8604 (t) cc_final: 0.8215 (p) REVERT: A 460 MET cc_start: 0.6811 (mmt) cc_final: 0.6539 (mmm) outliers start: 9 outliers final: 5 residues processed: 57 average time/residue: 1.2245 time to fit residues: 72.3503 Evaluate side-chains 57 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 4 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.181076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.136970 restraints weight = 13242.863| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.03 r_work: 0.3470 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3974 Z= 0.217 Angle : 0.565 6.572 5402 Z= 0.284 Chirality : 0.040 0.169 625 Planarity : 0.004 0.029 673 Dihedral : 5.079 49.127 561 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.64 % Allowed : 21.34 % Favored : 76.02 % 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: 2.28 (0.38), residues: 489 helix: 1.79 (0.26), residues: 376 sheet: -1.43 (1.36), residues: 10 loop : 1.05 (0.70), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.011 0.001 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.007 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.434 Fit side-chains REVERT: A 103 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6062 (pm20) REVERT: A 313 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6489 (mm) REVERT: A 389 ILE cc_start: 0.7465 (mt) cc_final: 0.7212 (mp) REVERT: A 437 SER cc_start: 0.8613 (t) cc_final: 0.8194 (p) REVERT: A 460 MET cc_start: 0.6742 (mmt) cc_final: 0.6450 (mmm) outliers start: 11 outliers final: 4 residues processed: 56 average time/residue: 1.1052 time to fit residues: 64.3096 Evaluate side-chains 56 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.183879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.140565 restraints weight = 9571.465| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.60 r_work: 0.3549 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3974 Z= 0.164 Angle : 0.550 7.458 5402 Z= 0.275 Chirality : 0.038 0.165 625 Planarity : 0.004 0.028 673 Dihedral : 4.961 48.335 561 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.68 % Allowed : 23.02 % Favored : 75.30 % 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: 2.37 (0.39), residues: 489 helix: 1.89 (0.26), residues: 374 sheet: -1.17 (1.44), residues: 10 loop : 0.89 (0.69), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.002 0.001 HIS A 217 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.009 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.446 Fit side-chains REVERT: A 103 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: A 313 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6547 (mm) REVERT: A 389 ILE cc_start: 0.7373 (mt) cc_final: 0.7138 (mp) REVERT: A 437 SER cc_start: 0.8608 (t) cc_final: 0.8221 (p) REVERT: A 460 MET cc_start: 0.6761 (mmt) cc_final: 0.6465 (mmm) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 1.2397 time to fit residues: 69.4225 Evaluate side-chains 52 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137011 restraints weight = 12687.185| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.97 r_work: 0.3508 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3974 Z= 0.214 Angle : 0.588 8.499 5402 Z= 0.296 Chirality : 0.040 0.167 625 Planarity : 0.004 0.028 673 Dihedral : 5.169 48.508 561 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.44 % Allowed : 23.02 % Favored : 75.54 % 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: 2.26 (0.38), residues: 489 helix: 1.80 (0.26), residues: 375 sheet: -1.31 (1.38), residues: 10 loop : 0.93 (0.70), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 213 HIS 0.002 0.001 HIS A 48 PHE 0.012 0.001 PHE A 351 TYR 0.019 0.001 TYR A 264 ARG 0.008 0.001 ARG A 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 978 Ramachandran restraints generated. 489 Oldfield, 0 Emsley, 489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6095 (pm20) REVERT: A 289 GLN cc_start: 0.7802 (tp-100) cc_final: 0.6925 (tm-30) REVERT: A 313 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6551 (mm) REVERT: A 389 ILE cc_start: 0.7459 (mt) cc_final: 0.7241 (mp) REVERT: A 437 SER cc_start: 0.8638 (t) cc_final: 0.8225 (p) REVERT: A 460 MET cc_start: 0.6792 (mmt) cc_final: 0.6489 (mmm) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 1.2545 time to fit residues: 66.4179 Evaluate side-chains 51 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 429 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.0010 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 ASN A 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.185583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.142449 restraints weight = 8738.188| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.51 r_work: 0.3578 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3974 Z= 0.159 Angle : 0.563 8.143 5402 Z= 0.281 Chirality : 0.038 0.160 625 Planarity : 0.004 0.033 673 Dihedral : 4.933 47.291 561 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.92 % Allowed : 23.26 % Favored : 74.82 % 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: 2.37 (0.39), residues: 489 helix: 1.87 (0.26), residues: 377 sheet: -0.98 (1.53), residues: 10 loop : 0.94 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 213 HIS 0.001 0.001 HIS A 48 PHE 0.015 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.008 0.000 ARG A 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3187.64 seconds wall clock time: 56 minutes 54.16 seconds (3414.16 seconds total)